Scaling the Unreachable: Acoustic Droplet Ejection for DNA-Encoded Library Multicomponent Synthesis

Objective

DNA-encoded libraries (DELs) allow the screening of millions to billions of small molecules via DNA barcodes that record each compound’s synthesis. Conventional DEL workflows rely on simple reactions (e.g., amide coupling, Suzuki) in microliter volumes using tip-based robots, limiting chemical diversity, sustainability, and throughput. This project overcomes these constraints by integrating acoustic droplet ejection (ADE), multicomponent reactions (MCRs), and DEL synthesis for the first time. ADE enables nanoliter-scale, tip-free transfers with high precision, drastically reducing reagent consumption and time. Coupled with MCR chemistry, such as Ugi-4CR, libraries of 10⁸–10⁹ structurally complex, 3D-rich molecules can be generated in hours under DNA-compatible conditions. The workflow includes ADE-based synthesis, enzymatic DNA ligation, and selection assays—achievable in a single afternoon. Biological validation will employ both target-based pull-down/NGS screening and proteome-wide selections in whole-cell lysates using covalent capture strategies. This dual approach ensures robust identification of ligands active in purified and complex systems. The CATRIN/IMTM Dömling lab offers unparalleled infrastructure, including advanced automation (Echo, TECAN EVO), UPLC-MS, NGS, and the world’s largest isocyanide collection, supported by expertise in synthetic chemistry, DEL screening, and MCR methodology. A provisional patent has been filed, and strong industrial interest underscores the platform’s commercial potential. This sustainable, high-throughput strategy redefines DEL synthesis, enabling AI-driven design loops and positioning Palacky University as a leader in next-generation drug discovery.