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Wang X, Shao X, Wang M, Li Y, Geng T, Wang Y, Ding X, He Y, Jin H, Sun Y, Li Z, Meng X. Design, synthesis, anticancer activity evaluation and molecular dynamics study of pyrazine N-oxide-based SHP2 allosteric inhibitors. Eur J Med Chem 2025; 293:117687. [PMID: 40344735 DOI: 10.1016/j.ejmech.2025.117687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2025] [Revised: 04/23/2025] [Accepted: 04/24/2025] [Indexed: 05/11/2025]
Abstract
Src homology-2-containing protein tyrosine phosphatase 2 (SHP2), the first oncoprotein identified in the protein phosphatase family, has emerged as a promising anticancer target in recent years. Here, we report the discovery of a novel series of pyrazine N-oxide derivatives as potent SHP2 allosteric inhibitors and the identification of compound C5 as a highly potent and selective SHP2 allosteric inhibitor (SHP2WT IC50 = 0.023 μM, SHP2E76K IC50 = 0.119 μM). At the cellular level, C5 exerted significant antiproliferative effect on KYSE-520 and MV-411 cells (KYSE-520 IC50 = 6.97 μM, MV-411 IC50 = 0.67 μM) and induced apoptosis of MV-411 cells by downregulating the SHP2-mediated ERK cell signaling. Molecular dynamics simulations revealed that C5 could form stable hydrogen bond interactions, cation-π interactions and water bridges with key residues Glu110, Arg111, Phe113, Gly115 and Thr253, thereby effectively binding to the tunnel allosteric site of SHP2. Notably, the pyrazine N-oxide scaffold could additionally form a strong and stable hydrogen bond with Arg111. Collectively, this work uncovers a novel and potent scaffold as well as presents compound C5 as a promising lead for the development of new chemotypes of SHP2 allosteric inhibitors.
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Affiliation(s)
- Xin Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Xiaoyu Shao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Meijing Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Yan Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Tongtong Geng
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Yashuai Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Xuyang Ding
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Yichao He
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Hongwei Jin
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Yang Sun
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Zhongjun Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China.
| | - Xiangbao Meng
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China.
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