Edith van der Nol ,  Nils Alexander Haupt ,  Qing Qing Gao ,  Benthe A. M. Smit ,  Martin Andre Hoffmann ,  Martin Engler-Lukajewski ,  Marcus Ludwig ,  Sean McKenna ,  J. Miguel Mata ,  Olivier J. M. Béquignon ,  Gerard van Westen ,  Tiemen J. Wendel ,  Sylvie M. Noordermeer ,  Sebastian Böcker ,  Sebastian Pomplun

Nature Communication

DOI: 10.1038/s41467-025-65282-1

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 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.

Summary

This article introduces a barcode-free self-encoded library (SEL) platform for affinity selection-based hit discovery in early drug discovery. The SEL platform leverages tandem mass spectrometry and custom software for automated structure annotation, eliminating the need for external tags. The platform enables the screening of large libraries with diverse scaffolds, identifying high-affinity binders for targets like carbonic anhydrase IX and inhibitors for flap endonuclease 1 (FEN1). This approach overcomes limitations of DNA-encoded libraries (DELs) by avoiding synthesis complexity and incompatibility with nucleic acid-binding targets, offering a streamlined workflow for rapid hit discovery.

Highlights

1. A barcode-free self-encoded library (SEL) platform enables screening of over half a million small molecules in a single experiment.
2. SELs combine tandem mass spectrometry with custom software for automated structure annotation, eliminating the need for external tags.
3. Efficient, high-diversity synthesis protocols are developed for a broad range of chemical scaffolds.
4. The platform identifies multiple nanomolar binders for carbonic anhydrase IX and potent inhibitors for flap endonuclease 1 (FEN1).
5. SELs offer advantages in synthesis complexity and scope compared to DNA-encoded libraries (DELs), expanding the accessible chemical space for drug discovery.

Conclusion

The SEL platform represents a significant advancement in early drug discovery by enabling the screening of large, diverse libraries without the need for external tags. This barcode-free approach overcomes limitations associated with DNA-encoded libraries, such as synthesis complexity and incompatibility with nucleic acid-binding targets. The successful identification of high-affinity binders and inhibitors for challenging targets like carbonic anhydrase IX and flap endonuclease 1 demonstrates the platform's potential for rapid hit discovery. The streamlined synthesis and automated decoding capabilities of SELs make this technology accessible to a broader range of researchers, promising substantial impact on both academic and industrial drug discovery efforts. Future work will focus on further optimizing the platform for even larger libraries and exploring its application to additional challenging targets.