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Shen Z, Zhuang W, Li K, Guo Y, Qu B, Chen S, Gao J, Liu J, Xu L, Dong X, Che J, Li Q. Identification of Novel Covalent XPO1 Inhibitors Based on a Hybrid Virtual Screening Strategy. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27082543. [PMID: 35458742 PMCID: PMC9024667 DOI: 10.3390/molecules27082543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/08/2022] [Accepted: 04/11/2022] [Indexed: 11/20/2022]
Abstract
Nuclear export protein 1 (XPO1), a member of the nuclear export protein-p (Karyopherin-P) superfamily, regulates the transport of “cargo” proteins. To facilitate this important process, which is essential for cellular homeostasis, XPO1 must first recognize and bind the cargo proteins. To inhibit this process, small molecule inhibitors have been designed that inhibit XPO1 activity through covalent binding. However, the scaffolds for these inhibitors are very limited. While virtual screening may be used to expand the diversity of the XPO1 inhibitor skeleton, enormous computational resources would be required to accomplish this using traditional screening methods. In the present study, we report the development of a hybrid virtual screening workflow and its application in XPO1 covalent inhibitor screening. After screening, several promising XPO1 covalent molecules were obtained. Of these, compound 8 performed well in both tumor cell proliferation assays and a nuclear export inhibition assay. In addition, molecular dynamics simulations were performed to provide information on the mode of interaction of compound 8 with XPO1. This research has identified a promising new scaffold for XPO1 inhibitors, and it demonstrates an effective and resource-saving workflow for identifying new covalent inhibitors.
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Affiliation(s)
- Zheyuan Shen
- Department of Urology, Rui’an People’s Hospital, the Third Affiliated Hospital of Wenzhou Medical University, Wenzhou 325200, China;
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Hangzhou 310018, China; (S.C.); (J.G.); (X.D.)
| | - Weihao Zhuang
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; (W.Z.); (Y.G.); (B.Q.); (J.L.)
| | - Kang Li
- Jiangsu Hengrui Pharmaceuticals Co., Ltd., Shanghai 222000, China;
| | - Yu Guo
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; (W.Z.); (Y.G.); (B.Q.); (J.L.)
| | - Bingxue Qu
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; (W.Z.); (Y.G.); (B.Q.); (J.L.)
| | - Sikang Chen
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Hangzhou 310018, China; (S.C.); (J.G.); (X.D.)
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; (W.Z.); (Y.G.); (B.Q.); (J.L.)
| | - Jian Gao
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Hangzhou 310018, China; (S.C.); (J.G.); (X.D.)
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; (W.Z.); (Y.G.); (B.Q.); (J.L.)
| | - Jing Liu
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; (W.Z.); (Y.G.); (B.Q.); (J.L.)
| | - Lei Xu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou 213001, China;
| | - Xiaowu Dong
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Hangzhou 310018, China; (S.C.); (J.G.); (X.D.)
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; (W.Z.); (Y.G.); (B.Q.); (J.L.)
| | - Jinxin Che
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Hangzhou 310018, China; (S.C.); (J.G.); (X.D.)
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; (W.Z.); (Y.G.); (B.Q.); (J.L.)
- Correspondence: (J.C.); (Q.L.)
| | - Qimeng Li
- Department of Urology, Rui’an People’s Hospital, the Third Affiliated Hospital of Wenzhou Medical University, Wenzhou 325200, China;
- Correspondence: (J.C.); (Q.L.)
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