De novo-designed pMHC binders facilitate T cell-mediated cytotoxicity toward cancer cells

Science. 2025 Jul 24;389(6758):380-385. doi: 10.1126/science.adv0422. Epub 2025 Jul 24.

Abstract

The recognition of intracellular antigens by CD8+ T cells through T cell receptors (TCRs) is central for adaptive immunity against infections and cancer. However, the identification of TCRs from patient material remains complex. We present a rapid de novo minibinder (miBd) design platform leveraging state-of-the-art generative models to engineer miBds targeting the cancer-associated peptide-bound major histocompatibility complex (pMHC) SLLMWITQC/HLA-A*02:01 (NY-ESO-1). Incorporating in silico cross-panning enabled computational prescreening of specificity, and molecular dynamics simulations allowed for improved predictability of in vitro success. We identified a high-affinity NY-ESO-1 binder and confirmed its structure using cryo-electron microscopy, which, when incorporated in a chimeric antigen receptor, induced killing of NY-ESO-1+ melanoma cells. We further designed and validated binders to a neoantigen pMHC complex, RVTDESILSY/HLA-A*01:01, with unknown structure, demonstrating the potential for precision immunotherapy.

MeSH terms

  • Antigens, Neoplasm* / chemistry
  • Antigens, Neoplasm* / immunology
  • CD8-Positive T-Lymphocytes* / immunology
  • Cell Line, Tumor
  • Cryoelectron Microscopy
  • Cytotoxicity, Immunologic*
  • HLA-A2 Antigen* / chemistry
  • HLA-A2 Antigen* / immunology
  • Humans
  • Major Histocompatibility Complex*
  • Melanoma* / immunology
  • Melanoma* / therapy
  • Membrane Proteins* / chemistry
  • Membrane Proteins* / immunology
  • Molecular Dynamics Simulation
  • Molecular Mimicry*
  • Peptides / chemistry
  • Peptides / immunology
  • Protein Binding
  • Protein Conformation, alpha-Helical
  • Protein Engineering
  • Receptors, Antigen, T-Cell* / chemistry
  • Receptors, Antigen, T-Cell* / immunology
  • Receptors, Chimeric Antigen / chemistry
  • Receptors, Chimeric Antigen / immunology

Substances

  • Antigens, Neoplasm
  • CTAG1B protein, human
  • HLA-A*02:01 antigen
  • HLA-A2 Antigen
  • Membrane Proteins
  • Peptides
  • Receptors, Antigen, T-Cell
  • Receptors, Chimeric Antigen