Rational optimization of tumor epitopes using in silico analysis‐assisted substitution of TCR contact residues

Abstract

Altered peptide ligands with increased affinity of the peptide-MHC complex for the TCR provide an alternative strategy to natural T-cell epitopes for cancer immunotherapy, as they can recruit and stimulate stronger T-cell repertoires. However, it remains unclear how alterations of the TCR contact residues improve the interaction between the peptide-MHC complex and the TCR molecule. In this study, we introduced a molecular simulation strategy to optimize a tumor immunodominant epitope NY-ESO-1 157-165 by the substitution of the potential TCR contact residues. We correlated molecule simulation with T-cell activation capacity assay and detected the effect of modifications of TCR contact residues on T-cell recognition. An agonist peptide W5F with substitution at Trp5 with Phe was identified and it exhibits a stronger ability to induce a cross-reactive CTL response with the WT peptide. Additionally, the W5F-induced CTL could be maintained with the WT peptide and possess higher capacity in lysing native NY-ESO-1-expressing tumor cells. These results provide important insights into the enhanced immunogenicity of epitopes through substitution at the TCR contact sites and revealed a novel molecular simulation approach for rational therapeutic peptide vaccine design.Key words: Cancer immunotherapy . Epitope . Molecular simulation . TCR contact residue IntroductionInduction of antigen-specific CTL by therapeutic peptide vaccination is a promising approach for cancer immunotherapy [1]. The specific cellular immune response starts from recognition by TCR of an immunogenic epitope presented in the context of the class I MHC molecules. Thus, modulation of CTL response by manipulating T-cell epitopes is a particularly attractive approach for cancer immunotherapy, because peptides from cancer cells are usually poorly immunogenic and often induce immune-tolerance [2,3]. Vaccination with altered peptide ligands (APL), which can be generated by appropriate amino acid substitutions at certain T-cell epitopes, has become an attractive strategy to enhance specic T-cell responses to tumors. This strategy can be achieved by two general approaches: (i) by increasing the affinity between the epitope and the MHC through substitution in the MHC anchor residues or (ii) by enhancing the interactions between the TCR and peptide-MHC (pMHC) complex through alteration at the TCR contact residues [4,5].Although APL with altered MHC contact residues can efficiently activate tumor-specific T cells in vitro, vaccination with this kind of APL has generally failed to elicit an effective anti-tumor CTL response 2248that can lead to clinical tumor regression [6,7]. APL with increased pMHC complex affinity for the TCR molecule, which are designed by modifications at the TCR contact sites rather than the MHC anchor residues, have unexpected potency to induce stronger T-cell responses and may even covert cross-reactive T cells from a tolerance state [8][9][10]. According to the structure of the TCR/pMHC complex established by X-ray crystallography, recogni...

Modification of MHC Anchor Residues Generates Heteroclitic Peptides That Alter TCR Binding and T Cell Recognition

“…At the molecular level, the specificity of T cell recognition is governed by the tripartite interaction between the TCR and peptide-MHC (pMHC). Enhanced binding of TCR to pMHC, and mutations that stabilize the fastening of the antigenic peptide to its restricting MHC molecule, are both known to increase immunogenicity (3)(4)(5)(6)(7)(8)(9)(10)(11). Thus, a number of sequence-modified, or heteroclitic, peptides have been developed for this purpose.…”

A Single L/D-Substitution at Q4 of the mInsA2-10 Epitope Prevents Type 1 Diabetes in Humanized NOD Mice

“…A modified H-2D d -restricted epitope of HIV-1 IIIB envelope glycoprotein P18-I10 (RGPGRAFVTI) with a single amino acid substitution by the respective D-enantiomer at positions 324F, 325V, 326T, or 327I markedly reduced the cytotoxic activity of P18-I10-specific murine CD8 + T lymphocytes (18). Subtle changes at the TCR contact residues can dramatically alter the downstream signaling events, leading to T-cell anergy, apoptosis, or high activation (28). Since amino acid residues at positions 4 and 6 of mInsA 2-10 were predicted to be in close contact with the TCR, we generated two APL candidates via in silicoassisted single D-amino acid substitution at the two positions, respectively.…”

PeptX: Using Genetic Algorithms to optimize peptides for MHC binding

“…Several approaches to address the challenge of optimization for pMHC/TCR interaction were reported: In early methods Alexander et al employed the main HLA-DR anchors to increase the peptide/MHC binding affinity as well as the use of bulky and charged residues to increase T cell recognition [ 27 , 28 ]. Shang et al used computational alanine scanning to indentify hotspots which were then systematically substituted and scored to optimize a tumor immunodominant epitope [ 29 ]. Also for the peptide and MHC interaction several approaches were reported: Reche et al published a webserver for the formulation of multi-epitope vaccines [ 30 ].…”