Orthogonal IMiD-Degron Pairs Induce Selective Protein Degradation in Cells

Immunomodulatory imide drugs (IMiDs), including thalidomide,
lenalidomide,
and pomalidomide, can be used to induce degradation of a protein of
interest that is fused to a short degron motif, which often comprises
a zinc finger (ZF). These IMiDs, however, also induce the degradation
of endogenous ZF-containing neosubstrates, including IKZF1, IKZF3,
and SALL4. To improve degradation selectivity, we took a bump-and-hole
approach to design and screen bumped IMiD analogues against 8380 ZF
mutants. This yielded a bumped IMiD analogue that induces efficient
degradation of a mutant ZF degron, while not affecting other cellular
proteins, including IKZF1, IKZF3, and SALL4. In proof-of-concept studies,
this system was applied to induce degradation of the optimum degron
fused to CDK9, HPRT1, NanoLuc, or TRIM28. We anticipate that this
system will be a valuable addition to the current arsenal of degron
systems for use in target validation.

免疫调节性酰亚胺类药物（Immunomodulatory imide drugs, IMiDs）包括沙利度胺、来那度胺与泊马度胺，可诱导与短降解基序（degron motif）融合的目的蛋白发生降解，该降解基序通常包含锌指结构（zinc finger, ZF）。不过此类IMiDs同时还会诱导内源性含锌指的新底物发生降解，例如IKZF1、IKZF3及SALL4。为提升降解选择性，我们采用凸凹适配策略（bump-and-hole approach），针对8380种锌指突变体设计并筛选带有凸位修饰的IMiD类似物。最终得到一款修饰有凸位的IMiD类似物，其可高效诱导突变型锌指降解基序发生降解，且不会对包括IKZF1、IKZF3与SALL4在内的其他细胞蛋白造成影响。在概念验证研究中，该体系被用于诱导融合于细胞周期蛋白依赖性激酶9（CDK9）、次黄嘌呤磷酸核糖基转移酶1（HPRT1）、纳米荧光素酶（NanoLuc）或三结构域蛋白28（TRIM28）的最优降解基序发生降解。我们预计，该体系将成为当前用于靶点验证的降解基序工具库中极具价值的新增成员。