Targeted protein degradation and stabilization are promising therapeutic modalities because of their potency, versatility and their potential to expand the druggable target space^1,2. However, only a few of the hundreds of E3 ligases and deubiquitinases in the human proteome have been harnessed for this purpose, which substantially limits the potential of the approach. Moreover, there may be other protein classes that could be exploited for protein stabilization or degradation^3,4,5, but there are currently no methods that can identify such effector proteins in a scalable and unbiased manner. Here we established a synthetic proteome-scale platform to functionally identify human proteins that can promote the degradation or stabilization of a target protein in a proximity-dependent manner. Our results reveal that the human proteome contains a large cache of effectors of protein stability. The approach further enabled us to comprehensively compare the activities of human E3 ligases and deubiquitinases, identify and characterize non-canonical protein degraders and stabilizers and establish that effectors have vastly different activities against diverse targets. Notably, the top degraders were more potent against multiple therapeutically relevant targets than the currently used E3 ligases cereblon and VHL. Our study provides a functional catalogue of stability effectors for targeted protein degradation and stabilization and highlights the potential of induced proximity screens for the discovery of new proximity-dependent protein modulators.

靶向蛋白质降解和稳定是有前途的治疗方式，因为它们具有效力、多功能性以及扩大药物靶点空间的潜力^1,2。然而，人类蛋白质组中数百种 E3 连接酶和去泛素酶中只有少数被用于此目的，这极大地限制了该方法的潜力。此外，可能还有其他蛋白质类别可用于蛋白质稳定或降解^3,4,5，但目前没有方法可以以可扩展且无偏见的方式识别此类效应蛋白。在这里，我们建立了一个合成蛋白质组规模的平台，以功能性地识别人类蛋白质，这些蛋白质可以以邻近依赖性方式促进目标蛋白质的降解或稳定。我们的结果表明，人类蛋白质组包含大量蛋白质稳定性效应子。该方法进一步使我们能够全面比较人类 E3 连接酶和去泛素酶的活性，识别和表征非典型蛋白质降解剂和稳定剂，并确定效应子针对不同靶点具有截然不同的活性。值得注意的是，顶级降解剂对多个治疗相关靶点比目前使用的 E3 连接酶 cereblon 和 VHL 更有效。我们的研究提供了用于靶向蛋白质降解和稳定的稳定效应子的功能目录，并强调了诱导邻近筛选在发现新的邻近依赖性蛋白质调节剂方面的潜力。