Johansen, Wolff, Scapolo, et al. used a known crystal structure, RFdiffusion, and other generative models to rapidly de novo design high-affinity minibinders (miBds) targeting the NY-ESO-1 peptide SllMWITQC on HLA-A*02:01. In silico cross-panning and molecular dynamics simulations allowed prescreening of specificity, which was later confirmed in vitro. The miBd structure was validated through cryo-electron microscopy, and when incorporated as a CAR on T cells, miBd binding induced killing of NY-ESO-1+ melanoma cells. The researchers also designed and validated a miBd to a neoantigen pMHC complex for which no experimental structure was available.
Contributed by Lauren Hitchings
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.
Author Info: (1) Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark. (2) Department of Biotechnology and Biomedicine, Technical University of Denmark, Kon
Author Info: (1) Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark. (2) Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark. (3) Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark. Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark. (4) Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA. (5) Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark. Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark. (6) Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA. (7) Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark. (8) Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark. (9) Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark. (10) Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark. (11) Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark. (12) Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark. (13) Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark. (14) Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark. (15) Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA. (16) Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA. (17) Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark. (18) Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark. (19) Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark. (20) Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark. (21) Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark. (22) Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark. (23) Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark. (24) Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA. (25) Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark. (26) Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark. (27) Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark.
