Protein degraders, also known as proteolysis targeting chimeras (PROTACs), are bifunctional small molecules that promote cellular degradation of a protein of interest (POI). PROTACs act as molecular mediators, bringing an E3 ligase and a POI into proximity, thus promoting ubiquitination and degradation of the targeted POI. Despite their great promise as next-generation pharmaceutical drugs, the development of new PROTACs is challenged by the complexity of the system, which involves binary and ternary interactions between components. Here, we demonstrate the strength of native mass spectrometry (nMS), a label-free technique, to provide novel insight into PROTAC-mediated protein interactions. We show that nMS can monitor the formation of ternary E3-PROTAC-POI complexes and detect various intermediate species in a single experiment. A unique benefit of the method is its ability to reveal preferentially formed E3-PROTAC-POI combinations in competition experiments with multiple substrate proteins, thereby positioning it as an ideal high-throughput screening strategy during the development of new PROTACs.

中文翻译：

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天然质谱可以有效预测PROTAC功效。

蛋白质降解剂，也称为靶向靶向嵌合体的蛋白水解（PROTAC），是双功能的小分子，可促进目标蛋白质（POI）的细胞降解。PROTAC充当分子介质，使E3连接酶和POI接近，从而促进了目标POI的泛素化和降解。尽管它们作为下一代药物具有广阔的前景，但新PROTAC的开发仍受到系统复杂性的挑战，该系统涉及组件之间的二元和三元相互作用。在这里，我们展示了天然质谱（nMS）（一种无标签技术）的实力，可提供对PROTAC介导的蛋白质相互作用的新颖见解。我们显示nMS可以监视三元E3-PROTAC-POI复合物的形成，并在单个实验中检测各种中间物种。