DNA-encoded chemical libraries (DELs) have become a powerful technology platform in drug discovery. Dual-pharmacophore DELs display two sets of small molecules at the termini of DNA duplexes, thereby enabling the identification of synergistic binders against biological targets, and have been successfully applied in fragment-based ligand discovery and affinity maturation of known ligands. However, dual-pharmacophore DELs identify separate binders that require subsequent linking to obtain the full ligands, which is often challenging. Here we report a protein-templated DEL selection approach that can identify full ligand/inhibitor structures from DNA-encoded dynamic libraries (DEDLs) without the need for subsequent fragment linking. Our approach is based on dynamic DNA hybridization and target-templated in situ ligand synthesis, and it incorporates and encodes the linker structures in the library, along with the building blocks, to be sampled by the target protein. To demonstrate the performance of this method, 4.35-million- and 3.00-million-member DEDLs with different library architectures were prepared, and hit selection was achieved against four therapeutically relevant target proteins.

DNA 编码化学库 (DEL) 已成为药物发现中强大的技术平台。双药效团 DEL 在 DNA 双链体末端显示两组小分子，从而能够识别针对生物靶标的协同结合剂，并已成功应用于基于片段的配体发现和已知配体的亲和力成熟。然而，双药效团 DEL 识别单独的结合物，需要随后连接以获得完整的配体，这通常具有挑战性。在这里，我们报告了一种蛋白质模板 DEL 选择方法，该方法可以从 DNA 编码动态库 (DEDL) 中识别完整的配体/抑制剂结构，而无需后续片段连接。我们的方法基于动态 DNA 杂交和靶标模板原位配体合成，它将库中的接头结构以及构建模块纳入并编码，以便由靶蛋白进行采样。为了证明该方法的性能，制备了具有不同文库架构的 435 万和 300 万成员 DEDL，并针对四种治疗相关的靶蛋白实现了命中选择。