In Silico Design of High-Affinity gp100 Antigenic Mimotopes for Targeting Melanoma

Human CD8+ cytotoxic T lymphocytes (CTLs) induce melanoma regression by utilizing T-cell receptors (TCRs) to recognize tumor-specific epitopes. One such epitope, gp100280-288(288 V) (YLEPGPVTV), is presented by human leukocyte antigen (HLA)-A*02:01 molecules. Computational approaches, particularly the predictions on peptide-HLA (pHLA) and TCR-pHLA binding affinities, are complementary to experimental approaches in guiding further optimization and design of the gp100280-288(288 V) peptide (mimotopes) for enhanced antitumor responses. Here, with all-atom molecular dynamics (MD) simulations and free energy perturbation (FEP) methods, we designed a series of potential mimotopes through in silico mutagenesis studies of gp100280-288(288 V) utilizing the latest affinity-matured TCR structure. Our results showed that E3I and E3L mutants increased HLA binding without affecting TCR binding, indicating their potential as epitope candidates. Conversely, the E3A and E3V mutations improved peptide-HLA binding but weakened the TCR-pHLA binding affinity. In-depth structural analysis revealed that insufficient occupancy of the HLA pocket by residue 3 in the E3A and E3V mutants would induce a twisted peptide conformation at positions 4 to 6, disrupting the interaction between TCR and pHLA. Therefore, it is crucial to consider the impact of single-residue mutations that alter peptide conformation on TCR binding when designing effective antigenic mimotopes. Furthermore, the E3I+V7L and E3L+V7L double mutants are also found to produce favorable binding affinity changes similar to those of the E3I and E3L mutants, suggesting their potential as advantageous mimotope candidates. Our work provides structural insights for the rational design of favorable gp100 mimotopes and may contribute to developing gp100 epitope-based vaccines.