Quantitative Validation and Application of the Photo-Cross-Linking Selection for Double-Stranded DNA-Encoded Libraries

The DNA-encoded compound library (DEL) technology has accelerated the target hits discovery in new drug development. While affinity-based DEL selection can distinguish high-affinity ligands, moderate-affinity ligands are also potential drug candidates with further modifications. Herein, we designed a photo-cross-linking selection method for DELs with double-stranded DNA (dsDELs) to screen moderate-affinity ligands. We constructed two photo-cross-linking libraries with linkers of different lengths that connect a diazirine group to the DNA encoded compound. The diazirine group can be activated by UV irradiation and thus bond with the target protein in a reachable distance. In the model selection, the feasibility of the photo-cross-linking screening system was verified by qPCR and NGS technology. Both high-affinity and moderate-affinity ligands were successfully selected from the libraries.DNA编码化合物库（DEL）技术已显著加速了新药研发中的靶点命中发现进程。尽管基于亲和力的DEL筛选可区分高亲和力配体，但中等亲和力配体经后续修饰后同样具备成为潜在药物候选分子的潜力。本文中，我们针对双链DNA型DNA编码化合物库（dsDELs）设计了一种光交联筛选方法，用于筛选中等亲和力配体。我们构建了两种光交联文库，其采用不同长度的连接臂将双吖丙啶基连接至DNA编码化合物上。该双吖丙啶基可经紫外照射激活，进而在可及距离内与靶标蛋白形成共价结合。在模型筛选实验中，我们通过定量聚合酶链式反应（qPCR）与下一代测序（NGS）技术验证了该光交联筛选系统的可行性。我们成功从该文库中筛选得到高亲和力与中等亲和力的配体。