Discovery of a Hidden Pocket beneath the NES Groove by Novel Noncovalent CRM1 Inhibitors

Protein
localization is frequently manipulated to favor
tumor initiation
and progression. In cancer cells, the nuclear export factor CRM1 is
often overexpressed and aberrantly localizes many tumor suppressors
via protein–protein interactions. Although targeting protein–protein
interactions is usually challenging, covalent inhibitors, including
the FDA-approved drug KPT-330 (selinexor), were successfully developed.
The development of noncovalent CRM1 inhibitors remains scarce. Here,
by shifting the side chain of two methionine residues and virtually
screening against a large compound library, we successfully identified
a series of noncovalent CRM1 inhibitors with a stable scaffold. Crystal
structures of inhibitor–protein complexes revealed that one
of the compounds, B28, utilized a deeply hidden protein interior cavity
for binding. SAR analysis guided the development of several B28 derivatives
with enhanced inhibition on nuclear export and growth of multiple
cancer cell lines. This work may benefit the development of new CRM1-targeted
therapies.

蛋白质定位在肿瘤的起始和进展过程中常被操控以利于其发展。在癌细胞中，核输出因子CRM1常常过表达，并通过蛋白质-蛋白质相互作用异常定位许多肿瘤抑制因子。尽管针对蛋白质-蛋白质相互作用的靶向通常具有挑战性，但共价抑制剂，包括已获美国食品药品监督管理局批准的药物KPT-330（塞利尼索），已被成功开发。非共价CRM1抑制剂的研发尚显不足。本研究通过改变两个蛋氨酸残基的侧链，并针对大量化合物库进行虚拟筛选，成功鉴定了一系列具有稳定骨架的非共价CRM1抑制剂。抑制剂-蛋白复合物的晶体结构揭示了其中一种化合物B28利用了深藏的蛋白质内部腔室进行结合。结构-活性关系分析指导了多个B28衍生物的开发，这些衍生物在增强对核输出和多种癌细胞系生长的抑制方面表现出显著效果。本研究成果有望促进针对CRM1的新疗法的开发。