Department of Chemistry, The Scripps Research Institute , Jupiter, Florida 33458, United States.
State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences , Beijing 102206, China.
J Am Chem Soc. 2017 Apr 19;139(15):5588-5595. doi: 10.1021/jacs.7b01791. Epub 2017 Apr 10.
Targeted covalent inhibitors have emerged as a powerful approach in the drug discovery pipeline. Key to this process is the identification of signaling pathways (or receptors) specific to (or overexpressed in) disease cells. In this context, fragment-based ligand discovery (FBLD) has significantly expanded our view of the ligandable proteome and affords tool compounds for biological inquiry. To date, such covalent ligand discovery has almost exclusively employed cysteine-reactive small-molecule fragments. However, functional cysteine residues in proteins are often redox-sensitive and can undergo oxidation in cells. Such reactions are particularly relevant in diseases, like cancer, which are linked to excessive production of reactive oxygen species. Once oxidized, the sulfur atom of cysteine is much less reactive toward electrophilic groups used in the traditional FBLD paradigm. To address this limitation, we recently developed a novel library of diverse carbon-based nucleophile fragments that react selectively with cysteine sulfenic acid formed in proteins via oxidation or hydrolysis reactions. Here, we report analysis of sulfenic acid-reactive C-nucleophile fragments screened against a colon cancer cell proteome. Covalent ligands were identified for >1280 S-sulfenylated cysteines present in "druggable" proteins and orphan targets, revealing disparate reactivity profiles and target preferences. Among the unique ligand-protein interactions identified was that of a pyrrolidinedione nucleophile that reacted preferentially with protein tyrosine phosphatases. Fragment-based covalent ligand discovery with C-nucleophiles affords an expansive snapshot of the ligandable "redoxome" with significant implications for covalent inhibitor pharmacology and also affords new chemical tools to investigate redox-regulation of protein function.
靶向共价抑制剂已成为药物发现领域的一种强大方法。这一过程的关键是识别特定于（或在）疾病细胞中过表达的信号通路（或受体）。在这种情况下，基于片段的配体发现（FBLD）大大扩展了我们对配体蛋白组的认识，并为生物研究提供了工具化合物。迄今为止，这种共价配体发现几乎完全采用了半胱氨酸反应性小分子片段。然而，蛋白质中的功能半胱氨酸残基通常对氧化还原敏感，并可在细胞中发生氧化。在癌症等与活性氧物种过度产生相关的疾病中，这种反应尤其相关。一旦被氧化，半胱氨酸的硫原子对传统 FBLD 范例中使用的亲电基团的反应性就会大大降低。为了解决这一限制，我们最近开发了一种新型的、多样化的碳亲核片段库，这些片段可以通过氧化或水解反应选择性地与蛋白质中形成的半胱氨酸亚磺酸反应。在这里，我们报告了针对结肠癌细胞蛋白质组筛选半胱氨酸亚磺酸反应性 C-亲核片段的分析结果。在“可成药”蛋白质和孤儿靶标中鉴定出了超过 1280 个 S-亚磺酰化半胱氨酸的共价配体，揭示了不同的反应性和靶标偏好。在所鉴定的独特配体-蛋白质相互作用中，有一种吡咯烷二酮亲核试剂与蛋白酪氨酸磷酸酶优先反应。基于 C-亲核试剂的共价片段配体发现提供了配体“氧化还原组”的广泛快照，对共价抑制剂药理学具有重要意义，并提供了新的化学工具来研究蛋白质功能的氧化还原调节。
