Sirocchi Ludovica S, Scharnweber Maximilian, Oberndorfer Sarah, Siszler Gabriella, Zak Krzysztof M, Rumpel Klaus, Neumüller Ralph A, Wilding Birgit
Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, Vienna A-1121, Austria.
J Am Chem Soc. 2025 May 7;147(18):15787-15795. doi: 10.1021/jacs.5c03562. Epub 2025 Apr 23.
Targeted covalent inhibitors are known to be successful therapeutics used in various indications. Covalent drugs typically target cysteine, as cysteine is well suited due to its high nucleophilicity. However, its low abundance in protein binding sites represents a major limitation. As a result, there is a need to covalently target additional nucleophilic amino acids. Recent literature has reported covalent inhibitors labeling aspartic acid in KRAS. However, these compounds also covalently bind to KRAS, indicating their cross-reactivity to cysteine along with aspartic acid. We report here carbodiimides as a novel reactive group to selectively target aspartic acid. Covalent inhibitors bearing a carbodiimide moiety are shown to covalently label KRAS in biochemical and cellular assays. A high-resolution X-ray crystal structure was obtained, which illustrates the mechanism of the covalent bond formation with KRAS. Carbodiimide warheads show selectivity toward KRAS over other KRAS alleles and represent a new covalent warhead suitable for covalently binding to aspartic acid in a biochemical and cellular context.
靶向共价抑制剂是已知的用于各种适应症的成功治疗药物。共价药物通常靶向半胱氨酸，因为半胱氨酸由于其高亲核性而非常适合。然而，其在蛋白质结合位点中的低丰度是一个主要限制。因此，需要共价靶向其他亲核氨基酸。最近的文献报道了共价抑制剂标记KRAS中的天冬氨酸。然而，这些化合物也与KRAS共价结合，表明它们对半胱氨酸和天冬氨酸具有交叉反应性。我们在此报告碳二亚胺作为一种新型反应基团，可选择性地靶向天冬氨酸。带有碳二亚胺部分的共价抑制剂在生化和细胞试验中显示出可共价标记KRAS。获得了高分辨率X射线晶体结构，其阐明了与KRAS形成共价键的机制。碳二亚胺弹头对KRAS显示出比对其他KRAS等位基因更高的选择性，并且代表了一种新的共价弹头，适用于在生化和细胞环境中与天冬氨酸共价结合。
