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Ma L, Zhang Y, Luo Z, Zheng L, Jiang Y, Zou M, Zheng Y, Kong L, Wang X. Discovery of phenylisoxazolidine analogs targeting receptor interacting protein kinase 1 with anti-inflammatory activity. Eur J Med Chem 2025; 290:117530. [PMID: 40153932 DOI: 10.1016/j.ejmech.2025.117530] [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: 01/15/2025] [Revised: 03/17/2025] [Accepted: 03/18/2025] [Indexed: 04/01/2025]
Abstract
Receptor Interacting Protein Kinase1 (RIPK1) is a key regulator of necroptosis and plays an important role in various inflammatory signaling and cell death processes. GSK963 has been reported to inhibit RIPK1 with limited anti-necroptotic effect. We designed and prepared a series of phenylisoxazolidine analogs based on GSK963 to improve their anti-necroptotic activity. After several turns of structure activity relationship (SAR) studies, compound 22, encoded with KWML-22, was found to have good anti-necroptotic activity (EC50 = 30.0 nM) and enzymatic activity (IC50 = 6.9 nM) against RIPK1. In a TNF-α-induced inflammation in vivo model, a dose of 10 mg/kg protected mice from hypothermia and death. Our results suggest that 22 is a promising lead compound for the study of inflammatory diseases.
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Affiliation(s)
- Liangliang Ma
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Yonglei Zhang
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Zhongwen Luo
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Long Zheng
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Yuhan Jiang
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Meiting Zou
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Yiwei Zheng
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Lingyi Kong
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China.
| | - Xiaobing Wang
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China.
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Li Y, Tian Z, Nan X, Zhang S, Zhou Q, Lu S. HSSPPI: hierarchical and spatial-sequential modeling for PPIs prediction. Brief Bioinform 2025; 26:bbaf079. [PMID: 40037640 PMCID: PMC11879409 DOI: 10.1093/bib/bbaf079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2024] [Revised: 02/10/2025] [Accepted: 02/13/2025] [Indexed: 03/06/2025] Open
Abstract
MOTIVATION Protein-protein interactions play a fundamental role in biological systems. Accurate detection of protein-protein interaction sites (PPIs) remains a challenge. And, the methods of PPIs prediction based on biological experiments are expensive. Recently, a lot of computation-based methods have been developed and made great progress. However, current computational methods only focus on one form of protein, using only protein spatial conformation or primary sequence. And, the protein's natural hierarchical structure is ignored. RESULTS In this study, we propose a novel network architecture, HSSPPI, through hierarchical and spatial-sequential modeling of protein for PPIs prediction. In this network, we represent protein as a hierarchical graph, in which a node in the protein is a residue (residue-level graph) and a node in the residue is an atom (atom-level graph). Moreover, we design a spatial-sequential block for capturing complex interaction relationships from spatial and sequential forms of protein. We evaluate HSSPPI on public benchmark datasets and the predicting results outperform the comparative models. This indicates the effectiveness of hierarchical protein modeling and also illustrates that HSSPPI has a strong feature extraction ability by considering spatial and sequential information simultaneously. AVAILABILITY AND IMPLEMENTATION The code of HSSPPI is available at https://github.com/biolushuai/Hierarchical-Spatial-Sequential-Modeling-of-Protein.
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Affiliation(s)
- Yuguang Li
- School of Computer and Artificial Intelligence, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Zhen Tian
- School of Computer and Artificial Intelligence, Zhengzhou University, Zhengzhou 450001, Henan, China
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou 324003, Zhejiang, China
| | - Xiaofei Nan
- School of Computer and Artificial Intelligence, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Shoutao Zhang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
- Zhongyuan Intelligent Medical Laboratory, Zhengzhou 450001, Henan, China
| | - Qinglei Zhou
- School of Computer and Artificial Intelligence, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Shuai Lu
- School of Computer and Artificial Intelligence, Zhengzhou University, Zhengzhou 450001, Henan, China
- National Supercomputing Center in Zhengzhou, Zhengzhou University, Zhengzhou 450001, Henan, China
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Jin Z, Dai Y, Ji Y, Peng X, Duan W, Ai J, Zhang H. Design, synthesis, and structure-activity relationship studies of 6,7-dihydro-5 H-pyrrolo[1,2- b][1,2,4]triazole derivatives as necroptosis inhibitors. RSC Med Chem 2024; 15:2514-2526. [PMID: 39026642 PMCID: PMC11253868 DOI: 10.1039/d4md00265b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 05/17/2024] [Indexed: 07/20/2024] Open
Abstract
The development of necroptosis inhibitors has emerged as a promising strategy to effectively mitigate necroptosis-related inflammatory diseases, neurodegenerative diseases, and cancers. In this paper, we reported a series of 6,7-dihydro-5H-pyrrolo[1,2-b][1,2,4]triazole derivatives as potent necroptosis inhibitors. The representative compound 26 displayed potent anti-necroptotic activity in both human and mouse cellular assays and exhibited potent inhibitory activity against receptor-interacting protein kinase 1 (RIPK1). In vivo pharmacokinetic studies were performed to determine the oral exposure of compound 26. Finally, molecular docking elucidated that compound 26 could effectively bind to the allosteric pocket of RIPK1 and serve as a type III inhibitor. Taken together, our findings highlighted that compound 26 represented a promising lead compound for future necroptosis inhibitor development.
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Affiliation(s)
- Zechen Jin
- Small-Molecule Drug Research Center, Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences 555 Zu Chong Zhi Road Shanghai 201203 China
- School of Pharmacy, University of Chinese Academy of Sciences No. 19A Yuquan Road Beijing 100049 China
| | - Yang Dai
- Cancer Research Center, Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences 555 Zu Chong Zhi Road Shanghai 201203 China
- School of Pharmacy, University of Chinese Academy of Sciences No. 19A Yuquan Road Beijing 100049 China
| | - Yinchun Ji
- Cancer Research Center, Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences 555 Zu Chong Zhi Road Shanghai 201203 China
| | - Xia Peng
- Cancer Research Center, Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences 555 Zu Chong Zhi Road Shanghai 201203 China
| | - Wenhu Duan
- Small-Molecule Drug Research Center, Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences 555 Zu Chong Zhi Road Shanghai 201203 China
- School of Pharmacy, University of Chinese Academy of Sciences No. 19A Yuquan Road Beijing 100049 China
- Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery Yantai Shandong 264117 China
| | - Jing Ai
- Cancer Research Center, Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences 555 Zu Chong Zhi Road Shanghai 201203 China
- School of Pharmacy, University of Chinese Academy of Sciences No. 19A Yuquan Road Beijing 100049 China
| | - Hefeng Zhang
- Small-Molecule Drug Research Center, Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences 555 Zu Chong Zhi Road Shanghai 201203 China
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Dong J, Liu W, Liu W, Wen Y, Liu Q, Wang H, Xiang G, Liu Y, Hao H. Acute lung injury: a view from the perspective of necroptosis. Inflamm Res 2024; 73:997-1018. [PMID: 38615296 DOI: 10.1007/s00011-024-01879-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 03/23/2024] [Accepted: 03/31/2024] [Indexed: 04/15/2024] Open
Abstract
BACKGROUND ALI/ARDS is a syndrome of acute onset characterized by progressive hypoxemia and noncardiogenic pulmonary edema as the primary clinical manifestations. Necroptosis is a form of programmed cell necrosis that is precisely regulated by molecular signals. This process is characterized by organelle swelling and membrane rupture, is highly immunogenic, involves extensive crosstalk with various cellular stress mechanisms, and is significantly implicated in the onset and progression of ALI/ARDS. METHODS The current body of literature on necroptosis and ALI/ARDS was thoroughly reviewed. Initially, an overview of the molecular mechanism of necroptosis was provided, followed by an examination of its interactions with apoptosis, pyroptosis, autophagy, ferroptosis, PANOptosis, and NETosis. Subsequently, the involvement of necroptosis in various stages of ALI/ARDS progression was delineated. Lastly, drugs targeting necroptosis, biomarkers, and current obstacles were presented. CONCLUSION Necroptosis plays an important role in the progression of ALI/ARDS. However, since ALI/ARDS is a clinical syndrome caused by a variety of mechanisms, we emphasize that while focusing on necroptosis, it may be more beneficial to treat ALI/ARDS by collaborating with other mechanisms.
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Affiliation(s)
- Jinyan Dong
- First Clinical Medical College, Shandong University of Traditional Chinese Medicine, Jinan, 250000, Shandong, China
| | - Weihong Liu
- Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, 250000, Shandong, China
| | - Wenli Liu
- First Clinical Medical College, Shandong University of Traditional Chinese Medicine, Jinan, 250000, Shandong, China
| | - Yuqi Wen
- Second Clinical Medical College, Shandong University of Traditional Chinese Medicine, Jinan, 250000, Shandong, China
| | - Qingkuo Liu
- First Clinical Medical College, Shandong University of Traditional Chinese Medicine, Jinan, 250000, Shandong, China
| | - Hongtao Wang
- First Clinical Medical College, Shandong University of Traditional Chinese Medicine, Jinan, 250000, Shandong, China
| | - Guohan Xiang
- First Clinical Medical College, Shandong University of Traditional Chinese Medicine, Jinan, 250000, Shandong, China
| | - Yang Liu
- Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, 250000, Shandong, China.
| | - Hao Hao
- Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, 250000, Shandong, China.
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