A UK Academic DNA-Encoded Library Screening Resource

This article is based on a poster originally authored by Taylor C., PhD² , Hassan H., PhD² , Celis S., PhD¹ , Detta E., PhD³ , Tierney A., BSc¹ , Noble M., Prof  ² , Leach A., PhD¹ , Brunschweiger A., PhD³ , Waring M., Prof² , Butterworth S., PhD¹

¹University of Manchester, School of Health Sciences
²Newcastle University, School of Natural and Environmental Sciences
³TU Dortmund University, Department of Chemistry and Chemical Biology

Background

The identification of small molecule protein ligands remains a key hurdle for the validation/translation of novel targets, which is pivotal to the successful development of new medicines. However, the costly resources to deliver an effective compound screening campaign and the contractual commitments to the screening organizations limit access to drug discovery projects for biomedical researchers.¹

To address this capability gap, we are establishing a DNA-encoded library (DEL) resource to provide cost-free and commitment-free access to high-throughput screening for academic research groups.

Materials and Methods

1. The DEL technology allows the preparation of millions of druglike molecules, each linked to a DNA sequence that uniquely identifies it. This is possible thanks to the exponential power of combinatorial chemistry in combination with established DNA ligation protocols. ²
2. Libraries of these compounds are then selected as a mixture for binding affinity against a protein of interest, which results in mixtures becoming enriched with the compounds with higher affinities.
3. Next-generation sequencing offers an ultra-high throughput, scalable and fast method to read DNA tags in a matter of days.
4. Since each DNA tag encodes the structure of its associated molecule, high-affinity protein binders(hits) are identified. Hits are later validated on- and off-DNA.

Ultimately, DEL screening results in a simpler and cost-effective strategy to accelerate the hit discovery stage of drug development.

Results

As a proof of concept, a 35-member DEL was selected against carbonic anhydrase CA IX:

Library Synthesis

The library was designed to contain some aromatic sulfonamides as building blocks (BB2), a known inhibitory chemotype for CA IX.

DNA Sequencing

Statistical analysis of the sequencing data allows us to determine compound enrichment as the ratio of the post-selection population fraction to the pre-selection population fraction.

Hit Identification

Compounds containing aromatic sulfonamides were found to be enriched among the rest of the library members and, therefore, identified as hits.

Conclusions

• Our collaborative team has developed on-DNA chemistry to enable the synthesis of up to 20 million compounds and has completed the synthesis of initial trial libraries of ~300,000 compounds.
• We have recently validated the discovery workflow by selecting a library against carbonic anhydrase CA IX and identifying aromatic sulfonamide-containing compounds as hits.

Future Work

• In the next year, we will synthesize and validate up to ten libraries designed to be chemically diverse so they can target a range of protein classes.
• These libraries will become available in 2024 for applicants from UK universities to request selection against their proteins of interest.

References

1. Machutta, C., Kollmann, C., Lind, K. et al., Nat. Commun., 2017, 8, 16081.
2. Satz, A.L., Brunschweiger, A., Flanagan, M.E., Gloger A., Hansen N.J.V., Kuai L., Kunig V.B.K., Lu X., Madsen D., Marcaurelle L.A., Mulrooney C., O’Donovan G., Sakata S., Scheuermann J., Nat. Rev. Methods Primers, 2022, 2, 3.