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Publication Abstract from PubMed

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.

Targeting peptide-MHC complexes with designed T cell receptors and antibodies.,Motmaen A, Jude KM, Wang N, Minervina A, Feldman D, Lichtenstein MA, Ebenezer A, Correnti C, Thomas PG, Garcia KC, Baker D, Bradley P bioRxiv [Preprint]. 2025 Nov 20:2025.11.19.689381. doi: , 10.1101/2025.11.19.689381. PMID:41332722^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.