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

ChemRxiv

Abstract

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 ~1 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 developed efficient, high-diversity synthesis protocols for a broad range of chemical scaffolds and benchmarked the platform in affinity selections against carbonic anhydrase IX, identifying multiple nanomolar binders. We further applied SELs to flap endonuclease 1 (FEN1) – a disease related DNA-processing enzyme inaccessible to DELs – and discovered potent inhibitors. Taken together, screening barcode-free libraries of this scale is unprecedented, enables access to novel target classes, and promises substantial impact on both academic and industrial early drug discovery.

Authors 14

1. Edith van der Nol Aachen

   Leiden University · Oncode Institute

   Affiliation as printed

   Leiden University

   Oncode Institute

2. Nicola Haupt

   Friedrich Schiller University Jena

   Affiliation as printed

   Friedrich Schiller University Jena

3. Benthe A. M. Smit Aachen

   Leiden University

   Affiliation as printed

   Leiden University

4. Martin Andre Hoffmann

   Friedrich Schiller University Jena

   Affiliation as printed

   Friedrich Schiller University Jena

5. Martin S. Engler

   Friedrich Schiller University Jena

   Affiliation as printed

   Friedrich Schiller University Jena

6. Marcus Ludwig

   Friedrich Schiller University Jena

   Affiliation as printed

   Friedrich Schiller University Jena

7. Sean M. McKenna Aachen

   Leiden University · Oncode Institute

   Affiliation as printed

   Leiden University

   Oncode Institute

8. J. Miguel Mata Aachen

   Leiden University · Oncode Institute

   Affiliation as printed

   Leiden University

   Oncode Institute

9. Olivier J. M. Béquignon Aachen

   Leiden University

   Affiliation as printed

   Leiden University

10. Gerard J. P. van Westen Aachen

    Leiden University

    Affiliation as printed

    Leiden University

11. Tiemen J. Wendel Aachen

    Leiden University Medical Center · Oncode Institute

    Affiliation as printed

    Leiden University Medical Center

    Oncode Institute

12. Sylvie M. Noordermeer Aachen

    Leiden University Medical Center · Oncode Institute

    Affiliation as printed

    Leiden University Medical Center

    Oncode Institute

13. Sebastian Böcker

    Friedrich Schiller University Jena

    Affiliation as printed

    Friedrich Schiller University Jena

14. Sebastian J. Pomplun Aachen

    Leiden University · Oncode Institute

    Affiliation as printed

    Leiden University

    Oncode Institute