Chemical tools to expand the ligandable proteome: elaborated fragment-based photoreactive stereoprobes

Efforts to expand the ligandable proteome have explored stereochemically defined fragments equipped with photoreactive and clickable handles (photo-stereoprobes) for mapping reversible small molecule-protein interactions in living systems. Here, we investigate the impact of structural elaboration of fragment photo-stereoprobes on interactions with the proteome of human cancer cells. We find that even conservative increases in size and complexity have profound effects on protein binding for fragment photo-stereoprobes, leading to enhanced stereoselective protein interactions, while abrogating others. We use stereochemically matched competitor ligands to assess the extent of protein binding in human cells, leading to the discovery of high-stoichiometry ligands for proteins from different functional classes, including a structurally novel set of epoxide hydrolase inhibitors. Our findings support the broad ligandability potential of the human proteome while also highlighting challenges in converting reversible small molecule-protein interaction maps into more advanced chemical probes.

为拓展可配体化蛋白质组（ligandable proteome），相关研究已探索了带有光反应性与可点击标记基团的立体化学定义片段——即光立体探针（photo-stereoprobes）——用于在活体系统中绘制可逆小分子-蛋白质相互作用图谱。本研究中，我们探究了片段光立体探针的结构衍生对其与人类癌细胞蛋白质组相互作用的影响。我们发现，即便仅对片段光立体探针进行尺寸与复杂度的保守性提升，也会对其蛋白质结合能力产生显著影响：既能增强立体选择性蛋白质相互作用，同时也会消除部分结合活性。我们利用立体化学匹配的竞争性配体，评估了人类细胞内蛋白质结合的程度，并由此发现了针对不同功能类别蛋白质的高结合计量比配体，其中包括一类结构新颖的环氧化物水解酶抑制剂。我们的研究结果证实了人类蛋白质组具备广泛的可配体化潜力，同时也凸显了将可逆小分子-蛋白质相互作用图谱转化为更先进化学探针所面临的挑战。