Journal Article

DKFZ-2026-02095

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png AI-enabled discovery and biochemical optimization of minibinders targeting cancer cell-surface proteins.

Broske, B. ; McEnroe, B. A. ; Frechen, S. C. ; Kempchen, T. N. ; Fandrey, C. I. ; Tan, E. ; Ferber, D. ; Yong, M. C. R. ; Kleinert, M. ; Messmer, J. M. ; Konopka, P. ; Hoch, A. ; Blumenstock, K. ; Tödtmann, J. M. P. ; Oldenburg, J. ; Rühl, H. ; Semaan, A. ; Toma, M. I. ; Markova, K. ; Kobold, S.DKFZ* ; Rollenske, T. ; Geyer, M. ; Menzel, S. ; Bald, T. ; Schmid-Burgk, J. L. ; Hagelueken, G. ; Hölzel, M.

2026
Springer Nature [London]

Abstract: Experimental validation and functional optimization remain bottlenecks in AI-based protein design. We present a scalable workflow for developing AI-designed minibinders against cancer-associated surface proteins. Screening thousands of designs using mammalian cell-surface display identifies several high-affinity PD-L1 minibinders but far fewer for CD276 (B7-H3) and VTCN1 (B7-H4), highlighting substantial target dependence. Interface predicted template modeling (ipTM) scores generated by Chai-1 with ESM embeddings correlate with binding success and capture deleterious effects of interface mutations. Fluorophore-labeled AI-minibinders enable flow-cytometric staining comparable to conventional antibodies. However, when incorporated into chimeric antigen receptors (CAR), some show poor cell-surface trafficking and limited functionality. Redesign through a genetic algorithm-based diversification strategy that preserves the binding interface while changing non-binding surfaces experimentally reveals an isoelectric point (pI) window that improves CAR expression and enhances target-selective tumor cell killing. Our findings identify biochemical optimization beyond the binding interface as a critical requirement for translating AI-minibinders into functional applications.

Keyword(s): Humans (MeSH) ; Neoplasms: metabolism (MeSH) ; Protein Binding (MeSH) ; Membrane Proteins: metabolism (MeSH) ; Animals (MeSH) ; Receptors, Chimeric Antigen: metabolism (MeSH) ; Receptors, Chimeric Antigen: genetics (MeSH) ; Cell Line, Tumor (MeSH) ; Protein Engineering: methods (MeSH) ; Algorithms (MeSH) ; Membrane Proteins ; Receptors, Chimeric Antigen

Note: #DKTKZFB9#

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Contributing Institute(s):

1. DKTK Koordinierungsstelle München (MU01)

Research Program(s):

1. 899 - ohne Topic (POF4-899) (POF4-899)

Appears in the scientific report 2026

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