Barcode-free hit discovery from massive libraries enabled by automated small molecule structure annotation
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.
Authors
- Martin S. Engler (ORCID: https://orcid.org/0000-0002-2200-9722)
- Qingsong Gao (ORCID: https://orcid.org/0000-0002-9930-8499)
- Sylvie M. Noordermeer (ORCID: https://orcid.org/0000-0003-2737-9690)
- Sebastian Pomplun (ORCID: https://orcid.org/0000-0003-0905-8551)
- Olivier J. M. Béquignon (ORCID: https://orcid.org/0000-0002-7554-9220)
- Sebastian Böcker (ORCID: https://orcid.org/0000-0002-9304-8091)
- Martin Hoffmann (ORCID: https://orcid.org/0000-0002-3554-2710)
- J. Miguel Mata (ORCID: https://orcid.org/0000-0002-9884-0184)
- Edith van der Nol (ORCID: https://orcid.org/0000-0002-0597-8185)
- Tiemen J. Wendel (ORCID: https://orcid.org/0009-0006-1434-2396)
- Nicola Haupt (ORCID: https://orcid.org/0009-0001-2280-5286)
- Marcus Ludwig (ORCID: https://orcid.org/0000-0001-9981-2153)
- Gerard J. P. van Westen (ORCID: https://orcid.org/0000-0003-0717-1817)
- Sean M. McKenna (ORCID: https://orcid.org/0000-0001-9197-5089)
- Benthe A. M. Smit (ORCID: https://orcid.org/0009-0007-7459-8841)
Institutions
- Leiden University (NL)
- Leiden University Medical Center (NL)
- Oncode Institute (NL)
- Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. - Hans-Knöll-Institut (HKI) (DE)
- Friedrich Schiller University Jena (DE)
Publication Details
- Journal
- Nature Communications
- Published
- 2025-10-27
- DOI
- https://doi.org/10.1038/s41467-025-65282-1
- Citations
- 1
- Primary Topic
- Chemical Synthesis and Analysis
- Type
- article
- Field-Weighted Citation Impact
- 0.81
Funders
- European Commission
- Thüringer Ministerium für Wirtschaft, Wissenschaft und Digitale Gesellschaft
- Oncode Institute
- European Regional Development Fund