Structure-Guided Design of the First Noncovalent Small-Molecule Inhibitor of CRM1

Nuclear export factor chromosome region maintenance 1 (CRM1) is an attractive anticancer and antiviral drug target that spurred several research efforts to develop its inhibitor. Noncovalent CRM1 inhibitors are desirable, but none is reported to date. Here, we present the crystal structure of yeast CRM1 in complex with S109, a substructure of CBS9106 (under clinical test). Superimposition with the LFS-829 (another covalent CRM1 inhibitor) complex inspired the design of a noncovalent CRM1 inhibitor. Among nine synthesized compounds, noncovalent CRM1 inhibitor 1 (NCI-1) showed a high affinity to human and yeast CRM1 in the absence or presence of GST-bound Ras-related nuclear protein (RanGTP). Unlike covalent inhibitors, the crystal structure showed that NCI-1 is bound in the “open” nuclear export signal (NES) groove of CRM1, simultaneously occupying two hydrophobic pockets. NCI-1 additionally inhibited the nuclear export and proliferation of cells harboring the human CRM1-C528S mutant. Our work opens up the avenue of noncovalent CRM1 inhibitor development toward a more potent, less toxic, and broad-spectrum anticancer/antiviral therapy.核输出因子染色体区域维持蛋白1（CRM1）是极具吸引力的抗癌与抗病毒药物靶点，由此催生了诸多开发其抑制剂的研究工作。非共价结合型CRM1抑制剂是理想的候选药物，但截至目前尚无相关报道。本研究解析了酵母CRM1与S109的复合物晶体结构，其中S109是处于临床试验阶段的CBS9106的亚结构片段。通过将本研究解析的酵母CRM1-S109复合物与另一种共价CRM1抑制剂LFS-829的复合物结构进行叠合分析，为非共价CRM1抑制剂的设计提供了重要思路。在合成的9种化合物中，非共价CRM1抑制剂1（NCI-1）无论是否存在谷胱甘肽S-转移酶（Glutathione S-transferase, GST）结合的Ras相关核蛋白（RanGTP），均对人源及酵母CRM1展现出较高的结合亲和力。与共价抑制剂不同，晶体结构显示NCI-1结合于CRM1的"开放型"核输出信号（NES）凹槽内，同时占据了两个疏水口袋。此外，NCI-1还可抑制携带人源CRM1-C528S突变体细胞的核输出过程与增殖能力。本研究为开发更高效、低毒且广谱的抗癌/抗病毒治疗用非共价CRM1抑制剂开辟了全新路径。