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Non-kinase targeting of oncogenic c-Jun N-terminal kinase (JNK) signaling: the future of clinically viable cancer treatments. Biochem Soc Trans 2022; 50:1823-1836. [PMID: 36454622 PMCID: PMC9788565 DOI: 10.1042/bst20220808] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/28/2022] [Accepted: 11/15/2022] [Indexed: 01/09/2023]
Abstract
c-Jun N-terminal Kinases (JNKs) have been identified as key disease drivers in a number of pathophysiological settings and central oncogenic signaling nodes in various cancers. Their roles in driving primary tumor growth, positively regulating cancer stem cell populations, promoting invasion and facilitating metastatic outgrowth have led JNKs to be considered attractive targets for anti-cancer therapies. However, the homeostatic, apoptotic and tumor-suppressive activities of JNK proteins limit the use of direct JNK inhibitors in a clinical setting. In this review, we will provide an overview of the different JNK targeting strategies developed to date, which include various ATP-competitive, non-kinase and substrate-competitive inhibitors. We aim to summarize their distinct mechanisms of action, review some of the insights they have provided regarding JNK-targeting in cancer, and outline the limitations as well as challenges of all strategies that target JNKs directly. Furthermore, we will highlight alternate drug targets within JNK signaling complexes, including recently identified scaffold proteins, and discuss how these findings may open up novel therapeutic options for targeting discrete oncogenic JNK signaling complexes in specific cancer settings.
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2
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Gehi BR, Gadhave K, Uversky VN, Giri R. Intrinsic disorder in proteins associated with oxidative stress-induced JNK signaling. Cell Mol Life Sci 2022; 79:202. [PMID: 35325330 PMCID: PMC11073203 DOI: 10.1007/s00018-022-04230-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 03/01/2022] [Accepted: 03/03/2022] [Indexed: 01/02/2023]
Abstract
The c-Jun N-terminal kinase (JNK) signaling cascade is a mitogen-activated protein kinase (MAPK) signaling pathway that can be activated in response to a wide range of environmental stimuli. Based on the type, degree, and duration of the stimulus, the JNK signaling cascade dictates the fate of the cell by influencing gene expression through its substrate transcription factors. Oxidative stress is a result of a disturbance in the pro-oxidant/antioxidant homeostasis of the cell and is associated with a large number of diseases, such as neurodegenerative disorders, cancer, diabetes, cardiovascular diseases, and disorders of the immune system, where it activates the JNK signaling pathway. Among different biological roles ascribed to the intrinsically disordered proteins (IDPs) and hybrid proteins containing ordered domains and intrinsically disordered protein regions (IDPRs) are signaling hub functions, as intrinsic disorder allows proteins to undertake multiple interactions, each with a different consequence. In order to ensure precise signaling, the cellular abundance of IDPs is highly regulated, and mutations or changes in abundance of IDPs/IDPRs are often associated with disease. In this study, we have used a combination of six disorder predictors to evaluate the presence of intrinsic disorder in proteins of the oxidative stress-induced JNK signaling cascade, and as per our findings, none of the 18 proteins involved in this pathway are ordered. The highest level of intrinsic disorder was observed in the scaffold proteins, JIP1, JIP2, JIP3; dual specificity phosphatases, MKP5, MKP7; 14-3-3ζ and transcription factor c-Jun. The MAP3Ks, MAP2Ks, MAPKs, TRAFs, and thioredoxin were the proteins that were predicted to be moderately disordered. Furthermore, to characterize the predicted IDPs/IDPRs in the proteins of the JNK signaling cascade, we identified the molecular recognition features (MoRFs), posttranslational modification (PTM) sites, and short linear motifs (SLiMs) associated with the disordered regions. These findings will serve as a foundation for experimental characterization of disordered regions in these proteins, which represents a crucial step for a better understanding of the roles of IDPRs in diseases associated with this important pathway.
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Affiliation(s)
- Bhuvaneshwari R Gehi
- School of Basic Sciences, Indian Institute of Technology Mandi, VPO Kamand, Mandi, Himachal Pradesh, 175005, India
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bengaluru, 560012, India
| | - Kundlik Gadhave
- School of Basic Sciences, Indian Institute of Technology Mandi, VPO Kamand, Mandi, Himachal Pradesh, 175005, India
| | - Vladimir N Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
- Laboratory of New Methods in Biology, Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow region, 142290, Russia.
| | - Rajanish Giri
- School of Basic Sciences, Indian Institute of Technology Mandi, VPO Kamand, Mandi, Himachal Pradesh, 175005, India.
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3
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Kirsch K, Zeke A, Tőke O, Sok P, Sethi A, Sebő A, Kumar GS, Egri P, Póti ÁL, Gooley P, Peti W, Bento I, Alexa A, Reményi A. Co-regulation of the transcription controlling ATF2 phosphoswitch by JNK and p38. Nat Commun 2020; 11:5769. [PMID: 33188182 PMCID: PMC7666158 DOI: 10.1038/s41467-020-19582-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 10/21/2020] [Indexed: 01/26/2023] Open
Abstract
Transcription factor phosphorylation at specific sites often activates gene expression, but how environmental cues quantitatively control transcription is not well-understood. Activating protein 1 transcription factors are phosphorylated by mitogen-activated protein kinases (MAPK) in their transactivation domains (TAD) at so-called phosphoswitches, which are a hallmark in response to growth factors, cytokines or stress. We show that the ATF2 TAD is controlled by functionally distinct signaling pathways (JNK and p38) through structurally different MAPK binding sites. Moreover, JNK mediated phosphorylation at an evolutionarily more recent site diminishes p38 binding and made the phosphoswitch differently sensitive to JNK and p38 in vertebrates. Structures of MAPK-TAD complexes and mechanistic modeling of ATF2 TAD phosphorylation in cells suggest that kinase binding motifs and phosphorylation sites line up to maximize MAPK based co-regulation. This study shows how the activity of an ancient transcription controlling phosphoswitch became dependent on the relative flux of upstream signals.
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Affiliation(s)
- Klára Kirsch
- Biomolecular Interactions Research Group, Institute of Organic Chemistry, Research Center for Natural Sciences, H-1117, Budapest, Hungary
| | - András Zeke
- Biomolecular Interactions Research Group, Institute of Organic Chemistry, Research Center for Natural Sciences, H-1117, Budapest, Hungary
| | - Orsolya Tőke
- Laboratory for NMR Spectroscopy, Research Center for Natural Sciences, H-1117, Budapest, Hungary
| | - Péter Sok
- Biomolecular Interactions Research Group, Institute of Organic Chemistry, Research Center for Natural Sciences, H-1117, Budapest, Hungary
| | - Ashish Sethi
- Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Anna Sebő
- Biomolecular Interactions Research Group, Institute of Organic Chemistry, Research Center for Natural Sciences, H-1117, Budapest, Hungary
| | | | - Péter Egri
- Biomolecular Interactions Research Group, Institute of Organic Chemistry, Research Center for Natural Sciences, H-1117, Budapest, Hungary
| | - Ádám L Póti
- Biomolecular Interactions Research Group, Institute of Organic Chemistry, Research Center for Natural Sciences, H-1117, Budapest, Hungary
| | - Paul Gooley
- Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Wolfgang Peti
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA
| | - Isabel Bento
- European Molecular Biology Laboratory, Hamburg, Germany
| | - Anita Alexa
- Biomolecular Interactions Research Group, Institute of Organic Chemistry, Research Center for Natural Sciences, H-1117, Budapest, Hungary
| | - Attila Reményi
- Biomolecular Interactions Research Group, Institute of Organic Chemistry, Research Center for Natural Sciences, H-1117, Budapest, Hungary.
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4
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Benn CL, Dawson LA. Clinically Precedented Protein Kinases: Rationale for Their Use in Neurodegenerative Disease. Front Aging Neurosci 2020; 12:242. [PMID: 33117143 PMCID: PMC7494159 DOI: 10.3389/fnagi.2020.00242] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 07/13/2020] [Indexed: 12/12/2022] Open
Abstract
Kinases are an intensively studied drug target class in current pharmacological research as evidenced by the large number of kinase inhibitors being assessed in clinical trials. Kinase-targeted therapies have potential for treatment of a broad array of indications including central nervous system (CNS) disorders. In addition to the many variables which contribute to identification of a successful therapeutic molecule, drug discovery for CNS-related disorders also requires significant consideration of access to the target organ and specifically crossing the blood-brain barrier (BBB). To date, only a small number of kinase inhibitors have been reported that are specifically designed to be BBB permeable, which nonetheless demonstrates the potential for success. This review considers the potential for kinase inhibitors in the context of unmet medical need for neurodegenerative disease. A subset of kinases that have been the focus of clinical investigations over a 10-year period have been identified and discussed individually. For each kinase target, the data underpinning the validity of each in the context of neurodegenerative disease is critically evaluated. Selected molecules for each kinase are identified with information on modality, binding site and CNS penetrance, if known. Current clinical development in neurodegenerative disease are summarized. Collectively, the review indicates that kinase targets with sufficient rationale warrant careful design approaches with an emphasis on improving brain penetrance and selectivity.
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5
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Duong MTH, Lee JH, Ahn HC. C-Jun N-terminal kinase inhibitors: Structural insight into kinase-inhibitor complexes. Comput Struct Biotechnol J 2020; 18:1440-1457. [PMID: 32637042 PMCID: PMC7327381 DOI: 10.1016/j.csbj.2020.06.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 06/07/2020] [Accepted: 06/07/2020] [Indexed: 12/12/2022] Open
Abstract
The activation of c-Jun N-terminal kinases (JNKs) plays an important role in physiological processes including neuronal function, immune activity, and development, and thus, JNKs have been a therapeutic target for various diseases such as neurodegenerative diseases, inflammation, and cancer. Efforts to develop JNK-specific inhibitors have been ongoing for several decades. In this process, the structures of JNK in complex with various inhibitors have contributed greatly to the design of novel compounds and to the elucidation of structure-activity relationships. Almost 100 JNK structures with various compounds have been determined. Here we summarize the information gained from these structures and classify the inhibitors into several groups based on the binding mode. These groups include inhibitors in the open conformation and closed conformation of the gatekeeper residue, non-ATP site binders, peptides, covalent inhibitors, and type II kinase inhibitors. Through this work, deep insight into the interaction of inhibitors with JNKs can be gained and this will be helpful for developing novel, potent, and selective inhibitors.
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Affiliation(s)
- Men Thi Hoai Duong
- Department of Pharmacy, Dongguk University-Seoul, Goyang, Gyeonggi 10326, South Korea
| | - Joon-Hwa Lee
- Department of Chemistry and RINS, Gyeongsang National University, Jinju, Gyeongnam 52828, South Korea
| | - Hee-Chul Ahn
- Department of Pharmacy, Dongguk University-Seoul, Goyang, Gyeonggi 10326, South Korea
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6
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Sailapathi A, Murugan G, Somarathinam K, Gunalan S, Jagadeesan R, Yoosuf N, Kanagaraj S, Kothandan G. Proposing the Promiscuous Protein Structures in JNK1 and JNK3 for Virtual Screening in Pursuit of Potential Leads. ACS OMEGA 2020; 5:3969-3978. [PMID: 32149224 PMCID: PMC7057334 DOI: 10.1021/acsomega.9b03458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 02/11/2020] [Indexed: 06/10/2023]
Abstract
Over the past decade, the available crystal structures have almost doubled in Protein Data Bank (PDB) providing the research community with a series of similar crystal structures to choose from for future docking studies. With the steady growth in the number of high-resolution three-dimensional protein structures, ligand docking-based virtual screening of chemical libraries to a receptor plays a critical role in the drug discovery process by identifying new drug candidates. Thus, identifying potential candidates among all the available structures in a database for docking studies is of utmost importance. Our work examined whether one could use the resolution of a number of known structures, without considering other parameters, to choose a good experimental structure for various docking studies to find more useful drug leads. We expected that a good experimental structure for docking studies to be the one that gave favorable docking with the largest number of ligands among the experimental structures to be selected. We chose three protein test systems for our study, all belonging to the family of MAPK: (1) JNK1, (2) JNK2, and (3) JNK3. On analysis of the results, the best resolution structures showed significant variations from the expected values in their result, whereas the poor resolution structures proved to be better candidates for docking studies.
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Affiliation(s)
- Ananthasri Sailapathi
- Biopolymer
Modelling Laboratory, Centre of Advanced Study in Crystallography
and Biophysics, Guindy Campus, University of Madras, Chennai 600025, Tamilnadu, India
| | - Gopinath Murugan
- Biopolymer
Modelling Laboratory, Centre of Advanced Study in Crystallography
and Biophysics, Guindy Campus, University of Madras, Chennai 600025, Tamilnadu, India
| | - Kanagasabai Somarathinam
- Biopolymer
Modelling Laboratory, Centre of Advanced Study in Crystallography
and Biophysics, Guindy Campus, University of Madras, Chennai 600025, Tamilnadu, India
| | - Seshan Gunalan
- Biopolymer
Modelling Laboratory, Centre of Advanced Study in Crystallography
and Biophysics, Guindy Campus, University of Madras, Chennai 600025, Tamilnadu, India
| | - Rahul Jagadeesan
- Biopolymer
Modelling Laboratory, Centre of Advanced Study in Crystallography
and Biophysics, Guindy Campus, University of Madras, Chennai 600025, Tamilnadu, India
| | - Niyaz Yoosuf
- Division
of Rheumatology, Department of Medicine, Solna, Karolinska Institutet and Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Sekar Kanagaraj
- Laboratory
for Structural Biology and Bio-computing, Department of Computational
and Data Sciences, Indian Institute of Science, Bangalore 560 012, India
| | - Gugan Kothandan
- Biopolymer
Modelling Laboratory, Centre of Advanced Study in Crystallography
and Biophysics, Guindy Campus, University of Madras, Chennai 600025, Tamilnadu, India
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7
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Park JY, Qu CX, Li RR, Yang F, Yu X, Tian ZM, Shen YM, Cai BY, Yun Y, Sun JP, Chung KY. Structural Mechanism of the Arrestin-3/JNK3 Interaction. Structure 2019; 27:1162-1170.e3. [PMID: 31080119 DOI: 10.1016/j.str.2019.04.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 02/25/2019] [Accepted: 04/03/2019] [Indexed: 01/14/2023]
Abstract
Arrestins, in addition to desensitizing GPCR-induced G protein activation, also mediate G protein-independent signaling by interacting with various signaling proteins. Among these, arrestins regulate MAPK signal transduction by scaffolding mitogen-activated protein kinase (MAPK) signaling components such as MAPKKK, MAPKK, and MAPK. In this study, we investigated the binding mode and interfaces between arrestin-3 and JNK3 using hydrogen/deuterium exchange mass spectrometry, 19F-NMR, and tryptophan-induced Atto 655 fluorescence-quenching techniques. Results suggested that the β1 strand of arrestin-3 is the major and potentially only interaction site with JNK3. The results also suggested that C-lobe regions near the activation loop of JNK3 form the potential binding interface, which is variable depending on the ATP binding status. Because the β1 strand of arrestin-3 is buried by the C-terminal strand in its basal state, C-terminal truncation (i.e., pre-activation) of arrestin-3 facilitates the arrestin-3/JNK3 interaction.
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Affiliation(s)
- Ji Young Park
- School of Pharmacy, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
| | - Chang-Xiu Qu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing 100191, China; Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University School of Medicine, 44 Wenhua Xi Road, Jinan, Shandong 250012, China
| | - Rui-Rui Li
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University School of Medicine, 44 Wenhua Xi Road, Jinan, Shandong 250012, China
| | - Fan Yang
- Key Laboratory of Infection and Immunity of Shandong Province, Department of Pharmacology, School of Basic Medical Science, Shandong University, Jinan 250012, China
| | - Xiao Yu
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Physiology, Shandong University School of Medicine, 44 Wenhua Xi Road, Jinan, Shandong 250012, China
| | - Zhao-Mei Tian
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University School of Medicine, 44 Wenhua Xi Road, Jinan, Shandong 250012, China
| | - Yue-Mao Shen
- Key Laboratory of Chemical Biology, (Ministry of Education), School of Pharmaceutical Science, Shandong University, Jinan, Shandong 250012, China
| | - Bo-Yang Cai
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing 100191, China
| | - Youngjoo Yun
- School of Pharmacy, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
| | - Jin-Peng Sun
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing 100191, China; Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University School of Medicine, 44 Wenhua Xi Road, Jinan, Shandong 250012, China.
| | - Ka Young Chung
- School of Pharmacy, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea.
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8
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Astl L, Tse A, Verkhivker GM. Interrogating Regulatory Mechanisms in Signaling Proteins by Allosteric Inhibitors and Activators: A Dynamic View Through the Lens of Residue Interaction Networks. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1163:187-223. [DOI: 10.1007/978-981-13-8719-7_9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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9
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Win S, Than TA, Kaplowitz N. The Regulation of JNK Signaling Pathways in Cell Death through the Interplay with Mitochondrial SAB and Upstream Post-Translational Effects. Int J Mol Sci 2018; 19:ijms19113657. [PMID: 30463289 PMCID: PMC6274687 DOI: 10.3390/ijms19113657] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 11/17/2018] [Accepted: 11/17/2018] [Indexed: 02/08/2023] Open
Abstract
c-Jun-N-terminal kinase (JNK) activity plays a critical role in modulating cell death, which depends on the level and duration of JNK activation. The kinase cascade from MAPkinase kinase kinase (MAP3K) to MAPkinase kinase (MAP2K) to MAPKinase (MAPK) can be regulated by a number of direct and indirect post-transcriptional modifications, including acetylation, ubiquitination, phosphorylation, and their reversals. Recently, a JNK-mitochondrial SH3-domain binding protein 5 (SH3BP5/SAB)-ROS activation loop has been elucidated, which is required to sustain JNK activity. Importantly, the level of SAB expression in the outer membrane of mitochondria is a major determinant of the set-point for sustained JNK activation. SAB is a docking protein and substrate for JNK, leading to an intramitochondrial signal transduction pathway, which impairs electron transport and promotes reactive oxygen species (ROS) release to sustain the MAPK cascade.
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Affiliation(s)
- Sanda Win
- Division of Gastrointestinal and Liver Disease, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA.
| | - Tin Aung Than
- Division of Gastrointestinal and Liver Disease, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA.
| | - Neil Kaplowitz
- Division of Gastrointestinal and Liver Disease, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA.
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10
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Sab concentrations indicate chemotherapeutic susceptibility in ovarian cancer cell lines. Biochem J 2018; 475:3471-3492. [PMID: 30322886 DOI: 10.1042/bcj20180603] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 10/08/2018] [Accepted: 10/11/2018] [Indexed: 01/05/2023]
Abstract
The occurrence of chemotherapy-resistant tumors makes ovarian cancer (OC) the most lethal gynecological malignancy. While many factors may contribute to chemoresistance, the mechanisms responsible for regulating tumor vulnerability are under investigation. Our analysis of gene expression data revealed that Sab, a mitochondrial outer membrane (MOM) scaffold protein, was down-regulated in OC patients. Sab-mediated signaling induces cell death, suggesting that this apoptotic pathway is diminished in OC. We examined Sab expression in a panel of OC cell lines and found that the magnitude of Sab expression correlated to chemo-responsiveness; wherein, OC cells with low Sab levels were chemoresistant. The Sab levels were reflected by a corresponding amount of stress-induced c-Jun N-terminal kinase (JNK) on the MOM. BH3 profiling and examination of Bcl-2 and BH3-only protein concentrations revealed that cells with high Sab concentrations were primed for apoptosis, as determined by the decrease in pro-survival Bcl-2 proteins and an increase in pro-apoptotic BH3-only proteins on mitochondria. Furthermore, overexpression of Sab in chemoresistant cells enhanced apoptotic priming and restored cellular vulnerability to a combination treatment of cisplatin and paclitaxel. Contrariwise, inhibiting Sab-mediated signaling or silencing Sab expression in a chemosensitive cell line resulted in decreased apoptotic priming and increased resistance. The effects of silencing on Sab on the resistance to chemotherapeutic agents were emulated by the silencing or inhibition of JNK, which could be attributed to changes in Bcl-2 protein concentrations induced by sub-chronic JNK inhibition. We propose that Sab may be a prognostic biomarker to discern personalized treatments for OC patients.
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11
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Lombard CK, Davis AL, Inukai T, Maly DJ. Allosteric Modulation of JNK Docking Site Interactions with ATP-Competitive Inhibitors. Biochemistry 2018; 57:5897-5909. [PMID: 30211540 DOI: 10.1021/acs.biochem.8b00776] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The c-Jun N-terminal kinases (JNKs) play a wide variety of roles in cellular signaling processes, dictating important, and even divergent, cellular fates. These essential kinases possess docking surfaces distal to their active sites that interact with diverse binding partners, including upstream activators, downstream substrates, and protein scaffolds. Prior studies have suggested that the interactions of certain protein-binding partners with one such JNK docking surface, termed the D-recruitment site (DRS), can allosterically influence the conformational state of the ATP-binding pocket of JNKs. To further explore the allosteric relationship between the ATP-binding pockets and DRSs of JNKs, we investigated how the interactions of the scaffolding protein JIP1, as well as the upstream activators MKK4 and MKK7, are allosterically influenced by the ATP-binding site occupancy of the JNKs. We show that the affinity of the JNKs for JIP1 can be divergently modulated with ATP-competitive inhibitors, with a >50-fold difference in dissociation constant observed between the lowest- and highest-affinity JNK1-inhibitor complexes. Furthermore, we found that we could promote or attenuate phosphorylation of JNK1's activation loop by MKK4 and MKK7, by varying the ATP-binding site occupancy. Given that JIP1, MKK4, and MKK7 all interact with JNK DRSs, these results demonstrate that there is functional allostery between the ATP-binding sites and DRSs of these kinases. Furthermore, our studies suggest that ATP-competitive inhibitors can allosterically influence the intracellular binding partners of the JNKs.
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Affiliation(s)
- Chloe K Lombard
- Department of Chemistry , University of Washington , Seattle , Washington 98117 , United States
| | - Audrey L Davis
- Department of Chemistry , University of Washington , Seattle , Washington 98117 , United States
| | - Takayuki Inukai
- Medicinal Chemistry Research Laboratories , Ono Pharmaceutical Company, Ltd. , 3-1-1 Sakurai , Shimamoto, Mishima, Osaka 618-8585 , Japan
| | - Dustin J Maly
- Department of Chemistry , University of Washington , Seattle , Washington 98117 , United States.,Department of Biochemistry , University of Washington , Seattle , Washington 98117 , United States
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12
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Structural determinants of Rab11 activation by the guanine nucleotide exchange factor SH3BP5. Nat Commun 2018; 9:3772. [PMID: 30217979 PMCID: PMC6138693 DOI: 10.1038/s41467-018-06196-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 08/14/2018] [Indexed: 12/18/2022] Open
Abstract
The GTPase Rab11 plays key roles in receptor recycling, oogenesis, autophagosome formation, and ciliogenesis. However, investigating Rab11 regulation has been hindered by limited molecular detail describing activation by cognate guanine nucleotide exchange factors (GEFs). Here, we present the structure of Rab11 bound to the GEF SH3BP5, along with detailed characterization of Rab-GEF specificity. The structure of SH3BP5 shows a coiled-coil architecture that mediates exchange through a unique Rab-GEF interaction. Furthermore, it reveals a rearrangement of the switch I region of Rab11 compared with solved Rab-GEF structures, with a constrained conformation when bound to SH3BP5. Mutation of switch I provides insights into the molecular determinants that allow for Rab11 selectivity over evolutionarily similar Rab GTPases present on Rab11-positive organelles. Moreover, we show that GEF-deficient mutants of SH3BP5 show greatly decreased Rab11 activation in cellular assays of active Rab11. Overall, our results give molecular insight into Rab11 regulation, and how Rab-GEF specificity is achieved.
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13
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Mishra P, Günther S. New insights into the structural dynamics of the kinase JNK3. Sci Rep 2018; 8:9435. [PMID: 29930333 PMCID: PMC6013471 DOI: 10.1038/s41598-018-27867-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 06/11/2018] [Indexed: 12/13/2022] Open
Abstract
In this work, we study the dynamics and the energetics of the all-atom structure of a neuronal-specific serine/threonine kinase c-Jun N-terminal kinase 3 (JNK3) in three states: unphosphorylated, phosphorylated, and ATP-bound phosphorylated. A series of 2 µs atomistic simulations followed by a conformational landscape mapping and a principal component analysis supports the mechanistic understanding of the JNK3 inactivation/activation process and also indicates key structural intermediates. Our analysis reveals that the unphosphorylated JNK3 undergoes the ‘open-to-closed’ movement via a two-step mechanism. Furthermore, the phosphorylation and ATP-binding allow the JNK3 kinase to attain a fully active conformation. JNK3 is a widely studied target for small-drugs used to treat a variety of neurological disorders. We believe that the mechanistic understanding of the large-conformational changes upon the activation of JNK3 will aid the development of novel targeted therapeutics.
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Affiliation(s)
- Pankaj Mishra
- Institute of Pharmaceutical Sciences, Research Group Pharmaceutical Bioinformatics, Albert-Ludwigs-University Freiburg, Hermann-Herder-Straße 9, 79104, Freiburg, Germany
| | - Stefan Günther
- Institute of Pharmaceutical Sciences, Research Group Pharmaceutical Bioinformatics, Albert-Ludwigs-University Freiburg, Hermann-Herder-Straße 9, 79104, Freiburg, Germany.
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14
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Ali I, Conrad RJ, Verdin E, Ott M. Lysine Acetylation Goes Global: From Epigenetics to Metabolism and Therapeutics. Chem Rev 2018; 118:1216-1252. [PMID: 29405707 DOI: 10.1021/acs.chemrev.7b00181] [Citation(s) in RCA: 220] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Post-translational acetylation of lysine residues has emerged as a key regulatory mechanism in all eukaryotic organisms. Originally discovered in 1963 as a unique modification of histones, acetylation marks are now found on thousands of nonhistone proteins located in virtually every cellular compartment. Here we summarize key findings in the field of protein acetylation over the past 20 years with a focus on recent discoveries in nuclear, cytoplasmic, and mitochondrial compartments. Collectively, these findings have elevated protein acetylation as a major post-translational modification, underscoring its physiological relevance in gene regulation, cell signaling, metabolism, and disease.
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Affiliation(s)
- Ibraheem Ali
- Gladstone Institute of Virology and Immunology , San Francisco, California 94158, United States.,University of California, San Francisco , Department of Medicine, San Francisco, California 94158, United States
| | - Ryan J Conrad
- Gladstone Institute of Virology and Immunology , San Francisco, California 94158, United States.,University of California, San Francisco , Department of Medicine, San Francisco, California 94158, United States
| | - Eric Verdin
- Buck Institute for Research on Aging , Novato, California 94945, United States
| | - Melanie Ott
- Gladstone Institute of Virology and Immunology , San Francisco, California 94158, United States.,University of California, San Francisco , Department of Medicine, San Francisco, California 94158, United States
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15
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Wu Y, Honegger A, Batyuk A, Mittl PRE, Plückthun A. Structural Basis for the Selective Inhibition of c-Jun N-Terminal Kinase 1 Determined by Rigid DARPin-DARPin Fusions. J Mol Biol 2017; 430:2128-2138. [PMID: 29126898 DOI: 10.1016/j.jmb.2017.10.032] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Revised: 10/30/2017] [Accepted: 10/31/2017] [Indexed: 12/31/2022]
Abstract
To untangle the complex signaling of the c-Jun N-terminal kinase (JNK) isoforms, we need tools that can selectively detect and inhibit individual isoforms. Because of the high similarity between JNK1, JNK2 and JNK3, it is very difficult to generate small-molecule inhibitors with this discriminatory power. Thus, we have recently selected protein binders from the designed ankyrin repeat protein (DARPin) library which were indeed isoform-specific inhibitors of JNK1 with low nanomolar potency. Here we provide the structural basis for their isotype discrimination and their inhibitory action. All our previous attempts to generate crystal structures of complexes had failed. We have now made use of a technology we recently developed which consists of rigid fusion of an additional special DARPin, which acts as a crystallization enhancer. This can be rigidly fused with different geometries, thereby generating a range of alternative crystal packings. The structures reveal the molecular basis for isoform specificity of the DARPins and their ability to prevent JNK activation and may thus form the basis of further investigation of the JNK family as well as novel approaches to drug design.
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Affiliation(s)
- Yufan Wu
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Annemarie Honegger
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Alexander Batyuk
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Peer R E Mittl
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Andreas Plückthun
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland.
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16
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Gomez-Gutierrez P, Rubio-Martinez J, Perez JJ. Identification of Potential Small Molecule Binding Pockets in p38α MAP Kinase. J Chem Inf Model 2017; 57:2566-2574. [DOI: 10.1021/acs.jcim.7b00439] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Patricia Gomez-Gutierrez
- Allinky
Biopharma, Madrid Scientific Park, Faraday, 7, 28049 Madrid, Spain
- Department
of Chemical Engineering, Universitat Politecnica de Catalunya, ETSEIB. Av. Diagonal, 647, 08028 Barcelona, Spain
| | - Jaime Rubio-Martinez
- Department
of Physical Chemistry, Faculty of Chemistry, Universitat de Barcelona and Institut de Recerca en Quimica Teorica i Computacional (IQTCUB), Marti i Franques 1-3, 08028 Barcelona, Spain
| | - Juan J. Perez
- Department
of Chemical Engineering, Universitat Politecnica de Catalunya, ETSEIB. Av. Diagonal, 647, 08028 Barcelona, Spain
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17
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Ye W, Qian T, Liu H, Luo R, Chen HF. Allosteric Autoinhibition Pathway in Transcription Factor ERG: Dynamics Network and Mutant Experimental Evaluations. J Chem Inf Model 2017; 57:1153-1165. [PMID: 28425706 DOI: 10.1021/acs.jcim.7b00073] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Allosteric autoinhibition exists in many transcription factors. The ERG proteins exhibit autoinhibition on DNA binding by the C-terminal and N-terminal inhibitory domains (CID and NID). However, the autoinhibition mechanism and allosteric pathway of ERG are unknown. In this study we intend to elucidate the residue-level allosteric mechanism and pathway via a combined approach of computational and experimental analyses. Specifically computational residue-level fluctuation correlation data was analyzed to reveal detailed dynamics signatures in the allosteric autoinhibition process. A hypothesis of "NID/CID binding induced allostery" is proposed to link similar structures and different protein functions, which is subsequently validated by perturbation and mutation analyses in both computation and experiment. Two possible allosteric autoinhibition pathways of L286-L382-A379-G377-I360-Y355-R353 and L286-L382-A379-G377-I360-Y355- A351-K347-R350 were identified computationally and were confirmed by the computational and experimental mutations. Specifically we identified two mutation sites on the allosteric inhibition pathways, L286P/Q383P (NID/CID binding site) and I360G (pathway junction), which completely restore the wild type DNA binding affinity. These results suggest that the putative protein structure-function relationship may be augmented with a general relationship of protein "structure/fluctuation-correlation/function" for more thorough analyses of protein functions.
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Affiliation(s)
- Wei Ye
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, SJTU-Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , 800 Dongchuan Road, Shanghai, 200240, China
| | - Tianle Qian
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, SJTU-Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , 800 Dongchuan Road, Shanghai, 200240, China
| | - Hao Liu
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, SJTU-Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , 800 Dongchuan Road, Shanghai, 200240, China
| | - Ray Luo
- Departments of Molecular Biology and Biochemistry, Chemical Engineering and Materials Science, and Biomedical Engineering, University of California , Irvine, California 92697-3900, United States
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, SJTU-Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , 800 Dongchuan Road, Shanghai, 200240, China.,Shanghai Center for Bioinformation Technology , 1278 Keyuan Road, Shanghai, 200235, China
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18
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Park JY, Yun Y, Chung KY. Conformations of JNK3α splice variants analyzed by hydrogen/deuterium exchange mass spectrometry. J Struct Biol 2016; 197:271-278. [PMID: 27998708 DOI: 10.1016/j.jsb.2016.12.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 12/13/2016] [Accepted: 12/15/2016] [Indexed: 10/20/2022]
Abstract
c-Jun N-terminal kinases (JNKs) are members of the mitogen-activated protein kinase (MAPK) family that regulate apoptosis, inflammation, cytokine production, and metabolism. MAPKs undergo various splicing within their kinase domains. Unlike other MAPKs, JNKs have alternative splicing at the C-terminus, resulting in long and short variants. Functional or conformational effects due to the elongated C-terminal tail in the long splice variants have not been investigated nor has the conformation of the C-terminal tail been analyzed. Here, we analyzed the conformation of the elongated C-terminal tail and investigated conformational differences between long and short splice variants of JNKs using JNK3α2 and JNK3α1 as models. We adopted hydrogen/deuterium exchange mass spectrometry (HDX-MS) to analyze the conformation. HDX-MS revealed that the C-terminal tail is mostly intrinsically disordered, and that the conformation of the kinase domain of JNK3α2 is more dynamic than that of JNK3α1. The different conformation dynamics between long and short splice variants of JNK3α might affect the cellular functions of JNK3.
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Affiliation(s)
- Ji Young Park
- School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
| | - Youngjoo Yun
- School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
| | - Ka Young Chung
- School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea.
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19
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Guo M, Wei J, Zhou Y, Qin Q. c-Jun N-terminal kinases 3 (JNK3) from orange-spotted grouper, Epinephelus coioides, inhibiting the replication of Singapore grouper iridovirus (SGIV) and SGIV-induced apoptosis. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2016; 65:169-181. [PMID: 27422159 DOI: 10.1016/j.dci.2016.06.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 06/10/2016] [Accepted: 06/10/2016] [Indexed: 06/06/2023]
Abstract
C-Jun N-terminal kinases (JNKs), a subgroup of serine-threonine protein kinases that activated by phosphorylation, are involve in physiological and pathophysiological processes. JNK3 is one of JNK proteins involved in JNK3 signaling transduction. In the present study, two JNK3 isoforms, Ec-JNK3 X1 and Ec-JNK3 X2, were cloned from orange-spotted grouper, Epinephelus coioides. Both Ec-JNK3 X1 and Ec-JNK3 X2 were mainly expressed in liver, gill, skin, brain and muscle of juvenile grouper. The relative expression of Ec-JNK3 X2 mRNA was much higher in muscle and gill than that of Ec-JNK3 X1. Isoform-specific immune response to challenges was revealed by the expression profiles in vivo. Immunofluorescence staining indicated that JNK3 was localized in the cytoplasm of grouper spleen (GS) cells and shown immune response to SGIV infection in vitro. Over-expressing Ec-JNK3 X1 and/or Ec-JNK3 X2 inhibited the SGIV infection and replication and the SGIV-induced apoptosis. To achieve the antiviral and anti-apoptosis activities, JNK3 promoted the activation of genes ISRE and type I IFN in the antiviral IFN signaling pathway, and inhibited the activation of transcription factors NF-κB and p53 relating to apoptosis, respectively. Ec-JNK3 X2 showed stronger activities in antivirus and anti-apoptosis than that of Ec-JNK3 X1. Our results not only define the characterization of JNK3 but also reveal new immune functions and the molecular mechanisms of JNK3 on iridoviruses infection and the virus-induced apoptosis.
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Affiliation(s)
- Minglan Guo
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China; Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China
| | - Jingguang Wei
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China; Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China
| | - Yongcan Zhou
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou, PR China
| | - Qiwei Qin
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China; College of Marine Sciences, South China Agricultural University, Guangzhou 510642, PR China.
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20
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JNK Signaling: Regulation and Functions Based on Complex Protein-Protein Partnerships. Microbiol Mol Biol Rev 2016; 80:793-835. [PMID: 27466283 DOI: 10.1128/mmbr.00043-14] [Citation(s) in RCA: 319] [Impact Index Per Article: 39.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The c-Jun N-terminal kinases (JNKs), as members of the mitogen-activated protein kinase (MAPK) family, mediate eukaryotic cell responses to a wide range of abiotic and biotic stress insults. JNKs also regulate important physiological processes, including neuronal functions, immunological actions, and embryonic development, via their impact on gene expression, cytoskeletal protein dynamics, and cell death/survival pathways. Although the JNK pathway has been under study for >20 years, its complexity is still perplexing, with multiple protein partners of JNKs underlying the diversity of actions. Here we review the current knowledge of JNK structure and isoforms as well as the partnerships of JNKs with a range of intracellular proteins. Many of these proteins are direct substrates of the JNKs. We analyzed almost 100 of these target proteins in detail within a framework of their classification based on their regulation by JNKs. Examples of these JNK substrates include a diverse assortment of nuclear transcription factors (Jun, ATF2, Myc, Elk1), cytoplasmic proteins involved in cytoskeleton regulation (DCX, Tau, WDR62) or vesicular transport (JIP1, JIP3), cell membrane receptors (BMPR2), and mitochondrial proteins (Mcl1, Bim). In addition, because upstream signaling components impact JNK activity, we critically assessed the involvement of signaling scaffolds and the roles of feedback mechanisms in the JNK pathway. Despite a clarification of many regulatory events in JNK-dependent signaling during the past decade, many other structural and mechanistic insights are just beginning to be revealed. These advances open new opportunities to understand the role of JNK signaling in diverse physiological and pathophysiological states.
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21
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Zhuo ZH, Sun YZ, Jin PN, Li FY, Zhang YL, Wang HL. Selective targeting of MAPK family kinases JNK over p38 by rationally designed peptides as potential therapeutics for neurological disorders and epilepsy. MOLECULAR BIOSYSTEMS 2016; 12:2532-40. [PMID: 27263470 DOI: 10.1039/c6mb00297h] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
A systematic strategy is described to optimize peptide selectivity between the MAPK family kinases JNK and p38 for epilepsy therapy.
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Affiliation(s)
- Zhi-Hong Zhuo
- Department of Pediatrics
- the First Affiliated Hospital of Zhengzhou University
- Zhengzhou 450052
- China
| | - Yi-Zhen Sun
- Department of Pediatrics
- the First Affiliated Hospital of Zhengzhou University
- Zhengzhou 450052
- China
| | - Pei-Na Jin
- Department of Pediatrics
- the First Affiliated Hospital of Zhengzhou University
- Zhengzhou 450052
- China
| | - Feng-Yan Li
- Department of Pediatrics
- the First Affiliated Hospital of Zhengzhou University
- Zhengzhou 450052
- China
| | - Yi-Le Zhang
- Reproductive Medical Center
- the First Affiliated Hospital of Zhengzhou University
- Zhengzhou 450052
- China
| | - Huai-Li Wang
- Department of Pediatrics
- the First Affiliated Hospital of Zhengzhou University
- Zhengzhou 450052
- China
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22
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Zeke A, Bastys T, Alexa A, Garai Á, Mészáros B, Kirsch K, Dosztányi Z, Kalinina OV, Reményi A. Systematic discovery of linear binding motifs targeting an ancient protein interaction surface on MAP kinases. Mol Syst Biol 2015; 11:837. [PMID: 26538579 PMCID: PMC4670726 DOI: 10.15252/msb.20156269] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Mitogen‐activated protein kinases (MAPK) are broadly used regulators of cellular signaling. However, how these enzymes can be involved in such a broad spectrum of physiological functions is not understood. Systematic discovery of MAPK networks both experimentally and in silico has been hindered because MAPKs bind to other proteins with low affinity and mostly in less‐characterized disordered regions. We used a structurally consistent model on kinase‐docking motif interactions to facilitate the discovery of short functional sites in the structurally flexible and functionally under‐explored part of the human proteome and applied experimental tools specifically tailored to detect low‐affinity protein–protein interactions for their validation in vitro and in cell‐based assays. The combined computational and experimental approach enabled the identification of many novel MAPK‐docking motifs that were elusive for other large‐scale protein–protein interaction screens. The analysis produced an extensive list of independently evolved linear binding motifs from a functionally diverse set of proteins. These all target, with characteristic binding specificity, an ancient protein interaction surface on evolutionarily related but physiologically clearly distinct three MAPKs (JNK, ERK, and p38). This inventory of human protein kinase binding sites was compared with that of other organisms to examine how kinase‐mediated partnerships evolved over time. The analysis suggests that most human MAPK‐binding motifs are surprisingly new evolutionarily inventions and newly found links highlight (previously hidden) roles of MAPKs. We propose that short MAPK‐binding stretches are created in disordered protein segments through a variety of ways and they represent a major resource for ancient signaling enzymes to acquire new regulatory roles.
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Affiliation(s)
- András Zeke
- Lendület Protein Interaction Group, Institute of Enzymology Research Center for Natural Sciences Hungarian Academy of Sciences, Budapest, Hungary
| | - Tomas Bastys
- Max Planck Institute for Informatics, Saarbrücken, Germany Graduate School of Computer Science, Saarland University, Saarbrücken, Germany
| | - Anita Alexa
- Lendület Protein Interaction Group, Institute of Enzymology Research Center for Natural Sciences Hungarian Academy of Sciences, Budapest, Hungary
| | - Ágnes Garai
- Lendület Protein Interaction Group, Institute of Enzymology Research Center for Natural Sciences Hungarian Academy of Sciences, Budapest, Hungary
| | - Bálint Mészáros
- Institute of Enzymology Research Center for Natural Sciences Hungarian Academy of Sciences, Budapest, Hungary
| | - Klára Kirsch
- Lendület Protein Interaction Group, Institute of Enzymology Research Center for Natural Sciences Hungarian Academy of Sciences, Budapest, Hungary
| | - Zsuzsanna Dosztányi
- MTA-ELTE Lendület Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
| | | | - Attila Reményi
- Lendület Protein Interaction Group, Institute of Enzymology Research Center for Natural Sciences Hungarian Academy of Sciences, Budapest, Hungary
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Chimnaronk S, Sitthiroongruang J, Srisucharitpanit K, Srisaisup M, Ketterman AJ, Boonserm P. The crystal structure of JNK from Drosophila melanogaster reveals an evolutionarily conserved topology with that of mammalian JNK proteins. BMC STRUCTURAL BIOLOGY 2015; 15:17. [PMID: 26377800 PMCID: PMC4573485 DOI: 10.1186/s12900-015-0045-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2015] [Accepted: 09/07/2015] [Indexed: 11/10/2022]
Abstract
Background The c-Jun N-terminal kinases (JNKs), members of the mitogen-activated protein kinase (MAPK) family, engage in diverse cellular responses to signals produced under normal development and stress conditions. In Drosophila, only one JNK member is present, whereas ten isoforms from three JNK genes (JNK1, 2, and 3) are present in mammalian cells. To date, several mammalian JNK structures have been determined, however, there has been no report of any insect JNK structure. Results We report the first structure of JNK from Drosophila melanogaster (DJNK). The crystal structure of the unphosphorylated form of DJNK complexed with adenylyl imidodiphosphate (AMP-PNP) has been solved at 1.79 Å resolution. The fold and topology of DJNK are similar to those of mammalian JNK isoforms, demonstrating their evolutionarily conserved structures and functions. Structural comparisons of DJNK and the closely related mammalian JNKs also allow identification of putative catalytic residues, substrate-binding sites and conformational alterations upon docking interaction with Drosophila scaffold proteins. Conclusions The DJNK structure reveals common features with those of the mammalian JNK isoforms, thereby allowing the mapping of putative catalytic and substrate binding sites. Additionally, structural changes upon peptide binding could be predicted based on the comparison with the closely-related JNK3 structure in complex with pepJIP1. This is the first structure of insect JNK reported to date, and will provide a platform for future mutational studies in Drosophila to ascertain the functional role of insect JNK. Electronic supplementary material The online version of this article (doi:10.1186/s12900-015-0045-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sarin Chimnaronk
- Institute of Molecular Biosciences, Mahidol University, Salaya, Phuttamonthon, Nakhon Pathom, 73170, Thailand.
| | - Jatuporn Sitthiroongruang
- Institute of Molecular Biosciences, Mahidol University, Salaya, Phuttamonthon, Nakhon Pathom, 73170, Thailand.
| | - Kanokporn Srisucharitpanit
- Faculty of Allied Health Sciences, Burapha University, Mueang District, Saen Sook, Chonburi, 20131, Thailand.
| | - Monrudee Srisaisup
- Institute of Molecular Biosciences, Mahidol University, Salaya, Phuttamonthon, Nakhon Pathom, 73170, Thailand.
| | - Albert J Ketterman
- Institute of Molecular Biosciences, Mahidol University, Salaya, Phuttamonthon, Nakhon Pathom, 73170, Thailand.
| | - Panadda Boonserm
- Institute of Molecular Biosciences, Mahidol University, Salaya, Phuttamonthon, Nakhon Pathom, 73170, Thailand.
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24
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Bardwell AJ, Bardwell L. Two hydrophobic residues can determine the specificity of mitogen-activated protein kinase docking interactions. J Biol Chem 2015; 290:26661-74. [PMID: 26370088 DOI: 10.1074/jbc.m115.691436] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Indexed: 11/06/2022] Open
Abstract
MAPKs bind to many of their upstream regulators and downstream substrates via a short docking motif (the D-site) on their binding partner. MAPKs that are in different families (e.g. ERK, JNK, and p38) can bind selectively to D-sites in their authentic substrates and regulators while discriminating against D-sites in other pathways. Here we demonstrate that the short hydrophobic region at the distal end of the D-site plays a critical role in determining the high selectivity of JNK MAPKs for docking sites in their cognate MAPK kinases. Changing just 1 or 2 key hydrophobic residues in this submotif is sufficient to turn a weak JNK-binding D-site into a strong one, or vice versa. These specificity-determining differences are also found in the D-sites of the ETS family transcription factors Elk-1 and Net. Moreover, swapping two hydrophobic residues between these D-sites switches the relative efficiency of Elk-1 and Net as substrates for ERK versus JNK, as predicted. These results provide new insights into docking specificity and suggest that this specificity can evolve rapidly by changes to just 1 or 2 amino acids.
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Affiliation(s)
- A Jane Bardwell
- From the Department of Developmental and Cell Biology, Center for Complex Biological Systems, University of California, Irvine, California 92697
| | - Lee Bardwell
- From the Department of Developmental and Cell Biology, Center for Complex Biological Systems, University of California, Irvine, California 92697
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25
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Kim MH, Lee J, Hah JM. De Novo Design and Synthesis of a γ-Turn Peptidomimetic Scaffold and Its Application as JNK3 Allosteric Ligand. Chem Asian J 2015; 10:1318-26. [DOI: 10.1002/asia.201403417] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 02/15/2015] [Indexed: 11/09/2022]
Affiliation(s)
- Mi-hyun Kim
- Department of Pharmacy; College of Pharmacy & Institute of Pharmaceutical Science and Technology; Hanyang University; 55 Hanyangdaehak-ro Sangnok-gu, Ansan, Kyeonggi-do 426-791 Korea
- Department of Pharmacy; College of Pharmacy & Gachon Institute of Pharmaceutical Science; Gachon University; 155 Gaetbeol-ro Yeonsu-gu, Incheon 406-840 Korea
| | - Junghun Lee
- Department of Pharmacy; College of Pharmacy & Institute of Pharmaceutical Science and Technology; Hanyang University; 55 Hanyangdaehak-ro Sangnok-gu, Ansan, Kyeonggi-do 426-791 Korea
| | - Jung-Mi Hah
- Department of Pharmacy; College of Pharmacy & Institute of Pharmaceutical Science and Technology; Hanyang University; 55 Hanyangdaehak-ro Sangnok-gu, Ansan, Kyeonggi-do 426-791 Korea
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26
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Co-conserved MAPK features couple D-domain docking groove to distal allosteric sites via the C-terminal flanking tail. PLoS One 2015; 10:e0119636. [PMID: 25799139 PMCID: PMC4370755 DOI: 10.1371/journal.pone.0119636] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 02/02/2015] [Indexed: 11/19/2022] Open
Abstract
Mitogen activated protein kinases (MAPKs) form a closely related family of kinases that control critical pathways associated with cell growth and survival. Although MAPKs have been extensively characterized at the biochemical, cellular, and structural level, an integrated evolutionary understanding of how MAPKs differ from other closely related protein kinases is currently lacking. Here, we perform statistical sequence comparisons of MAPKs and related protein kinases to identify sequence and structural features associated with MAPK functional divergence. We show, for the first time, that virtually all MAPK-distinguishing sequence features, including an unappreciated short insert segment in the β4-β5 loop, physically couple distal functional sites in the kinase domain to the D-domain peptide docking groove via the C-terminal flanking tail (C-tail). The coupling mediated by MAPK-specific residues confers an allosteric regulatory mechanism unique to MAPKs. In particular, the regulatory αC-helix conformation is controlled by a MAPK-conserved salt bridge interaction between an arginine in the αC-helix and an acidic residue in the C-tail. The salt-bridge interaction is modulated in unique ways in individual sub-families to achieve regulatory specificity. Our study is consistent with a model in which the C-tail co-evolved with the D-domain docking site to allosterically control MAPK activity. Our study provides testable mechanistic hypotheses for biochemical characterization of MAPK-conserved residues and new avenues for the design of allosteric MAPK inhibitors.
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27
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Abstract
Signaling specificity in the mitogen-activated protein kinase (MAPK) pathways is controlled by disordered domains of the MAPK kinases (MKKs) that specifically bind to their cognate MAPKs via linear docking motifs. MKK7 activates the c-Jun N-terminal kinase (JNK) pathway and is the only MKK containing three motifs within its regulatory domain. Here, we characterize the conformational behavior and interaction mechanism of the MKK7 regulatory domain. Using NMR spectroscopy, we develop an atomic resolution ensemble description of MKK7, revealing highly diverse intrinsic conformational propensities of the three docking sites, suggesting that prerecognition sampling of the bound-state conformation is not prerequisite for binding. Although the different sites exhibit similar affinities for JNK1, interaction kinetics differ considerably. Importantly, we determine the crystal structure of JNK1 in complex with the second docking site of MKK7, revealing two different binding modes of the docking motif correlating with observations from NMR exchange spectroscopy. Our results provide unique insight into how signaling specificity is regulated by linear motifs and, in general, into the role of conformational disorder in MAPK signaling.
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28
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Chen WK, Yeap YY, Bogoyevitch MA. The JNK1/JNK3 interactome – Contributions by the JNK3 unique N-terminus and JNK common docking site residues. Biochem Biophys Res Commun 2014; 453:576-81. [DOI: 10.1016/j.bbrc.2014.09.122] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 09/27/2014] [Indexed: 12/14/2022]
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Gao YG, Yang H, Zhao J, Jiang YJ, Hu HY. Autoinhibitory structure of the WW domain of HYPB/SETD2 regulates its interaction with the proline-rich region of huntingtin. Structure 2014; 22:378-86. [PMID: 24412394 DOI: 10.1016/j.str.2013.12.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Revised: 11/19/2013] [Accepted: 12/05/2013] [Indexed: 01/25/2023]
Abstract
Huntington's disease (HD) is an autosomally dominant neurodegenerative disorder caused by expansion of polyglutamine (polyQ) in the huntingtin (Htt) protein. Htt yeast two-hybrid protein B (HYPB/SETD2), a histone methyltransferase, directly interacts with Htt and is involved in HD pathology. Using NMR techniques, we characterized a polyproline (polyP) stretch at the C terminus of HYPB, which directly interacts with the following WW domain and leads this domain predominantly to be in a closed conformational state. The solution structure shows that the polyP stretch extends from the back and binds to the WW core domain in a typical binding mode. This autoinhibitory structure regulates interaction between the WW domain of HYPB and the proline-rich region (PRR) of Htt, as evidenced by NMR and immunofluorescence techniques. This work provides structural and mechanistic insights into the intramolecular regulation of the WW domain in Htt-interacting partners and will be helpful for understanding the pathology of HD.
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Affiliation(s)
- Yong-Guang Gao
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Hui Yang
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jian Zhao
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ya-Jun Jiang
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hong-Yu Hu
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
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30
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Peti W, Page R. Molecular basis of MAP kinase regulation. Protein Sci 2013; 22:1698-710. [PMID: 24115095 DOI: 10.1002/pro.2374] [Citation(s) in RCA: 216] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 09/09/2013] [Accepted: 09/10/2013] [Indexed: 12/11/2022]
Abstract
Mitogen-activated protein kinases (MAPKs; ERK1/2, p38, JNK, and ERK5) have evolved to transduce environmental and developmental signals (growth factors, stress) into adaptive and programmed responses (differentiation, inflammation, apoptosis). Almost 20 years ago, it was discovered that MAPKs contain a docking site in the C-terminal lobe that binds a conserved 13-16 amino acid sequence known as the D- or KIM-motif (kinase interaction motif). Recent crystal structures of MAPK:KIM-peptide complexes are leading to a precise understanding of how KIM sequences contribute to MAPK selectivity. In addition, new crystal and especially NMR studies are revealing how residues outside the canonical KIM motif interact with specific MAPKs and contribute further to MAPK selectivity and signaling pathway fidelity. In this review, we focus on these recent studies, with an emphasis on the use of NMR spectroscopy, isothermal titration calorimetry and small angle X-ray scattering to investigate these processes.
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Affiliation(s)
- Wolfgang Peti
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, Rhode Island, 02912; Department of Chemistry, Brown University, Providence, Rhode Island, 02912
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31
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Feng Y, Chambers JW, Iqbal S, Koenig M, Park H, Cherry L, Hernandez P, Figuera-Losada M, LoGrasso PV. A small molecule bidentate-binding dual inhibitor probe of the LRRK2 and JNK kinases. ACS Chem Biol 2013; 8:1747-54. [PMID: 23751758 DOI: 10.1021/cb3006165] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Both JNK and LRRK2 are associated with Parkinson's disease (PD). Here we report a reasonably selective and potent kinase inhibitor (compound 6) that bound to both JNK and LRRK2 (a dual inhibitor). A bidentate-binding strategy that simultaneously utilized the ATP hinge binding and a unique protein surface site outside of the ATP pocket was applied to the design and identification of this kind of inhibitor. Compound 6 was a potent JNK3 and modest LRRK2 dual inhibitor with an enzyme IC50 value of 12 nM and 99 nM (LRRK2-G2019S), respectively. Compound 6 also exhibited good cell potency, inhibited LRRK2:G2019S-induced mitochondrial dysfunction in SHSY5Y cells, and was demonstrated to be reasonably selective against a panel of 116 kinases from representative kinase families. Design of such a probe molecule may help enable testing if dual JNK and LRRK2 inhibitions have added or synergistic efficacy in protecting against neurodegeneration in PD.
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Affiliation(s)
- Yangbo Feng
- Medicinal Chemistry, ‡Discovery Biology, §Modeling/Crystallography
Facility, Translational Research Institute, and ∥Department of Molecular Therapeutics, The Scripps Research Institute, Florida,
Jupiter, Florida 33458, United States
| | - Jeremy W. Chambers
- Medicinal Chemistry, ‡Discovery Biology, §Modeling/Crystallography
Facility, Translational Research Institute, and ∥Department of Molecular Therapeutics, The Scripps Research Institute, Florida,
Jupiter, Florida 33458, United States
| | - Sarah Iqbal
- Medicinal Chemistry, ‡Discovery Biology, §Modeling/Crystallography
Facility, Translational Research Institute, and ∥Department of Molecular Therapeutics, The Scripps Research Institute, Florida,
Jupiter, Florida 33458, United States
| | - Marcel Koenig
- Medicinal Chemistry, ‡Discovery Biology, §Modeling/Crystallography
Facility, Translational Research Institute, and ∥Department of Molecular Therapeutics, The Scripps Research Institute, Florida,
Jupiter, Florida 33458, United States
| | - HaJeung Park
- Medicinal Chemistry, ‡Discovery Biology, §Modeling/Crystallography
Facility, Translational Research Institute, and ∥Department of Molecular Therapeutics, The Scripps Research Institute, Florida,
Jupiter, Florida 33458, United States
| | - Lisa Cherry
- Medicinal Chemistry, ‡Discovery Biology, §Modeling/Crystallography
Facility, Translational Research Institute, and ∥Department of Molecular Therapeutics, The Scripps Research Institute, Florida,
Jupiter, Florida 33458, United States
| | - Pamela Hernandez
- Medicinal Chemistry, ‡Discovery Biology, §Modeling/Crystallography
Facility, Translational Research Institute, and ∥Department of Molecular Therapeutics, The Scripps Research Institute, Florida,
Jupiter, Florida 33458, United States
| | - Mariana Figuera-Losada
- Medicinal Chemistry, ‡Discovery Biology, §Modeling/Crystallography
Facility, Translational Research Institute, and ∥Department of Molecular Therapeutics, The Scripps Research Institute, Florida,
Jupiter, Florida 33458, United States
| | - Philip V. LoGrasso
- Medicinal Chemistry, ‡Discovery Biology, §Modeling/Crystallography
Facility, Translational Research Institute, and ∥Department of Molecular Therapeutics, The Scripps Research Institute, Florida,
Jupiter, Florida 33458, United States
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32
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A novel retro-inverso peptide is a preferential JNK substrate-competitive inhibitor. Int J Biochem Cell Biol 2013; 45:1939-50. [DOI: 10.1016/j.biocel.2013.06.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 06/04/2013] [Accepted: 06/11/2013] [Indexed: 12/22/2022]
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33
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Ligand-binding dynamics rewire cellular signaling via estrogen receptor-α. Nat Chem Biol 2013; 9:326-32. [PMID: 23524984 PMCID: PMC3631275 DOI: 10.1038/nchembio.1214] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2012] [Accepted: 02/22/2013] [Indexed: 11/24/2022]
Abstract
Ligand-binding dynamics control allosteric signaling through the estrogen receptor-α (ERα), but the biological consequences of such dynamic binding orientations are unknown. Here, we compare a set of ER ligands having dynamic binding orientation (dynamic ligands) with a control set of isomers that are constrained to bind in a single orientation (constrained ligands). Proliferation of breast cancer cells directed by constrained ligands is associated with DNA binding, coactivator recruitment and activation of the estrogen-induced gene GREB1, reflecting a highly interconnected signaling network. In contrast, proliferation driven by dynamic ligands is associated with induction of ERα-mediated transcription in a DNA-binding domain (DBD)-dependent manner. Further, dynamic ligands displayed enhanced anti-inflammatory activity. The DBD-dependent profile was predictive of these signaling patterns in a larger diverse set of natural and synthetic ligands. Thus, ligand dynamics directs unique signaling pathways, and reveals a novel role of the DBD in allosteric control of ERα-mediated signaling.
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