Chapter 5 Vaccine Peptide Evaluating towards Epitope and/or Agretope Plastic
5.4 Conclusion and Future Works
Knowledge of the 3D structure of epitopes is essential in structural immunoinformatics. With the structure of peptides binding to MHC molecules, further elucidation about immune reactions such as epitope-MHC molecular interactions can be done. There are many methods developed for protein structure prediction, however, there are relatively few methods for short sequence peptide structure prediction. In the immunoinformatic field, epitope is primarily the target of concern, which is consisted of about 8-12 amino acids. There is little previous effort for structural prediction of peptides binding to MHC Class I molecules.[49]
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The bmPDA structure prediction result of epitope revealed our method was good at predicting structure of short sequence of peptide such as epitope. This is compatible with the previous experience that protein threading method is more accurate in short sequence of protein than homology modeling.
Based on the structure prediction result, we can actually simulate the binding between peptide and MHC molecules, instead of other indirect method. For binding affinity evaluation between peptide and MHC class I molecule, docking is done with MVD regression model based on tabu clustering in order to avoid GA sub-optima and GA local optima.[48]
The intended vaccine peptide of epitope and agretope may be delivered in the format of
“in silico DNA vaccine” which is constructed with expression DNA sequence deduced from the intended vaccine peptide sequence and as well with upstream control sequence of LMP1/2 promoter sequence. The developed “in silico DNA vaccine” with intended specific expression in EBV latent infection lymphocytes may be verified with NPC cell line of EBV-latent infected B lymphocytes for immunogenic induction in order to demonstrate the potential ability in shifting cell-mediated immunity (CMI) pathway towards MHC-I Tc cell of CTL while away from MHC-II Th cell.
The BAff evaluation of predicted nona-peptide agretope structure towards docking HLA1 pit structure exploits MVD regression model with tabu clustering parameter in order to avoid sub-optima and local optima with GA method. In that, the HLA1 BAff of predicted activity with tabu clustering parameter may show good correlation with experiment activity and as well may show better reproducibility of computation result when compared with default rerank score of MVD regression model. The BAff computation time with nona-peptide structure on docking HLA1 pit structure is respectively 150 minutes or 40 minutes in average with default parameter or tabu clustering parameter in MVD regression model.
In addition to antigenecity priority on LMP1np epitope candidates in original amino acid sequence, the LMP1 agretope anchor plastics candidates based on bmPDA structure modeling may comply with inferred position-specific preference on A*02:01 pit binding nona-peptide at positions {2nd; 9th} with {L/M; I/L/V} towards improving MVD BAff vale while in disregard of tolerated {I/Q/V; A/M}. Notably, putative LMP1np structures of bmPDA prediction match with compatible biological experiment verified IEDB entries of A*02:01 epitopes ID 1377922~1377926 from Herpesvirus 4 Strain B95-8 with LMP1np-125(~133) published by Khanna R et al. in 1988. Despite of top ranking antigenecity scores with NetCTL and SYFPEITHI severs with LMP1np-125 {L; L} within preferred {L/M; I/L/V}
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anchor group, the MDV BAff value of LMP1np-125 structural docking appears at the last ranking position within the indicated group in original amino acid sequence whereas the LMP1np-125 {L; V}.
With the priority LMP1 epitope candidates for HLA1 predicted with the antigenicity scores of NetCTL and/or SYFPEITHI servers, our bmPDA designed nona-peptide structures may further contribute on the need of structural evaluation in order to move on the diligence in practical feasibility towards application direction of mining Ama candidates of in vitro DNA vaccine for in vitro cell activation and Ace candidates of in vivo twin adhesive for in vivo subject therapy based on MDV BAff values. Despite of accords in good antigenicity scores level of NetCTL and SYFPEITHI, NetCTL score rankings within Ama group of {L/M; I/L/V}
seem to be more consistent with MVD BAff value rankings of our bmPDA designed LMP1np:Ama structures while at noticeable inconsistency with SYFPEITHI score rankings.
Moreover, high NetCTL antigenicity scores of top 8 candidates with the distribution range from 1.575 to 1.303) may fail to offer adequate {L/M; I/L/V} intra-group resolution as in contrast to the distribution range of low score antigenicity cases; whereas BAff value range from -24.347 to -10.253 of top 8 candidates may offer appropriate power for differentiation among LMP1np:Ama candidates as to be a supplemental indicator for analyzing HLA1-binding nona-peptides.
Instead of external delivery in vaccine peptide towards regular AMI induction, the intended vaccine peptide of HLA1 binder epitope and agretope for CMI induction shall in future take internal delivery strategy in the format of DNA vaccine which is constructed with coding sequence DNA insert deduced from intended HLA1 binder peptide sequence and as well with upstream control sequence of appropriate promoters. The intended CMI vaccine peptide thus in the format of in vitro DNA vaccine may serve good application for in vitro cell activation towards in vivo adoptive cell transfer with mixed lymphocyte reaction (MLR) plate separated with dialysis membrane from host cell and antigen presenting cell (APC), T cytotoxic (Tc) cell, and T helper (Th) cell. The in vitro DNA vaccine is hypothesized with practical feasibility while bypassing immune suppression within in vivo tumor microenvironment and while avoiding adverse clinical cytotoxicity on innocent bystander cells due to in vivo non-specific delivery of DNA vaccines.
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