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（DNA-encoded compound library, DEL）技术已加速新药研发中的靶点命中物发现进程。基于亲和力的DEL筛选虽可甄别高亲和力配体，但中等亲和力配体同样是具备进一步修饰潜力的潜在候选药物。本文中，我们设计了一种针对双链DNA编码化合物库（double-stranded DNA DEL, dsDELs）的光交联筛选方法，用于筛选中等亲和力配体。我们构建了两款带有不同长度连接臂的光交联文库，该连接臂将双吖丙啶基连接至DNA编码化合物之上。双吖丙啶基可经紫外照射激活，并在可及距离内与靶标蛋白结合。在模型筛选实验中，我们通过定量PCR（qPCR）与下一代测序技术（Next-Generation Sequencing, NGS）验证了该光交联筛选体系的可行性，并成功从文库中筛选获得高亲和力与中等亲和力两类配体。