Barcode-free hit discovery from massive libraries enabled by automated small molecule structure annotation

Nol, E.A. van der; Haupt, N.A.; Gao, Q.Q.; Smit, B.A.M.; Hoffmann, M.A.; Engler-Lukajewski, M.; ... ; Pomplun, S.J. (2025)

Article / Letter to editor

Affinity-selection platforms are powerful tools in early drug discovery, but current technologies - most notably DNA-encoded libraries (DELs) - are limited by synthesis complexity and incompatibility with nucleic acid-binding targets. We present a barcode-free self-encoded library (SEL) platform that enables direct screening of over half a million small molecules in a single experiment. SELs combine tandem mass spectrometry with custom software for automated structure annotation, eliminating the need for external tags for the identification of screening hits. We develop efficient, high-diversity synthesis protocols for a broad range of chemical scaffolds and benchmark the platform in affinity selections against carbonic anhydrase IX, identifying multiple nanomolar binders. We further apply SELs to flap endonuclease 1 (FEN1) - a disease related DNA-processing enzyme inaccessible to DELs - and discover potent inhibitors. Taken together, screening barcode-free libraries of this scale all at once represents an important development, enables access to novel target classes, and promises substantial impact on both academic and industrial early drug discovery.

• All authors: Nol, E.A. van der; Haupt, N.A.; Gao, Q.Q.; Smit, B.A.M.; Hoffmann, M.A.; Engler-Lukajewski, M.; Ludwig, M.; McKenna, S.; Apolónia da Mata, J.M.; Béquignon, O.J.M.; Westen, G. van; Wendel, T.J.; Noordermeer, S.M.; Böcker, S.; Pomplun, S.J.
• Date: 2025-10-27
• Journal: Nature Communications
• Volume: 16
• Issue: 1
• DOI: doi:10.1038/s41467-025-65282-1