Immunoinformatics-Driven Rational Design of Altered Peptide Ligands and In Vitro Validation of a Multi-Epitope CTL Formulation Targeting HPV16 E6/E7

Background: Therapeutic vaccination against human papillomavirus type 16 (HPV16) is frequently limited by the weak HLA-A*02:01 presentation of native E6/E7 oncoprotein epitopes. This study aims to utilize an integrated computational-experimental pipeline to design and evaluate anchor-optimized altered peptide ligands (APLs) for improving peptide presentation and HPV16-specific T-cell responses. Methods: Anchor-residue substitutions were introduced into three wild-type E6/E7 epitopes. Candidates were prioritized in silico based on predicted presentation, affinity, immunogenicity, and toxicity, and subsequently evaluated via in vitro functional assays using HLA-A*02:01-positive donor cells and molecular dynamics (MD) simulations. Results: Anchor optimization successfully converted weak binders into strong binders; for instance, E6apl improved predicted affinity from 329.33 to 6.21 nM. Crucially, candidate E7apl1 exhibited normal CD8+ T-cell expansion but reduced IFN-γ secretion, revealing a distinct binding–immunogenicity dissociation. MD simulations suggested that altered peptide conformational dynamics may contribute to differences in functional activity. Subsequently, an optimized six-peptide formulation (three APLs and three wild-type epitopes) was assembled. The resulting multi-epitope HPV-specific cytotoxic T lymphocytes (meHPV-CTLs) mediated target-specific cytotoxicity against cervical cancer cells, achieving 74.1% ± 5.1% specific lysis at an effector-to-target ratio of 30:1, which was largely abrogated by HLA class I blockade. Conclusions: These proof-of-concept findings demonstrate that stable peptide–MHC binding is a necessary but insufficient condition for optimal T-cell activation. The experimentally characterized multi-epitope formulation provides a proof-of-concept strategy for further preclinical evaluation of HPV16-targeted peptide-based immunotherapies. Moreover, because these anchor-optimized APLs are defined at the sequence level, these sequence-defined APLs may potentially be explored in alternative vaccine delivery platforms, including mRNA-based approaches, in future studies.