Ban Chen, Shuangshuang Liu, Huiyin Xia, Xican Li, Rongxin Cai, Yingqing Zhang, Yuchen Hu, Jiangtao Su
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The approach incorporated ultrahigh-performance liquid chromatography-quadrupole-orbitrap mass spectrometry analysis, data mining, drug-like property evaluation, molecular docking, chemical structure clustering, molecular dynamics (MD) simulations, in vitro experimental validation, and density functional theory (DFT) calculations. A total of 517 compounds were identified in ABR, of which 248 met the drug-likeness criteria. Additionally, seventeen compounds from six structural clusters were identified as having theoretical Keap1-Nrf2 PPI inhibitory activity. Among these compounds, shidasterone, nortrachelogenin, wogonin, and <i>N</i>-<i>trans</i>-feruloylmethoxytyramine were subjected to experimental evaluation for their Keap1-Nrf2 PPI inhibitory and free radical scavenging activities. MD simulations and DFT calculations demonstrated that these compounds directly inhibited Keap1-Nrf2 PPI through hydrophobic interactions, hydrogen bonds, and salt bridges. Moreover, DFT calculations confirmed that these compounds scavenged free radicals via the hydrogen atom transfer mechanism. In conclusion, the strategy presented herein offers a robust framework for screening direct Keap1-Nrf2 PPI inhibitors with structural diversity from ABR and other TCM sources.</p><h3>Graphical abstract</h3><p>An integrated strategy was developed to screen direct Keap1-Nrf2 PPI inhibitors from TCM taking <i>Achyranthis bidentatae Radix</i> as an example.</p><div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":621,"journal":{"name":"Journal of Computer-Aided Molecular Design","volume":"39 1","pages":""},"PeriodicalIF":3.1000,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Integrated strategy for screening direct Keap1-Nrf2 PPI inhibitors from traditional Chinese medicine: a case study of Achyranthis bidentatae Radix\",\"authors\":\"Ban Chen, Shuangshuang Liu, Huiyin Xia, Xican Li, Rongxin Cai, Yingqing Zhang, Yuchen Hu, Jiangtao Su\",\"doi\":\"10.1007/s10822-025-00662-9\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><p>Direct inhibition of the Kelch-like ECH-associated protein 1 (Keap1)-nuclear factor erythroid 2-related factor 2 (Nrf2) protein–protein interaction (PPI) represents a critical pathway for enhancing the antioxidant response. Therefore, screening for direct Keap1-Nrf2 PPI inhibitors holds significant potential for addressing oxidative stress-related diseases. This study aims to develop an integrated approach to identify direct Keap1-Nrf2 PPI inhibitors from traditional Chinese medicine (TCM) using <i>Achyranthis bidentatae Radix</i> (ABR) as a case study. The approach incorporated ultrahigh-performance liquid chromatography-quadrupole-orbitrap mass spectrometry analysis, data mining, drug-like property evaluation, molecular docking, chemical structure clustering, molecular dynamics (MD) simulations, in vitro experimental validation, and density functional theory (DFT) calculations. A total of 517 compounds were identified in ABR, of which 248 met the drug-likeness criteria. Additionally, seventeen compounds from six structural clusters were identified as having theoretical Keap1-Nrf2 PPI inhibitory activity. 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Integrated strategy for screening direct Keap1-Nrf2 PPI inhibitors from traditional Chinese medicine: a case study of Achyranthis bidentatae Radix
Direct inhibition of the Kelch-like ECH-associated protein 1 (Keap1)-nuclear factor erythroid 2-related factor 2 (Nrf2) protein–protein interaction (PPI) represents a critical pathway for enhancing the antioxidant response. Therefore, screening for direct Keap1-Nrf2 PPI inhibitors holds significant potential for addressing oxidative stress-related diseases. This study aims to develop an integrated approach to identify direct Keap1-Nrf2 PPI inhibitors from traditional Chinese medicine (TCM) using Achyranthis bidentatae Radix (ABR) as a case study. The approach incorporated ultrahigh-performance liquid chromatography-quadrupole-orbitrap mass spectrometry analysis, data mining, drug-like property evaluation, molecular docking, chemical structure clustering, molecular dynamics (MD) simulations, in vitro experimental validation, and density functional theory (DFT) calculations. A total of 517 compounds were identified in ABR, of which 248 met the drug-likeness criteria. Additionally, seventeen compounds from six structural clusters were identified as having theoretical Keap1-Nrf2 PPI inhibitory activity. Among these compounds, shidasterone, nortrachelogenin, wogonin, and N-trans-feruloylmethoxytyramine were subjected to experimental evaluation for their Keap1-Nrf2 PPI inhibitory and free radical scavenging activities. MD simulations and DFT calculations demonstrated that these compounds directly inhibited Keap1-Nrf2 PPI through hydrophobic interactions, hydrogen bonds, and salt bridges. Moreover, DFT calculations confirmed that these compounds scavenged free radicals via the hydrogen atom transfer mechanism. In conclusion, the strategy presented herein offers a robust framework for screening direct Keap1-Nrf2 PPI inhibitors with structural diversity from ABR and other TCM sources.
Graphical abstract
An integrated strategy was developed to screen direct Keap1-Nrf2 PPI inhibitors from TCM taking Achyranthis bidentatae Radix as an example.
期刊介绍：
The Journal of Computer-Aided Molecular Design provides a form for disseminating information on both the theory and the application of computer-based methods in the analysis and design of molecules. The scope of the journal encompasses papers which report new and original research and applications in the following areas:
- theoretical chemistry;
- computational chemistry;
- computer and molecular graphics;
- molecular modeling;
- protein engineering;
- drug design;
- expert systems;
- general structure-property relationships;
- molecular dynamics;
- chemical database development and usage.
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