JEDEL: Zero-Shot DNA-Encoded Library Design for Early-Stage Drug Discovery
For early-stage drug discovery, JEDEL enables experimentally realizable library design, addressing the synthesis bottleneck of virtual molecule generation.
JEDEL generates synthesis-ready DNA-encoded libraries directly from pharmacophore representations, outperforming baselines in binding affinity and pharmacophore recovery across 18 protein targets without retraining.
We present JEDEL, a framework for generating synthesis-ready DNA-encoded libraries (DELs) directly from three-dimensional pharmacophore representations of active ligands. JEDEL is the first model to map pharmacophore interaction patterns to actionable, scalable synthesis instructions, enabling the design of targeted libraries comprising potentially millions of molecules. Unlike existing generative approaches that produce virtual compounds requiring downstream synthesis planning, JEDEL operates within the space of purchasable building blocks and validated reactions, ensuring that every output is experimentally realizable by construction. JEDEL learns a predictive alignment between pharmacophore geometry and molecular structure and decodes this into combinatorial synthesis routes at scale. Across 18 protein targets, it generates focused libraries that outperform random and diversity-based baselines in predicted binding affinity, pharmacophore recovery, and sample efficiency, without target-specific retraining. JEDEL enables a shift from virtual molecule generation to experimentally deployable library design.