The success of targeted covalent inhibitors in the global pharmaceutical industry has led to a resurgence of covalent drug discovery. However, covalent inhibitor design for flexible binding sites remains a difficult task due to a lack of methodological development. Here, we compared covalent docking to empirical electrophile screening against the highly dynamic target K-Ras^G12C. While the overall hit rate of both methods was comparable, we were able to rapidly progress a docking hit to a potent irreversible covalent binder that modifies the inactive, GDP-bound state of K-Ras^G12C. Hydrogen–deuterium exchange mass spectrometry was used to probe the protein dynamics of compound binding to the switch-II pocket and subsequent destabilization of the nucleotide-binding region. SOS-mediated nucleotide exchange assays showed that, contrary to prior switch-II pocket inhibitors, these new compounds appear to accelerate nucleotide exchange. This study highlights the efficiency of covalent docking as a tool for the discovery of chemically novel hits against challenging targets.

中文翻译：

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新型K-Ras G12C Switch-II共价结合剂使Ras不稳定并加速核苷酸交换

靶向共价抑制剂在全球制药行业的成功导致了共价药物发现的复兴。然而，由于缺乏方法学的发展，针对柔性结合位点的共价抑制剂设计仍然是一项艰巨的任务。在这里，我们将共价对接与经验亲电筛选与高度动态的目标K-Ras ^{G12C进行了比较}。尽管两种方法的总命中率相当，但我们能够快速将对接命中发展为有效的不可逆共价结合剂，从而改变了K-Ras ^G12C处于非活动状态且受GDP约束的状态。氢-氘交换质谱用于探测化合物与switch-II口袋结合以及随后核苷酸结合区不稳定的蛋白质动力学。SOS介导的核苷酸交换分析表明，与以前的switch-II口袋抑制剂相反，这些新化合物似乎促进了核苷酸交换。这项研究强调了共价对接作为发现具有挑战性目标的化学新命中工具的效率。