Motmaen et al. developed a structure-based deep learning strategy (ADAPT) for pMHC binder design that leverages AlphaFold2 for conformational sampling, ProteinMPNN for CDR design, and iterative re-docking and a genetic algorithm for interface amino acid refinement. For 9 pre-selected pMHC targets, 6 successful TCR binders were identified. While target binding was tightly correlated with T cell activation, and binders exhibited high pMHC affinity, some designs led to background activation. ADAPT also produced antibody binders (5-700 nM monovalent affinity) to 3 pre-selected targets, where peptide binding was mediated by heavy chain CDRs.
Contributed by Morgan Janes
ABSTRACT: Class I major histocompatibility complexes (MHCs), expressed on the surface of all nucleated cells, present peptides derived from intracellular proteins for surveillance by T cells. The precise recognition of foreign or mutated peptide-MHC (pMHC) complexes by T cell receptors (TCRs) is central to immune defense against pathogens and tumors. Although patient-derived TCRs specific for cancer-associated antigens have been used to engineer tumor-targeting therapies, their reactivity toward self- or near-self antigens may be constrained by negative selection in the thymus. Here, we introduce a structure-based deep learning framework, ADAPT (Antigen-receptor Design Against Peptide-MHC Targets), for the design of TCRs and antibodies that bind to pMHC targets of interest. We evaluate the ADAPT pipeline by designing and characterizing TCRs and antibodies against a diverse panel of pMHCs. Cryogenic electron microscopy structures of two designed antibodies bound to their respective pMHC targets demonstrate atomic-level accuracy at the recognition interface, supporting the robustness of our structure-based approach. Computationally designed TCRs and antibodies targeting pMHC complexes could enable a broad range of therapeutic applications, from cancer immunotherapy to autoimmune disease treatment, and insights gained from TCR-pMHC design should advance predictive understanding of TCR specificity with implications for basic immunology and clinical diagnostics.


