Computational design of a single-domain antibody that specifically recognizes WT1 peptide-loaded class I MHC

Abstract

T cell receptor (TCR)-like antibodies that recognize peptide-loaded class I MHC (pMHC) complexes can enable precise targeting of cancer cells, but developing single-domain binders with high specificity and affinity is challenging. Here, we report the computational design and experimental validation of a TCR-like single-domain antibody (sdAb) that specifically recognizes the WT1-derived peptide RMFPNAPYL presented by HLA-A*02:01. Starting from the crystal structure of a Fab antibody bound to RMF/HLA- A02:01, we repurposed the VH domain into a stable, soluble Trastuzumab-derived VH scaffold. The resulting sdAb, RMFsdAb, spans all nine peptide residues and shows no binding to a control pMHC with a different peptide. Its biophysical properties were improved by fusion to human serum albumin domain III (HSA D3), yielding a monodisperse HSA D3-RMFsdAb with 81 nM affinity and specificity for RMF/HLA- A*02:01. We further engineered a bivalent format (RMFsdAb-HSA D3-RMFsdAb), which dramatically increased apparent binding affinity to 0.4 nM. When expressed on a CAR T cell, HSA D3-RMFsdAb functioned as the antigen-recognition domain to selectively activate T cells in the presence of RMF/HLA-A*02:01-positive cells. Our results demonstrate a viable strategy to develop high-specificity, peptide-focused TCR-like sdAbs for pMHC-targeted therapeutics.