Computational Design of the Affinity and Specificity of a Therapeutic T Cell Receptor

Author Summary T cell receptors (TCRs) play a major role in immunity, recognizing peptide antigens presented by major histocompatibility complex proteins. Due to their capacity to target intracellularly produced proteins and initiate cell killing, there is significant interest developing TCR-based therapeutic strategies, particularly towards cancer. A concern with TCRs is their weak-to-moderate affinities, which limits therapeutic potential. While in vitro evolution has been used to enhance TCR affinity, with sometimes spectacular results, these techniques can reduce peptide specificity and offer little control over affinity enhancements. Here we explored the use of structure-based computational design to enhance TCR affinity, which in principle can permit control over both specificity and affinity gains. We examined a clinically relevant TCR recently used in melanoma immunotherapy, identifying and characterizing mutations which enhanced affinity with no detectable impacts on binding specificity. We solved a crystal structure of our highest affinity designed TCR in complex with antigen, which indicated high accuracy of the structural modeling during the design process, and we critically evaluated several design protocols and functions to further improve design success. These results provide valuable insights into the use of computational design for TCRs. Lastly, the enhanced affinity variants identified may be of potential clinical benefit. T cell receptors (TCRs) are key to antigen-specific immunity and are increasingly being explored as therapeutics, most visibly in cancer immunotherapy. As TCRs typically possess only low-to-moderate affinity for their peptide/MHC (pMHC) ligands, there is a recognized need to develop affinity-enhanced TCR variants. Previous in vitro engineering efforts have yielded remarkable improvements in TCR affinity, yet concerns exist about the maintenance of peptide specificity and the biological impacts of ultra-high affinity. As opposed to in vitro engineering, computational design can directly address these issues, in theory permitting the rational control of peptide specificity together with relatively controlled increments in affinity. Here we explored the efficacy of computational design with the clinically relevant TCR DMF5, which recognizes nonameric and decameric epitopes from the melanoma-associated Melan-A/MART-1 protein presented by the class I MHC HLA-A2. We tested multiple mutations selected by flexible and rigid modeling protocols, assessed impacts on affinity and specificity, and utilized the data to examine and improve algorithmic performance. We identified multiple mutations that improved binding affinity, and characterized the structure, affinity, and binding kinetics of a previously reported double mutant that exhibits an impressive 400-fold affinity improvement for the decameric pMHC ligand without detectable binding to non-cognate ligands. The structure of this high affinity mutant indicated very little conformational consequences and emphasized the high fidelity of our modeling procedure. Overall, our work showcases the capability of computational design to generate TCRs with improved pMHC affinities while explicitly accounting for peptide specificity, as well as its potential for generating TCRs with customized antigen targeting capabilities.