Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, California, USA.
Chemistry and Chemical Biology Graduate Program, University of California-San Francisco, San Francisco, California, USA.
Nat Chem Biol. 2014 Dec;10(12):1066-72. doi: 10.1038/nchembio.1666. Epub 2014 Oct 26.
Chemical probes that form a covalent bond with a protein target often show enhanced selectivity, potency and utility for biological studies. Despite these advantages, protein-reactive compounds are usually avoided in high-throughput screening campaigns. Here we describe a general method (DOCKovalent) for screening large virtual libraries of electrophilic small molecules. We apply this method prospectively to discover reversible covalent fragments that target distinct protein nucleophiles, including the catalytic serine of AmpC β-lactamase and noncatalytic cysteines in RSK2, MSK1 and JAK3 kinases. We identify submicromolar to low-nanomolar hits with high ligand efficiency, cellular activity and selectivity, including what are to our knowledge the first reported reversible covalent inhibitors of JAK3. Crystal structures of inhibitor complexes with AmpC and RSK2 confirm the docking predictions and guide further optimization. As covalent virtual screening may have broad utility for the rapid discovery of chemical probes, we have made the method freely available through an automated web server (http://covalent.docking.org/).
与蛋白质靶标形成共价键的化学探针通常显示出增强的选择性、效力和用于生物学研究的实用性。尽管有这些优势，但在高通量筛选活动中通常避免使用蛋白质反应性化合物。在这里，我们描述了一种筛选亲电小分子大型虚拟文库的通用方法（DOCKovalent）。我们前瞻性地应用这种方法来发现靶向不同蛋白质亲核试剂的可逆共价片段，包括 AmpC β-内酰胺酶的催化丝氨酸和 RSK2、MSK1 和 JAK3 激酶中的非催化半胱氨酸。我们鉴定出具有高配体效率、细胞活性和选择性的亚毫摩尔至低纳摩尔的命中物，其中包括据我们所知首次报道的 JAK3 可逆共价抑制剂。与 AmpC 和 RSK2 的抑制剂复合物的晶体结构证实了对接预测，并指导进一步优化。由于共价虚拟筛选可能广泛用于快速发现化学探针，因此我们通过自动化网络服务器（http://covalent.docking.org/）免费提供该方法。
