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Shi Y, Wu C, Shi J, Gao T, Ma H, Li L, Zhao Y. Protein phosphorylation and kinases: Potential therapeutic targets in necroptosis. Eur J Pharmacol 2024; 970:176508. [PMID: 38493913 DOI: 10.1016/j.ejphar.2024.176508] [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: 11/10/2023] [Revised: 03/05/2024] [Accepted: 03/14/2024] [Indexed: 03/19/2024]
Abstract
Necroptosis is a pivotal contributor to the pathogenesis of various human diseases, including those affecting the nervous system, cardiovascular system, pulmonary system, and kidneys. Extensive investigations have elucidated the mechanisms and physiological ramifications of necroptosis. Among these, protein phosphorylation emerges as a paramount regulatory process, facilitating the activation or inhibition of specific proteins through the addition of phosphate groups to their corresponding amino acid residues. Currently, the targeting of kinases has gained recognition as a firmly established and efficacious therapeutic approach for diverse diseases, notably cancer. In this comprehensive review, we elucidate the intricate role of phosphorylation in governing key molecular players in the necroptotic pathway. Moreover, we provide an in-depth analysis of recent advancements in the development of kinase inhibitors aimed at modulating necroptosis. Lastly, we deliberate on the prospects and challenges associated with the utilization of kinase inhibitors to modulate necroptotic processes.
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Affiliation(s)
- Yihui Shi
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Chengkun Wu
- School of Medicine, Nankai University, Tianjin, 300071, China
| | - Jiayi Shi
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Taotao Gao
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Huabin Ma
- Central Laboratory, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China.
| | - Long Li
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, Zhejiang, 315211, China.
| | - Yufen Zhao
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, Zhejiang, 315211, China
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2
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Kurup S, Gesinski D, Assaad K, Reynolds A. Design, synthesis, and evaluation of dual EGFR/AURKB inhibitors as anticancer agents for non-small cell lung cancer. Bioorg Med Chem Lett 2024; 100:129612. [PMID: 38199330 PMCID: PMC10951975 DOI: 10.1016/j.bmcl.2024.129612] [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: 11/03/2023] [Revised: 12/20/2023] [Accepted: 01/06/2024] [Indexed: 01/12/2024]
Abstract
The epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) are first-line agents for mutant EGFR-positive (mEGFR+) NSCLC. However, secondary resistant mutations develop following therapy that prevent EGFR-TKI binding. The EGFR-TKIs are rendered ineffective in NSCLC expressing EGFR resistant mutations (rmEGFR+). Mutations in Kirsten rat sarcoma virus protein (mKRAS) support persistent signaling downstream of EGFR regardless of EGFR-TKI earlier in the signaling cascade. The EGFR-TKIs are ineffective in mKRAS+ NSCLC. Thus, newer anticancer agents are needed for rmEGFR+ and mKRAS+ NSCLC. Aurora kinase B (AURKB) is a mitosis related kinase that is overexpressed in NSCLC and supports cancer cell proliferation and survival. Literature reports have suggested that AURKB inhibitors if given concurrently with an EGFR-TKI could overcome EGFR-TKI resistance in mKRAS+ NSCLC and rmEGFR + NSCLC, and showed improved anticancer effects compared to current single-targeted EGFR-TKIs. Molecular modeling was used to identify similarities between the kinase pockets of EGFR and AURKB. An overlap was observed for the inactive conformation of EGFR and the active conformation of AURKB. Compounds 3-7 were synthesized as dual EGFR/AURKB inhibitors for mKRAS+ and rmEGFR+ NSCLC. Compounds 5, 6 and 7 were identified as dual EGFR/AURKB inhibitors. Compound 5 demonstrated modest micromolar inhibition of rmEGFR+ NSCLC. All investigated compounds showed moderate inhibition of mKRAS+ NSCLC cells. Compound 7 demonstrated single-digit micromolar inhibition of mKRAS+ NSCLC.
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Affiliation(s)
- Sonali Kurup
- College of Pharmacy, Ferris State University, United States.
| | - Dayna Gesinski
- College of Pharmacy, Ferris State University, United States
| | - Kaitlin Assaad
- College of Pharmacy, Ferris State University, United States
| | - Aidan Reynolds
- College of Pharmacy, Ferris State University, United States
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3
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Zhou Y, Cai Z, Zhai Y, Yu J, He Q, He Y, Jitkaew S, Cai Z. Necroptosis inhibitors: mechanisms of action and therapeutic potential. Apoptosis 2024; 29:22-44. [PMID: 38001341 DOI: 10.1007/s10495-023-01905-6] [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] [Accepted: 10/15/2023] [Indexed: 11/26/2023]
Abstract
Necroptosis is a type of programmed cell death that is morphologically similar to necrosis. This type of cell death is involved in various pathophysiological disorders, including inflammatory, neurodegenerative, infectious, and malignant diseases. Receptor-interacting protein kinase 1 (RIPK1), RIPK3, and mixed lineage kinase domain-like protein (MLKL) pseudokinase constitute the core components of the necroptosis signaling pathway and are considered the most promising targets for therapeutic intervention. The discovery and characterization of necroptosis inhibitors not only accelerate our understanding of the necroptosis signaling pathway but also provide important drug candidates for the treatment of necroptosis-related diseases. Here, we will review recent research progress on necroptosis inhibitors, mechanisms of action and their potential applications for disease treatment.
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Affiliation(s)
- Yingbo Zhou
- School of Medicine, Tongji University, Shanghai, 200092, China
| | - Zhangtao Cai
- School of Medicine, Tongji University, Shanghai, 200092, China
| | - Yijia Zhai
- School of Medicine, Tongji University, Shanghai, 200092, China
| | - Jintao Yu
- School of Medicine, Tongji University, Shanghai, 200092, China
| | - Qiujing He
- School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Yuan He
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Siriporn Jitkaew
- Center of Excellence for Cancer and Inflammation, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Zhenyu Cai
- School of Medicine, Tongji University, Shanghai, 200092, China.
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200092, China.
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4
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Sun X, Wu Y, Xu F, Liu C. Screening of potent RIPK3 inhibitors to attenuate necroptosis and inflammation in mouse traumatic brain injury models. Exp Neurol 2024; 372:114633. [PMID: 38061556 DOI: 10.1016/j.expneurol.2023.114633] [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: 09/23/2023] [Revised: 11/15/2023] [Accepted: 11/29/2023] [Indexed: 01/03/2024]
Abstract
Necroptosis is a type of cell death that occurs when cells are exposed to external stressors such as inflammation, infections, or injury. In necroptosis, cells use a different set of proteins including: receptor-interacting kinase 1 (RIPK1 or RIP1), receptor-interacting kinase 3 (RIPK3 or RIP3) and the phosphorylation of its substrate mixed lineage kinase domain-like protein (MLKL) and pathways to trigger their own death. Mutations in the gene encoding RIPK3 have been associated with many diseases, including neurodegenerative diseases, neuroinflammatory diseases, inflammatory diseases,tumors, and it is being studied as a potential target for inflammatory injury therapy. RIPK3 has also been implicated in the pathology of neuroinflammation following Traumatic brain injury and is currently being explored as a potential therapy. We screened through necroptosis blocking compounds, a library of FDA-approved compounds. We found four compounds:1D6-Foretinib GSK1363089; 15F6-Poziotinib (HM781-36B); 15F9-Dasatinib monohydrate; 15A10-Pexmetinib (ARRY-614); acts as potent inhibitors of necroptosis (Necroptosis Blocking Compounds, NBCs) by blocking the RIPK3 kinase activity. These four compounds effectively block necroptosis induced by death receptor ligands Toll-like receptors as well as viral infections in human, rat and mouse cells. The cellular activation of RIPK3 and MLKL stimulated by necroptosis was strongly inhibited by NBCs. The compounds are promising for targeting RIPK3 kinase activity, thereby preventing necroptosis and inflammatory responses. In our study, we explored the role of NBCs in neuroprotection after traumatic brain injury. It's effectiveness in traumatic brain injury animal models and favorable safety profiles make it a potential candidate for the advances of new therapies for necroptosis-associated neuroinflammatory disorders.
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Affiliation(s)
- Xue Sun
- The Second Affiliated Hospital of Soochow University, Department of Neurology and Suzhou Clinical Research Center of Neurological Disease, Soochow University, Suzhou, China; The First Affiliated hospital of Soochow University, Department of Emergency Medicine, Soochow University, Jiangsu Province, Suzhou, China; Institute of Trauma Medicine, Soochow University, China; Jiangsu Provincial Medical Innovation Center of Trauma Medicine, China
| | - Yu Wu
- The First Affiliated Hospital of Soochow University, Department of neurosurgery, Soochow University, Jiangsu Province, Suzhou, China
| | - Feng Xu
- The First Affiliated hospital of Soochow University, Department of Emergency Medicine, Soochow University, Jiangsu Province, Suzhou, China; Institute of Trauma Medicine, Soochow University, China; Jiangsu Provincial Medical Innovation Center of Trauma Medicine, China.
| | - Chunfeng Liu
- The Second Affiliated Hospital of Soochow University, Department of Neurology and Suzhou Clinical Research Center of Neurological Disease, Soochow University, Suzhou, China.
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5
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Qin Y, Li D, Qi C, Xiang H, Meng H, Liu J, Zhou S, Gong X, Li Y, Xu G, Zu R, Xie H, Xu Y, Xu G, Zhang Z, Chen S, Pan L, Li Y, Tan L. Structure-based development of potent and selective type-II kinase inhibitors of RIPK1. Acta Pharm Sin B 2024; 14:319-334. [PMID: 38261830 PMCID: PMC10793102 DOI: 10.1016/j.apsb.2023.10.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 10/21/2023] [Accepted: 10/26/2023] [Indexed: 01/25/2024] Open
Abstract
Receptor-interacting serine/threonine-protein kinase 1 (RIPK1) functions as a key regulator in inflammation and cell death and is involved in mediating a variety of inflammatory or degenerative diseases. A number of allosteric RIPK1 inhibitors (RIPK1i) have been developed, and some of them have already advanced into clinical evaluation. Recently, selective RIPK1i that interact with both the allosteric pocket and the ATP-binding site of RIPK1 have started to emerge. Here, we report the rational development of a new series of type-II RIPK1i based on the rediscovery of a reported but mechanistically atypical RIPK3i. We also describe the structure-guided lead optimization of a potent, selective, and orally bioavailable RIPK1i, 62, which exhibits extraordinary efficacies in mouse models of acute or chronic inflammatory diseases. Collectively, 62 provides a useful tool for evaluating RIPK1 in animal disease models and a promising lead for further drug development.
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Affiliation(s)
- Ying Qin
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dekang Li
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chunting Qi
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
| | - Huaijiang Xiang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huyan Meng
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingli Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
| | - Shaoqing Zhou
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinyu Gong
- University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Ying Li
- University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Guifang Xu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
| | - Rui Zu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
| | - Hang Xie
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Yechun Xu
- University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Gang Xu
- Institute of Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, the Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen 518112, China
| | - Zheng Zhang
- Institute of Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, the Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen 518112, China
| | - Shi Chen
- Department of Burn and Plastic Surgery, Shenzhen Institute of Translational Medicine, Shenzhen University Medical School, Shenzhen Second People’s Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen 518035, China
| | - Lifeng Pan
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Ying Li
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
| | - Li Tan
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
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6
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Guerrero-Mauvecin J, Fontecha-Barriuso M, López-Diaz AM, Ortiz A, Sanz AB. RIPK3 and kidney disease. Nefrologia 2024; 44:10-22. [PMID: 37150671 DOI: 10.1016/j.nefroe.2023.04.006] [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: 09/29/2022] [Accepted: 12/28/2022] [Indexed: 05/09/2023] Open
Abstract
Receptor interacting protein kinase 3 (RIPK3) is an intracellular kinase at the crossroads of cell death and inflammation. RIPK3 contains a RIP homotypic interaction motif (RHIM) domain which allows interactions with other RHIM-containing proteins and a kinase domain that allows phosphorylation of target proteins. RIPK3 may be activated through interaction with RHIM-containing proteins such as RIPK1, TRIF and DAI (ZBP1, DLM-1) or through RHIM-independent mechanisms in an alkaline intracellular pH. RIPK3 mediates necroptosis and promotes inflammation, independently of necroptosis, through either activation of NFκB or the inflammasome. There is in vivo preclinical evidence of the contribution of RIPK3 to both acute kidney injury (AKI) and chronic kidney disease (CKD) and to the AKI-to-CKD transition derived from RIPK3 deficient mice or the use of small molecule RIPK3 inhibitors. In these studies, RIPK3 targeting decreased inflammation but kidney injury improved only in some contexts. Clinical translation of these findings has been delayed by the potential of some small molecule inhibitors of RIPK3 kinase activity to trigger apoptotic cell death by inducing conformational changes of the protein. A better understanding of the conformational changes in RIPK3 that trigger apoptosis, dual RIPK3/RIPK1 inhibitors or repurposing of multiple kinase inhibitors such as dabrafenib may facilitate clinical development of the RIPK3 inhibition concept for diverse inflammatory diseases, including kidney diseases.
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Affiliation(s)
- Juan Guerrero-Mauvecin
- Department of Nephrology and Hypertension, IIS-Fundacion Jimenez Diaz UAM, 28040 Madrid, Spain
| | | | - Ana M López-Diaz
- Department of Nephrology and Hypertension, IIS-Fundacion Jimenez Diaz UAM, 28040 Madrid, Spain
| | - Alberto Ortiz
- Department of Nephrology and Hypertension, IIS-Fundacion Jimenez Diaz UAM, 28040 Madrid, Spain; RICORS2040, 28040 Madrid, Spain; Departamento de Medicina, Facultad de Medicina, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Ana B Sanz
- Department of Nephrology and Hypertension, IIS-Fundacion Jimenez Diaz UAM, 28040 Madrid, Spain; RICORS2040, 28040 Madrid, Spain.
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7
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Misehe M, Matoušová M, Dvořáková A, Hercík K, Škach K, Chalupská D, Dejmek M, Šála M, Hájek M, Boura E, Mertlíková-Kaiserová H, Nencka R. Exploring positions 6 and 7 of a quinazoline-based scaffold leads to changes in selectivity and potency towards RIPK2/3 kinases. Eur J Med Chem 2023; 260:115717. [PMID: 37598483 DOI: 10.1016/j.ejmech.2023.115717] [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: 06/14/2023] [Revised: 08/08/2023] [Accepted: 08/08/2023] [Indexed: 08/22/2023]
Abstract
Receptor-interacting protein kinases 2 and 3 (RIPK2 and RIPK3) are considered attractive therapeutic enzyme targets for the treatment of a multitude of inflammatory diseases and cancers. In this study, we developed three interrelated series of novel quinazoline-based derivatives to investigate the effects of extensive modifications of positions 6 and 7 of the central core on the inhibitory activity and the selectivity against these RIPKs. The design of the derivatives was inspired by analyses of available literary knowledge on both RIPK2 and RIPK3 in complex with known quinazoline or quinoline inhibitors. Enzymatic investigations for bioactivity of the prepared molecules against purified RIPKs (RIPK1-4) shed light on multiple potent and selective RIPK2 and dual RIPK2/3 inhibitors. Furthermore, evaluations in living cells against the RIPK2-NOD1/2-mediated signaling pathways, identified as the potential primary targets, demonstrated nanomolar inhibition for a majority of the compounds. In addition, we have demonstrated overall good stability of various lead inhibitors in both human and mouse microsomes and plasma. Several of these compounds also were evaluated for selectivity across 58 human kinases other than RIPKs, exhibiting outstanding specificity profiles. We have thus clearly demonstrated that tuning appropriate substitutions at positions 6 and 7 of the developed quinazoline derivatives may lead to interesting potency and specificities against RIPK2 and RIPK3. This knowledge might therefore be employed for the targeted preparation of new, highly potent and selective tools against these RIPKs, which could be of utility in biological and clinical research.
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Affiliation(s)
- Mbilo Misehe
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Nam. 2, 166 10, Prague 6, Czech Republic; Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 2030/8, 128 43, Prague 2, Czech Republic
| | - Marika Matoušová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Nam. 2, 166 10, Prague 6, Czech Republic
| | - Alexandra Dvořáková
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Nam. 2, 166 10, Prague 6, Czech Republic
| | - Kamil Hercík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Nam. 2, 166 10, Prague 6, Czech Republic
| | - Kryštof Škach
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Nam. 2, 166 10, Prague 6, Czech Republic
| | - Dominika Chalupská
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Nam. 2, 166 10, Prague 6, Czech Republic
| | - Milan Dejmek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Nam. 2, 166 10, Prague 6, Czech Republic
| | - Michal Šála
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Nam. 2, 166 10, Prague 6, Czech Republic
| | - Miroslav Hájek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Nam. 2, 166 10, Prague 6, Czech Republic
| | - Evzen Boura
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Nam. 2, 166 10, Prague 6, Czech Republic
| | - Helena Mertlíková-Kaiserová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Nam. 2, 166 10, Prague 6, Czech Republic
| | - Radim Nencka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Nam. 2, 166 10, Prague 6, Czech Republic.
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8
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Kim N, Park CJ, Kim Y, Ryu S, Cho H, Nam Y, Han M, Shin JS, Sim T. Identification of Pyrido[3,4-d]pyrimidine derivatives as RIPK3-Mediated necroptosis inhibitors. Eur J Med Chem 2023; 259:115635. [PMID: 37494773 DOI: 10.1016/j.ejmech.2023.115635] [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: 05/15/2023] [Revised: 07/01/2023] [Accepted: 07/10/2023] [Indexed: 07/28/2023]
Abstract
Necroptosis executed by RIPK3-mediated phosphorylation of MLKL is a programmed necrotic cell death and implicated with various diseases such as sterile inflammation. We designed and synthesized pyrido[3,4-d]pyrimidine derivatives as novel necroptosis inhibitors capable of suppressing the phosphorylation of MLKL. Our SAR studies reveal that 20 possesses comparable inhibitory activity against RIPK3-mediated pMLKL in HT-29 cells relative to GSK872 (2), a representative selective RIPK3 inhibitor. Based on biochemical kinase assay results, 20 is comparable to GSK872 (2) with regard to activity against RIPK3 and less potent against RIPK1 than GSK872, indicating selectivity of 20 towards RIPK3 over RIPK1 is higher than that of GSK872. In HT-29 cells, 20 inhibits necroptosis via MLKL oligomerization impediment. Moreover, 20 suppresses migration and invasion of AsPC-1 cells by necroptosis induced- CXCL5 secretion downregulation. Significantly, 20 could relieve the TNFα-induced systemic inflammatory response syndrome in vivo. Taken together, this study would provide a useful insight into the design of novel necroptosis inhibitors possessing RIPK3-mediated pMLKL inhibitory activity.
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Affiliation(s)
- Namkyoung Kim
- KU-KIST Graduate School of Converging Science and Technology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea; Severance Biomedical Science Institute, Graduate School of Medicinal Science, Brain Korea 21 Project, Yonsei University College of Medicine, 50, Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Chan-Jung Park
- KU-KIST Graduate School of Converging Science and Technology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea; Severance Biomedical Science Institute, Graduate School of Medicinal Science, Brain Korea 21 Project, Yonsei University College of Medicine, 50, Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Younghoon Kim
- KU-KIST Graduate School of Converging Science and Technology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea; Severance Biomedical Science Institute, Graduate School of Medicinal Science, Brain Korea 21 Project, Yonsei University College of Medicine, 50, Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - SeongShick Ryu
- KU-KIST Graduate School of Converging Science and Technology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea; Severance Biomedical Science Institute, Graduate School of Medicinal Science, Brain Korea 21 Project, Yonsei University College of Medicine, 50, Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Hanna Cho
- Severance Biomedical Science Institute, Graduate School of Medicinal Science, Brain Korea 21 Project, Yonsei University College of Medicine, 50, Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Yunju Nam
- KU-KIST Graduate School of Converging Science and Technology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea; Severance Biomedical Science Institute, Graduate School of Medicinal Science, Brain Korea 21 Project, Yonsei University College of Medicine, 50, Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Myeonggil Han
- Department of Microbiology, Yonsei University College of Medicine, Seoul, South Korea
| | - Jeon-Soo Shin
- Department of Microbiology, Yonsei University College of Medicine, Seoul, South Korea
| | - Taebo Sim
- KU-KIST Graduate School of Converging Science and Technology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea; Severance Biomedical Science Institute, Graduate School of Medicinal Science, Brain Korea 21 Project, Yonsei University College of Medicine, 50, Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea.
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9
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Xu L, Zhuang C. Profiling of small-molecule necroptosis inhibitors based on the subpockets of kinase-ligand interactions. Med Res Rev 2023; 43:1974-2024. [PMID: 37119044 DOI: 10.1002/med.21968] [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: 08/01/2022] [Revised: 03/13/2023] [Accepted: 04/12/2023] [Indexed: 04/30/2023]
Abstract
Necroptosis is a highly regulated cell death (RCD) form in various inflammatory diseases. Receptor-interacting protein kinase 1 (RIPK1) and RIPK3 are involved in the pathway. Targeting the kinase domains of RIPK1 and/or 3 is a drug design strategy for related diseases. It is generally accepted that essential reoccurring features are observed across the human kinase domains, including RIPK1 and RIPK3. They present common N- and C-terminal domains that are built up mostly by α-helices and β-sheets, respectively. The current RIPK1/3 kinase inhibitors mainly interact with the kinase catalytic cleft. This article aims to present an in-depth profiling for ligand-kinase interactions in the crucial cleft areas by carefully aligning the kinase-ligand cocrystal complexes or molecular docking models. The similarity and differential structural segments of ligands are systematically evaluated. New insights on the adaption of the conserved and selective kinase domains to the diversity of chemical scaffolds are also provided. In a word, our analysis can provide a better structural requirement for RIPK1 and RIPK3 inhibition and a guide for inhibitor discovery and optimization of their potency and selectivity.
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Affiliation(s)
- Lijuan Xu
- School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Chunlin Zhuang
- School of Pharmacy, Second Military Medical University, Shanghai, China
- School of Pharmacy, Ningxia Medical University, Yinchuan, China
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10
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Shen X, Chen H, Wen T, Liu L, Hu Q, Xie F, Wang L. A natural chalcone cardamonin inhibits necroptosis and ameliorates dextran sulfate sodium (DSS)-induced colitis by targeting RIPK1/3 kinases. Eur J Pharmacol 2023:175840. [PMID: 37302524 DOI: 10.1016/j.ejphar.2023.175840] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 06/08/2023] [Indexed: 06/13/2023]
Abstract
Necroptosis, a new form of programmed cell death, is involved in the pathogenesis of ulcerative colitis (UC). Inhibition of necroptosis represents an attractive strategy for UC therapy. Herein, cardamonin, a natural chalcone isolated from Zingiberaceae family, was firstly identified as a potent necroptosis inhibitor. In vitro, cardamonin significantly inhibited necroptosis in TNF-α plus Smac mimetic and z-VAD-FMK (TSZ)-, cycloheximide plus TZ (TCZ)-, or lipopolysaccharide plus SZ (LSZ)-stimulated HT29, L929, or RAW264.7 cell lines. Furthermore, TSZ-induced elevated population of necrotic cells, release of LDH and HMGB1 also could be inhibited by cardamonin in HT29 cells. Cellular thermal shift assay (CETSA) and drug affinity responsive target stability (DARTS) assay combined with molecular docking demonstrated that cardamonin interacted with RIPK1/3. Furthermore, cardamonin blocked the phosphorylation of RIPK1/3, thereby disrupting RIPK1-RIPK3 necrosome formation and MLKL phosphorylation. In vivo, orally administration of cardamonin attenuated dextran sulfate sodium (DSS)-induced colitis, which mainly manifested as mitigated intestinal barrier damage, suppressed necroinflammation, and reduced phosphorylation of MLKL. Taken together, our findings revealed that dietary cardamonin is a novel necroptosis inhibitor and has great potential for UC therapy by targeting RIPK1/3 kinases.
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Affiliation(s)
- Xiaofei Shen
- TCM Regulating Metabolic Diseases Key Laboratory of Sichuan Province, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Hongqing Chen
- TCM Regulating Metabolic Diseases Key Laboratory of Sichuan Province, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China; College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Tian Wen
- TCM Regulating Metabolic Diseases Key Laboratory of Sichuan Province, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China; College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Lu Liu
- TCM Regulating Metabolic Diseases Key Laboratory of Sichuan Province, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China; College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Qiongying Hu
- TCM Regulating Metabolic Diseases Key Laboratory of Sichuan Province, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China; College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Fan Xie
- TCM Regulating Metabolic Diseases Key Laboratory of Sichuan Province, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China.
| | - Lun Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China.
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11
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Shao H, Xu L, Li G, Wang S, Han T, Zhuang C. Analysis on benzothiazole necroptosis inhibitors with chiral substitutions in the solvent-accessible region of RIP kinase domain. Bioorg Chem 2023; 137:106647. [PMID: 37270986 DOI: 10.1016/j.bioorg.2023.106647] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/28/2023] [Accepted: 05/29/2023] [Indexed: 06/06/2023]
Abstract
Receptor-interacting protein kinase 1 (RIPK1) and RIPK3, two imperative targets of the necroptosis pathway, are associated with various inflammatory-related diseases. Regulating kinase activity with inhibitors has been confirmed as a promising strategy for inflammation treatment. However, most of the reported type I and II kinase inhibitors of RIPK1 and RIPK3, including benzothiazole compounds discovered by our group, have selective limitations due to interaction with ATP-binding pockets. Fortunately, a solvent exposure E0 region of the kinase domain, which extends into the linker region, has been reported to be related to the potency and selectivity of inhibitors. Hence, based on our previous study, a series of benzothiazole necroptosis inhibitors with chiral substitutions in the linker region were developed to investigate RIPK1/3 inhibitory potency. The results showed a 2-to 6-fold increase in anti-necroptotic activity for these chiral compounds. The improved selectivity on RIPK1 or RIPK3 was demonstrated on different derivatives. Predicted binding conformations of enantiomers with RIPK1/3 gave an explanation for their activity differences, guiding further rational design of chiral necroptosis inhibitors.
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Affiliation(s)
- Hongming Shao
- School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| | - Lijuan Xu
- School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| | - Gechang Li
- School of Pharmacy, Guangdong Pharmaceutical University, Guangdong 510006, China
| | - Shuyu Wang
- School of Pharmacy, Ningxia Medical University, Yinchuan 750004, China
| | - Ting Han
- School of Pharmacy, Second Military Medical University, Shanghai 200433, China.
| | - Chunlin Zhuang
- School of Pharmacy, Second Military Medical University, Shanghai 200433, China; School of Pharmacy, Ningxia Medical University, Yinchuan 750004, China.
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12
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Gardner C, Davies KA, Zhang Y, Brzozowski M, Czabotar PE, Murphy JM, Lessene G. From (Tool)Bench to Bedside: The Potential of Necroptosis Inhibitors. J Med Chem 2023; 66:2361-2385. [PMID: 36781172 PMCID: PMC9969410 DOI: 10.1021/acs.jmedchem.2c01621] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Necroptosis is a regulated caspase-independent form of necrotic cell death that results in an inflammatory phenotype. This process contributes profoundly to the pathophysiology of numerous neurodegenerative, cardiovascular, infectious, malignant, and inflammatory diseases. Receptor-interacting protein kinase 1 (RIPK1), RIPK3, and the mixed lineage kinase domain-like protein (MLKL) pseudokinase have been identified as the key components of necroptosis signaling and are the most promising targets for therapeutic intervention. Here, we review recent developments in the field of small-molecule inhibitors of necroptosis signaling, provide guidelines for their use as chemical probes to study necroptosis, and assess the therapeutic challenges and opportunities of such inhibitors in the treatment of a range of clinical indications.
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Affiliation(s)
- Christopher
R. Gardner
- The
Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia,Department
of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Katherine A. Davies
- The
Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia,Department
of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Ying Zhang
- The
Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia,Department
of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Martin Brzozowski
- The
Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia,Department
of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Peter E. Czabotar
- The
Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia,Department
of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - James M. Murphy
- The
Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia,Department
of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Guillaume Lessene
- The
Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia,Department
of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia,Department
of Pharmacology and Therapeutics, University
of Melbourne, Parkville, VIC 3052, Australia,Email;
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13
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Zhang J, Li H, Zhao X, Wu Q, Huang SY. Holo Protein Conformation Generation from Apo Structures by Ligand Binding Site Refinement. J Chem Inf Model 2022; 62:5806-5820. [PMID: 36342197 DOI: 10.1021/acs.jcim.2c00895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An important part in structure-based drug design is the selection of an appropriate protein structure. It has been revealed that a holo protein structure that contains a well-defined binding site is a much better choice than an apo structure in structure-based drug discovery. Therefore, it is valuable to obtain a holo-like protein conformation from apo structures in the case where no holo structure is available. Meeting the need, we present a robust approach to generate reliable holo-like structures from apo structures by ligand binding site refinement with restraints derived from holo templates with low homology. Our method was tested on a test set of 32 proteins from the DUD-E data set and compared with other approaches. It was shown that our method successfully refined the apo structures toward the corresponding holo conformations for 23 of 32 proteins, reducing the average all-heavy-atom RMSD of binding site residues by 0.48 Å. In addition, when evaluated against all the holo structures in the protein data bank, our method can improve the binding site RMSD for 14 of 19 cases that experience significant conformational changes. Furthermore, our refined structures also demonstrate their advantages over the apo structures in ligand binding mode predictions by both rigid docking and flexible docking and in virtual screening on the database of active and decoy ligands from the DUD-E. These results indicate that our method is effective in recovering holo-like conformations and will be valuable in structure-based drug discovery.
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Affiliation(s)
- Jinze Zhang
- School of Physics, Huazhong University of Science and Technology, Wuhan430074, Hubei, P. R. China
| | - Hao Li
- School of Physics, Huazhong University of Science and Technology, Wuhan430074, Hubei, P. R. China
| | - Xuejun Zhao
- School of Physics, Huazhong University of Science and Technology, Wuhan430074, Hubei, P. R. China
| | - Qilong Wu
- School of Physics, Huazhong University of Science and Technology, Wuhan430074, Hubei, P. R. China
| | - Sheng-You Huang
- School of Physics, Huazhong University of Science and Technology, Wuhan430074, Hubei, P. R. China
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14
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Wen W, Chen J, Zhou Y, Li G, Zhang Y. Loss of Ripk3 attenuated neutrophil accumulation in a lipopolysaccharide-induced zebrafish inflammatory model. Cell Death Dis 2022; 8:88. [PMID: 35220408 PMCID: PMC8882176 DOI: 10.1038/s41420-022-00891-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/27/2022] [Accepted: 02/09/2022] [Indexed: 11/09/2022]
Abstract
Neutrophils are important effector cells during inflammation, which play complex roles. Therefore, investigating the regulation of neutrophil accumulation during inflammation might provide targets for treating related diseases. In the present study, we generated a ripk3-deficient zebrafish line to study the roles of Ripk3 in neutrophil-related inflammation. The homeostatic hematopoiesis and cytokine expression of the ripk3-deficient larvae were unaltered. The ripk3-deficient larvae with caudal fin fold injury exhibited similar neutrophil enrichment with wild-type larvae, suggesting that Ripk3 is not essential for non-infectious inflammatory responses. When challenged with lipopolysaccharide (LPS), the ripk3-deficient larvae showed significantly less neutrophil accumulation in the injection site and differential expression of several key cytokines. Ripk3 inhibitors could also attenuate neutrophil accumulation in wild-type larvae, indicating that Ripk3 could serve as a candidate target for inflammation treatment. In summary, our study indicated that Ripk3 has an essential role in LPS-induced inflammatory responses. It was suggested that the ripk3-deficient zebrafish might be applied in developing infectious disease models, while Ripk3 also has potential as an inflammation-treatment target.
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15
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Synthesis and characterization of potent RIPK3 inhibitors based on a tricyclic scaffold. Future Med Chem 2022; 14:421-442. [PMID: 35167311 DOI: 10.4155/fmc-2021-0196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Background: Necroptosis is an important form of regulated cell death involved in inflammatory diseases, degenerative diseases and cancer. RIPK3 is an interesting target for intervention of necroptosis-associated diseases. Methodology: Herein the authors report the synthesis of a series RIPK3 inhibitors under the guidance of structure-based drug design which leads to the identification of compound 37. Results: Compound 37 potently rescued human and mouse cells from necroptotic stimuli TNFα, Smac mimetic, z-VAD and LPS + z-VAD, displayed high affinity to RIPK3 (Kd = 14 nM) but no observable affinity to RIPK1 and inhibited RIPK3 kinase function. Importantly, compound 37 significantly alleviated TNF-induced systemic inflammatory response syndrome in the mouse model. Conclusion: These results support compound 37 as a prototype RIPK3 inhibitor for lead optimization.
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16
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Meng Y, Davies KA, Fitzgibbon C, Young SN, Garnish SE, Horne CR, Luo C, Garnier JM, Liang LY, Cowan AD, Samson AL, Lessene G, Sandow JJ, Czabotar PE, Murphy JM. Human RIPK3 maintains MLKL in an inactive conformation prior to cell death by necroptosis. Nat Commun 2021; 12:6783. [PMID: 34811356 PMCID: PMC8608796 DOI: 10.1038/s41467-021-27032-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 10/29/2021] [Indexed: 12/11/2022] Open
Abstract
The ancestral origins of the lytic cell death mode, necroptosis, lie in host defense. However, the dysregulation of necroptosis in inflammatory diseases has led to widespread interest in targeting the pathway therapeutically. This mode of cell death is executed by the terminal effector, the MLKL pseudokinase, which is licensed to kill following phosphorylation by its upstream regulator, RIPK3 kinase. The precise molecular details underlying MLKL activation are still emerging and, intriguingly, appear to mechanistically-diverge between species. Here, we report the structure of the human RIPK3 kinase domain alone and in complex with the MLKL pseudokinase. These structures reveal how human RIPK3 structurally differs from its mouse counterpart, and how human RIPK3 maintains MLKL in an inactive conformation prior to induction of necroptosis. Residues within the RIPK3:MLKL C-lobe interface are crucial to complex assembly and necroptotic signaling in human cells, thereby rationalizing the strict species specificity governing RIPK3 activation of MLKL.
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Affiliation(s)
- Yanxiang Meng
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Katherine A Davies
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Cheree Fitzgibbon
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Samuel N Young
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
| | - Sarah E Garnish
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Christopher R Horne
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Cindy Luo
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
| | - Jean-Marc Garnier
- SYNthesis med chem, 30 Flemington Rd, Parkville, VIC, 3052, Australia
| | - Lung-Yu Liang
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Angus D Cowan
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Andre L Samson
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Guillaume Lessene
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Jarrod J Sandow
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Peter E Czabotar
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia.
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia.
| | - James M Murphy
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia.
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia.
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17
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Recent progress in small-molecule inhibitors for critical therapeutic targets of necroptosis. Future Med Chem 2021; 13:817-837. [PMID: 33845591 DOI: 10.4155/fmc-2020-0386] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Nonapoptotic types of regulated cell death have attracted widespread interest since the discovery that certain forms of cell necrosis can be regulated. In particular, research into cell necroptosis has made significant progress in connection with kidney, inflammatory, degenerative and neoplastic diseases. Inhibitors targeting the critical necroptosis-associated proteins RIPK1/3 and MLKL have been in development for more than a decade. Herein the authors compile a list of the known small-molecule inhibitors of these enzymes and representative structures of compounds co-crystallized with these proteins and put forward some thoughts regarding their future development.
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18
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Wu S, Xu C, Xia K, Lin Y, Tian S, Ma H, Ji Y, Zhu F, He S, Zhang X. Ring closure strategy leads to potent RIPK3 inhibitors. Eur J Med Chem 2021; 217:113327. [PMID: 33730678 DOI: 10.1016/j.ejmech.2021.113327] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 02/10/2021] [Accepted: 02/19/2021] [Indexed: 01/02/2023]
Abstract
Necroptosis is a form of regulated necrotic cell death that is independent of caspases. Receptor-interacting protein kinase 3 (RIPK3) has been identified as a key regulator for necroptosis, and has been proposed as a potential therapeutic target for the treatment of diseases associated with necroptosis. In this report, we describe the design, synthesis, and evaluation of a series of novel RIPK3 inhibitors. The lead compound 38 exhibited potent activity (EC50 = 0.42 μM) in blocking TNFα, Smac mimetic and z-VAD (TSZ) induced cell death in HT-29 cells. Mechanistic studies showed that compound 38 bound to RIPK3 with high affinity (Kd = 7.1 nM), and inhibited RIPK3 kinase activity in a ADP-Glo functional assay. In addition, compound 38 displayed good selectivity over another necroptosis regulator RIPK1 (Kd = 6000 nM). Furthermore, compound 38 demonstrated excellent in vitro safety profiles with minimal inhibition of CYP isozymes and hERG potassium channel. Lastly, compound 38 efficiently blocked hypothermia and death in mice in the TNFα-induced systemic inflammatory response syndrome model.
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Affiliation(s)
- Shuwei Wu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, 215123, PR China
| | - Chen Xu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, 215123, PR China
| | - Kaijiang Xia
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, 215123, PR China
| | - Yu Lin
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, 215123, PR China
| | - Sheng Tian
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, 215123, PR China
| | - Haikuo Ma
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, 215123, PR China
| | - Yuting Ji
- Center of Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medial College, Beijing, Suzhou Institute of Systems Medicine, Suzhou, 215123, Jiangsu, PR China; Cyrus Tang Hematology Center, Jiangsu Institute of Hematology and Collaborative Innovation Center of Hematology, Soochow University, Suzhou, 215123, PR China
| | - Fang Zhu
- Center of Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medial College, Beijing, Suzhou Institute of Systems Medicine, Suzhou, 215123, Jiangsu, PR China; Cyrus Tang Hematology Center, Jiangsu Institute of Hematology and Collaborative Innovation Center of Hematology, Soochow University, Suzhou, 215123, PR China
| | - Sudan He
- Center of Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medial College, Beijing, Suzhou Institute of Systems Medicine, Suzhou, 215123, Jiangsu, PR China; Cyrus Tang Hematology Center, Jiangsu Institute of Hematology and Collaborative Innovation Center of Hematology, Soochow University, Suzhou, 215123, PR China.
| | - Xiaohu Zhang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, 215123, PR China.
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19
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Meng Y, Sandow JJ, Czabotar PE, Murphy JM. The regulation of necroptosis by post-translational modifications. Cell Death Differ 2021; 28:861-883. [PMID: 33462412 PMCID: PMC7937688 DOI: 10.1038/s41418-020-00722-7] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 12/14/2020] [Accepted: 12/18/2020] [Indexed: 01/30/2023] Open
Abstract
Necroptosis is a caspase-independent, lytic form of programmed cell death whose errant activation has been widely implicated in many pathologies. The pathway relies on the assembly of the apical protein kinases, RIPK1 and RIPK3, into a high molecular weight cytoplasmic complex, termed the necrosome, downstream of death receptor or pathogen detector ligation. The necrosome serves as a platform for RIPK3-mediated phosphorylation of the terminal effector, the MLKL pseudokinase, which induces its oligomerization, translocation to, and perturbation of, the plasma membrane to cause cell death. Over the past 10 years, knowledge of the post-translational modifications that govern RIPK1, RIPK3 and MLKL conformation, activity, interactions, stability and localization has rapidly expanded. Here, we review current knowledge of the functions of phosphorylation, ubiquitylation, GlcNAcylation, proteolytic cleavage, and disulfide bonding in regulating necroptotic signaling. Post-translational modifications serve a broad array of functions in modulating RIPK1 engagement in, or exclusion from, cell death signaling, whereas the bulk of identified RIPK3 and MLKL modifications promote their necroptotic functions. An enhanced understanding of the modifying enzymes that tune RIPK1, RIPK3, and MLKL necroptotic functions will prove valuable in efforts to therapeutically modulate necroptosis.
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Affiliation(s)
- Yanxiang Meng
- grid.1042.7Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052 Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, University of Melbourne, Parkville, VIC 3052 Australia
| | - Jarrod J. Sandow
- grid.1042.7Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052 Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, University of Melbourne, Parkville, VIC 3052 Australia
| | - Peter E. Czabotar
- grid.1042.7Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052 Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, University of Melbourne, Parkville, VIC 3052 Australia
| | - James M. Murphy
- grid.1042.7Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052 Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, University of Melbourne, Parkville, VIC 3052 Australia
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20
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Chaudhry C, Tebben A, Tokarski JS, Borzilleri R, Pitts WJ, Lippy J, Zhang L. An innovative kinome platform to accelerate small-molecule inhibitor discovery and optimization from hits to leads. Drug Discov Today 2021; 26:1115-1125. [PMID: 33497831 DOI: 10.1016/j.drudis.2021.01.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 07/23/2020] [Accepted: 01/18/2021] [Indexed: 01/09/2023]
Abstract
Kinases, accounting for 20% of the human genome, have been the focus of pharmaceutical drug discovery efforts for over three decades. Despite concerns surrounding the tractability of kinases as drug targets, it is evident that kinase drug discovery offers great potential, underscored by the US Food and Drug Administration (FDA) approval of 48 small-molecule kinase inhibitors. Despite these successes, it is challenging to identify novel kinome selective inhibitors with good pharmacokinetic/pharmacodynamic (PK/PD) properties, and resistance to kinase inhibitor treatment frequently arises. A new era of kinase drug discovery predicates the need for diverse and powerful tools to discover the next generation of kinase inhibitors. Here, we outline key tenets of the Bristol Meyers Squibb (BMS) kinase platform, to enable efficient generation of highly optimized kinase inhibitors.
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Affiliation(s)
- Charu Chaudhry
- Lead Discovery and Optimization, Bristol Myers Squibb, NJ, USA.
| | - Andrew Tebben
- Molecular Structure and Design, Molecular Discovery Technologies, Bristol Myers Squibb, NJ, USA
| | - John S Tokarski
- Molecular Structure and Design, Molecular Discovery Technologies, Bristol Myers Squibb, NJ, USA
| | | | - William J Pitts
- Immunosciences Discovery Chemistry, Bristol Myers Squibb, NJ, USA
| | - Jonathan Lippy
- Lead Discovery and Optimization, Bristol Myers Squibb, NJ, USA
| | - Litao Zhang
- Lead Discovery and Optimization, Bristol Myers Squibb, NJ, USA
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21
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Xia K, Zhu F, Yang C, Wu S, Lin Y, Ma H, Yu X, Zhao C, Ji Y, Ge W, Wang J, Du Y, Zhang W, Yang T, Zhang X, He S. Discovery of a Potent RIPK3 Inhibitor for the Amelioration of Necroptosis-Associated Inflammatory Injury. Front Cell Dev Biol 2020; 8:606119. [PMID: 33364238 PMCID: PMC7753040 DOI: 10.3389/fcell.2020.606119] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 11/16/2020] [Indexed: 12/18/2022] Open
Abstract
Necroptosis is a form of regulated necrosis that requires the activation of receptor-interacting kinase 3 (RIPK3 or RIP3) and its phosphorylation of the substrate MLKL (mixed lineage kinase domain-like protein). Necroptosis has emerged as important cell death involved in the pathogenesis of various diseases including inflammatory diseases, degenerative diseases, and cancer. Here, we discovered a small molecule Zharp-99 as a potent inhibitor of necroptosis through blocking the kinase activity of RIPK3. Zharp-99 efficiently blocks necroptosis induced by ligands of the death receptor and Toll-like receptor as well as viral infection in human, rat and mouse cells. Zharp-99 strongly inhibits cellular activation of RIPK3, and MLKL upon necroptosis stimuli. Zharp-99 directly blocks the kinase activity of RIPK3 without affecting RIPK1 kinase activity at the tested concentration. Importantly, Zharp-99 exerts effective protection against TNF-α induced systemic inflammatory response syndrome in the mouse model. Zharp-99 displays favorable in vitro safety profiles and in vivo pharmacokinetic parameters. Thus, our study demonstrates Zharp-99 as a potent inhibitor of RIPK3 kinase and also highlights its potential for further development of new approaches for treating necroptosis-associated inflammatory disorders.
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Affiliation(s)
- Kaijiang Xia
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, China
| | - Fang Zhu
- Center of Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medial College, Beijing, China.,Suzhou Institute of Systems Medicine, Suzhou, China.,Key Laboratory of Synthetic Biology Regulatory Elements, Chinese Academy of Medical Sciences, Beijing, China.,Cyrus Tang Hematology Center and Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou, China
| | - Chengkui Yang
- Center of Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medial College, Beijing, China.,Suzhou Institute of Systems Medicine, Suzhou, China.,Key Laboratory of Synthetic Biology Regulatory Elements, Chinese Academy of Medical Sciences, Beijing, China
| | - Shuwei Wu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, China
| | - Yu Lin
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, China
| | - Haikuo Ma
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, China
| | - Xiaoliang Yu
- Center of Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medial College, Beijing, China.,Suzhou Institute of Systems Medicine, Suzhou, China.,Key Laboratory of Synthetic Biology Regulatory Elements, Chinese Academy of Medical Sciences, Beijing, China
| | - Cong Zhao
- Center of Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medial College, Beijing, China.,Suzhou Institute of Systems Medicine, Suzhou, China.,Key Laboratory of Synthetic Biology Regulatory Elements, Chinese Academy of Medical Sciences, Beijing, China
| | - Yuting Ji
- Center of Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medial College, Beijing, China.,Suzhou Institute of Systems Medicine, Suzhou, China.,Key Laboratory of Synthetic Biology Regulatory Elements, Chinese Academy of Medical Sciences, Beijing, China.,School of Life Sciences and Technology, China Pharmaceutical University, Nanjing, China
| | - Wenxiang Ge
- Center of Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medial College, Beijing, China.,Suzhou Institute of Systems Medicine, Suzhou, China.,Key Laboratory of Synthetic Biology Regulatory Elements, Chinese Academy of Medical Sciences, Beijing, China
| | - Jingrui Wang
- Center of Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medial College, Beijing, China.,Suzhou Institute of Systems Medicine, Suzhou, China.,Key Laboratory of Synthetic Biology Regulatory Elements, Chinese Academy of Medical Sciences, Beijing, China
| | - Yayun Du
- Center of Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medial College, Beijing, China.,Suzhou Institute of Systems Medicine, Suzhou, China.,Key Laboratory of Synthetic Biology Regulatory Elements, Chinese Academy of Medical Sciences, Beijing, China.,Cyrus Tang Hematology Center and Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou, China
| | - Wei Zhang
- Center of Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medial College, Beijing, China.,Suzhou Institute of Systems Medicine, Suzhou, China.,Key Laboratory of Synthetic Biology Regulatory Elements, Chinese Academy of Medical Sciences, Beijing, China
| | - Tao Yang
- Center of Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medial College, Beijing, China.,Suzhou Institute of Systems Medicine, Suzhou, China.,Key Laboratory of Synthetic Biology Regulatory Elements, Chinese Academy of Medical Sciences, Beijing, China.,Cyrus Tang Hematology Center and Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou, China
| | - Xiaohu Zhang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, China
| | - Sudan He
- Center of Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medial College, Beijing, China.,Suzhou Institute of Systems Medicine, Suzhou, China.,Key Laboratory of Synthetic Biology Regulatory Elements, Chinese Academy of Medical Sciences, Beijing, China.,Cyrus Tang Hematology Center and Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou, China
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22
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Cuny GD, Degterev A. RIPK protein kinase family: Atypical lives of typical kinases. Semin Cell Dev Biol 2020; 109:96-105. [PMID: 32732131 DOI: 10.1016/j.semcdb.2020.06.014] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 06/22/2020] [Accepted: 06/24/2020] [Indexed: 01/11/2023]
Abstract
Receptor Interacting Protein Kinases (RIPKs) are a family of Ser/Thr/Tyr kinases whose functions, regulation and pathophysiologic roles have remained an enigma for a long time. In recent years, these proteins garnered significant interest due to their roles in regulating a variety of host defense functions including control of inflammatory gene expression, different forms of cell death, and cutaneous and intestinal barrier functions. In addition, there is accumulating evidence that while these kinases seemingly follow typical kinase blueprints, their functioning in cells can take forms that are atypical for protein kinases. Lastly, while these kinases generally belong to distinct areas of innate immune regulation, there are emerging overarching themes that may unify the functions of this kinase family. Our review seeks to discuss the biology of RIPKs, and how typical and atypical features of this family informs the activity of a rapidly growing repertoire of RIPK inhibitors.
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Affiliation(s)
- Gregory D Cuny
- Department of Pharmacological and Pharmaceutical Sciences, University of Houston, Houston, TX, USA.
| | - Alexei Degterev
- Department of Developmental, Molecular & Chemical Biology, Tufts University School of Medicine, Boston, MA, USA.
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23
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Shi Y, Chen X, Huang C, Pollock C. RIPK3: A New Player in Renal Fibrosis. Front Cell Dev Biol 2020; 8:502. [PMID: 32613000 PMCID: PMC7308494 DOI: 10.3389/fcell.2020.00502] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 05/26/2020] [Indexed: 12/28/2022] Open
Abstract
Chronic kidney disease (CKD) is the end result of a plethora of renal insults, including repeated episodes of acute or toxic kidney injury, glomerular, or diabetic kidney disease. It affects a large number of the population worldwide, resulting in significant personal morbidity and mortality and economic cost to the community. Hence it is appropriate to focus on treatment strategies that interrupt the development of kidney fibrosis, the end result of all forms of CKD, in addition to upstream factors that may be specific to certain diseases. However, the current clinical approach to prevent or manage renal fibrosis remains unsatisfactory. The rising importance of receptor-interacting serine/threonine-protein kinase (RIPK) 3 in the inflammatory response and TGF-β1 signaling is increasingly recognized. We discuss here the biological functions of RIPK3 and its role in the development of renal fibrosis.
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Affiliation(s)
- Ying Shi
- Nephrology, School of Medicine, Stanford University, Palo Alto, CA, United States
| | - Xinming Chen
- Kolling Institute of Medical Research, Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
| | - Chunling Huang
- Kolling Institute of Medical Research, Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
| | - Carol Pollock
- Kolling Institute of Medical Research, Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
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24
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Affiliation(s)
- Matthew D. Lloyd
- Drug & Target Development, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, U.K
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25
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Zhuang C, Chen F. Small-Molecule Inhibitors of Necroptosis: Current Status and Perspectives. J Med Chem 2019; 63:1490-1510. [PMID: 31622096 DOI: 10.1021/acs.jmedchem.9b01317] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Necroptosis, an important form of programmed cell death (PCD), is a highly regulated caspase-independent type of cell death that plays a critical role in the pathophysiology of various inflammatory, infectious, and degenerative diseases. Currently, receptor-interacting protein kinase 1 (RIPK1), RIPK3, and mixed lineage kinase domain-like protein (MLKL) have been widely recognized as critical therapeutic targets of the necroptotic machinery. Targeting RIPK1, RIPK3, and/or MLKL is a promising strategy for necroptosis-related diseases. Following the identification of the first RIPK1 inhibitor Nec-1 in 2005, the antinecroptosis field is attracting increasing research interest from multiple disciplines, including the biological and medicinal chemistry communities. Herein, we will review the functions of necroptosis in human diseases, as well as the related targets and representative small-molecule inhibitors, mainly focusing on research articles published during the past 10 years. Outlooks and perspectives on the associated challenges are also discussed.
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Affiliation(s)
- Chunlin Zhuang
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry , Fudan University , Shanghai 200433 , China.,Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs , Shanghai 200433 , China
| | - Fener Chen
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry , Fudan University , Shanghai 200433 , China.,Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs , Shanghai 200433 , China
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