Pharmacophore-focused chemical libraries are continuously being created in drug discovery programs, yet screening assays to maximize the usage of such libraries are not fully explored. Here, we report a chemical proteomics approach to reutilizing a focused chemical library of 1,800 indole-containing molecules for discovering uncharacterized ligand-protein pairs. Gel-based protein profiling of the library using a photo-affinity indole probe 1 enabled us to find new ligands for glyoxalase 1 (Glo1), an enzyme involved in the detoxification of methylglyoxal. Structure optimization of the ligands yielded an inhibitor for Glo1 (9). Molecule 9 increased the cellular methylglyoxal levels in human cells and suppressed the osteoclast formation of mouse bone marrow-derived macrophages. X-ray structure analyses revealed that the molecule lies at a site abutting the substrate binding site, which is consistent with the enzyme kinetic profile of 9. Overall, this study exemplifies how chemical proteomics can be used to exploit existing focused chemical libraries.

在药物发现程序中不断创建以药理学为中心的化学文库，但尚未充分探索最大化此类文库使用率的筛选试验。在这里，我们报告一种化学蛋白质组学方法，以重新利用包含1,800个吲哚分子的聚焦化学文库，以发现未表征的配体-蛋白质对。使用光亲和吲哚探针1对文库进行基于凝胶的蛋白质谱分析，使我们能够找到乙二醛酶1（Glo1）的新配体，乙二醛酶1是参与甲基乙二醛解毒的酶。配体的结构优化产生了Glo1的抑制剂（9）。分子9增加人体内细胞甲基乙二醛的水平并抑制小鼠骨髓来源的巨噬细胞的破骨细胞形成。X射线结构分析显示该分子位于与底物结合位点邻接的位点，这与9的酶动力学特征相符。总的来说，这项研究举例说明了如何使用化学蛋白质组学来开发现有的重点化学文库。