201
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Lee Y, Chou TF, Pittman SK, Keith AL, Razani B, Weihl CC. Keap1/Cullin3 Modulates p62/SQSTM1 Activity via UBA Domain Ubiquitination. Cell Rep 2017; 19:188-202. [PMID: 28380357 DOI: 10.1016/j.celrep.2017.03.030] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 11/30/2016] [Accepted: 03/08/2017] [Indexed: 10/19/2022] Open
Abstract
p62/SQSTM1 (p62) is a scaffolding protein that facilitates the formation and degradation of ubiquitinated aggregates via its self-interaction and ubiquitin binding domains. The regulation of this process is unclear but may relate to the post-translational modification of p62. In the present study, we find that Keap1/Cullin3 ubiquitinates p62 at lysine 420 within its UBA domain. Substitution of lysine 420 with an arginine diminishes p62 sequestration and degradation activity similar what is seen when the UBA domain is deleted. Overexpression of Keap1/Cullin3 in p62-WT-expressing cells increases ubiquitinated inclusion formation and p62's association with LC3 and rescues proteotoxicity. This effect is not seen in cells expressing a mutant p62 that fails to interact with Keap1. Interestingly, p62 disease mutants have diminished or absent UBA domain ubiquitination. These data suggest that the ubiquitination of p62's UBA domain at lysine 420 may regulate p62's function and be disrupted in p62-associated disease.
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Affiliation(s)
- YouJin Lee
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Tsui-Fen Chou
- Division of Medical Genetics, Department of Pediatrics, Harbor-UCLA Medical Center and Los Angeles Biomedical Research Institute, Torrance, CA 90502, USA
| | - Sara K Pittman
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Amy L Keith
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Babak Razani
- Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Conrad C Weihl
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA.
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202
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Bello M, Morales-González JA. Molecular recognition between potential natural inhibitors of the Keap1-Nrf2 complex. Int J Biol Macromol 2017; 105:981-992. [PMID: 28746889 DOI: 10.1016/j.ijbiomac.2017.07.117] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 07/13/2017] [Accepted: 07/18/2017] [Indexed: 02/07/2023]
Abstract
Disrupting the Keap1-Nrf2 pathway enhances Nrf2 activity, which has been identified as an important approach for the prevention of different chronic diseases in which oxidative stress and inflammation are present, such as cancer, diabetes, Alzheimer's and Parkinson's. Based on the high potential to modulate antioxidant, anti-inflammatory and anticancer properties that the discovery of Keap1-Nrf2 protein-protein interaction inhibitors would represent, the utilization of some natural compounds has emerged as a promising strategy to identify new drugs. To gain insight into the structural and energetic basis of the molecular recognition between some natural inhibitors that could work as inhibitors of the Keap1-Nrf2 complex, we evaluated the binding properties between four natural compounds present in the extract of Geranium schiedeanum (Gs): 3-O-a-L arabinofuranoside-7-O-a-l-rhamnopyranoside of kaempferol (KAM), gallic acid (GAL), ellagic acid (ELL) and geranium acetonitrile (ACE), which based on experimental findings have been proposed as possible Keap1-Nrf2 PPI inhibitors. Computational studies combining docking and MD simulations accompanied by the MMGBSA approach revealed that KAM and ACE directly interact with residues in the Kelch domain that participate in the molecular recognition of Nrf2, indicating that both natural compounds could act as activators of Nrf2, whereas GAL and ELL are possible free radical scavengers.
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Affiliation(s)
- Martiniano Bello
- Laboratorio de Modelado Molecular, Bioinformática y Diseño de Fármacos de la Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón, Col. Casco de Santo Tomás, Del. Miguel Hidalgo, México D.F. 11340, Mexico.
| | - José Antonio Morales-González
- Laboratorio Medicina de Conservación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón, Col. Casco de Santo Tomás, Del. Miguel Hidalgo, México D.F. 11340, Mexico
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203
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Deck LM, Hunsaker LA, Vander Jagt TA, Whalen LJ, Royer RE, Vander Jagt DL. Activation of anti-oxidant Nrf2 signaling by enone analogues of curcumin. Eur J Med Chem 2017; 143:854-865. [PMID: 29223100 DOI: 10.1016/j.ejmech.2017.11.048] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 10/31/2017] [Accepted: 11/18/2017] [Indexed: 12/24/2022]
Abstract
Inflammation and oxidative stress are common in many chronic diseases. Targeting signaling pathways that contribute to these conditions may have therapeutic potential. The transcription factor Nrf2 is a major regulator of phase II detoxification and anti-oxidant genes as well as anti-inflammatory and neuroprotective genes. Nrf2 is widespread in the CNS and is recognized as an important regulator of brain inflammation. The natural product curcumin exhibits numerous biological activities including ability to induce the expression of Nrf2-dependent phase II and anti-oxidant enzymes. Curcumin has been examined in a number of clinical studies with limited success, mainly owing to limited bioavailability and rapid metabolism. Enone analogues of curcumin were examined with an Nrf2 reporter assay to identify Nrf2 activators. Analogues were separated into groups with a 7-carbon dienone spacer, as found in curcumin; a 5-carbon enone spacer with and without a ring; and a 3-carbon enone spacer. Activators of Nrf2 were found in all three groups, many of which were more active than curcumin. Dose-response studies demonstrated that a range of substituents on the aromatic rings of these enones influenced not only the sensitivity to activation, reflected in EC50 values, but also the extent of activation, which suggests that multiple mechanisms are involved in the activation of Nrf2 by these analogues.
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Affiliation(s)
- Lorraine M Deck
- Department of Chemistry and Chemical Biology, University of New Mexico, MSC03 2060, 1 University of New Mexico, Albuquerque, NM 87131, USA.
| | - Lucy A Hunsaker
- Department of Biochemistry and Molecular Biology, University of New Mexico School of Medicine, MSC08 4670, Fitz Hall, Room 249, 1 University of New Mexico, Albuquerque, NM 87131, USA
| | - Thomas A Vander Jagt
- Department of Biochemistry and Molecular Biology, University of New Mexico School of Medicine, MSC08 4670, Fitz Hall, Room 249, 1 University of New Mexico, Albuquerque, NM 87131, USA
| | - Lisa J Whalen
- Department of Chemistry and Chemical Biology, University of New Mexico, MSC03 2060, 1 University of New Mexico, Albuquerque, NM 87131, USA
| | - Robert E Royer
- Department of Biochemistry and Molecular Biology, University of New Mexico School of Medicine, MSC08 4670, Fitz Hall, Room 249, 1 University of New Mexico, Albuquerque, NM 87131, USA
| | - David L Vander Jagt
- Department of Biochemistry and Molecular Biology, University of New Mexico School of Medicine, MSC08 4670, Fitz Hall, Room 249, 1 University of New Mexico, Albuquerque, NM 87131, USA
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204
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Lu MC, Jiao Q, Liu T, Tan SJ, Zhou HS, You QD, Jiang ZY. Discovery of a head-to-tail cyclic peptide as the Keap1-Nrf2 protein-protein interaction inhibitor with high cell potency. Eur J Med Chem 2017; 143:1578-1589. [PMID: 29117896 DOI: 10.1016/j.ejmech.2017.10.052] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Revised: 10/16/2017] [Accepted: 10/16/2017] [Indexed: 01/06/2023]
Abstract
Directly disrupting Keap1-Nrf2 protein-protein interaction (PPI) has emerged as a novel way to activate Nrf2. Peptide Keap1-Nrf2 PPI inhibitors have been reported with high Keap1 binding affinity. However, these peptide inhibitors show weak activity in cells. In this study, the head-to-tail cyclic strategy was applied in the development of peptide inhibitors. The privileged residue sequence with minimal acidic residues was used as the template for the cyclic peptide, and the appropriate conjugation method was designed based on the peptide-Keap1 binding mode. The glycine was introduced as the linker to connect both sides, which can avoid the terminal charge, enhance the peptide stability and constrain the binding conformation simultaneously. The obtained novel cyclic peptide 3 showed high binding affinity with Keap1 and possessed high potency in Nrf2 activation at cellular level. We also showed that peptide 3 exhibited effective anti-inflammatory effects in mouse RAW 264.7 cells by activating the Nrf2-regulated defense system and enhancing the antioxidant capacity. This study proved that the head-to-tail cyclic strategy is quite useful in improving the cell potency of peptide Keap1-Nrf2 inhibitors and provided a possible way to develop drug-like peptides as therapeutic Nrf2 activators.
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Affiliation(s)
- Meng-Chen Lu
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
| | - Qiong Jiao
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
| | - Tian Liu
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
| | - Shi-Jie Tan
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
| | - Hai-Shan Zhou
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
| | - Qi-Dong You
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
| | - Zheng-Yu Jiang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
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205
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The Chinese herbal formula Free and Easy Wanderer ameliorates oxidative stress through KEAP1-NRF2/HO-1 pathway. Sci Rep 2017; 7:11551. [PMID: 28912423 PMCID: PMC5599498 DOI: 10.1038/s41598-017-10443-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 05/10/2017] [Indexed: 12/21/2022] Open
Abstract
Posttraumatic stress disorder (PTSD) gains a lot of attention due to high prevalence and strong psychological upset, but the etiology remains undefined and effective treatment is quite limited. Growing studies demonstrated the involvement of oxidative stress in various psychiatry diseases, suggesting anti-oxidation therapy might be a strategy for PTSD treatment. Free and Easy Wanderer (FAEW) is a poly-herbal drug clinically used in China for hundreds of years in the treatment of psychiatric disorder. We hypothesized that FAEW exerts clinical effects through the activity against oxidative stress with fluoxetine as antidepressant control drug. Our results revealed that FAEW significantly reduced both endogenous and H2O2-induced exogenous ROS levels in the human glioblastoma T98G and neuroblastoma SH-SY5Y cell lines. Transcriptome-wide microarray analysis indicated NRF2/HO-1 as the common target of FAEW and fluoxetine. Western blotting assay proved that the two drugs promoted NRF2 release from KEAP1 in the cytoplasm and translocation to the nuclei in a KEAP1-dependent manner, the expression of the protein HO-1 increased accordingly, suggesting the participation of KEAP1-NRF2/HO-1 pathway. The chemical constituents of FAEW (i.e. paeoniflorin, baicalin) bound to KEAP1 in silico, which hence might be the effective substances of FAEW. In conclusion, FAEW counteracted H2O2-induced oxidative stress through KEAP1-NRF2/HO-1 pathway.
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206
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Bresciani A, Missineo A, Gallo M, Cerretani M, Fezzardi P, Tomei L, Cicero DO, Altamura S, Santoprete A, Ingenito R, Bianchi E, Pacifici R, Dominguez C, Munoz-Sanjuan I, Harper S, Toledo-Sherman L, Park LC. Nuclear factor (erythroid-derived 2)-like 2 (NRF2) drug discovery: Biochemical toolbox to develop NRF2 activators by reversible binding of Kelch-like ECH-associated protein 1 (KEAP1). Arch Biochem Biophys 2017; 631:31-41. [PMID: 28801166 DOI: 10.1016/j.abb.2017.08.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Revised: 08/03/2017] [Accepted: 08/04/2017] [Indexed: 12/22/2022]
Abstract
Mechanisms that activate innate antioxidant responses, as a way to mitigate oxidative stress at the site of action, hold much therapeutic potential in diseases, such as Parkinson's disease, Alzheimer's disease and Huntington's disease, where the use of antioxidants as monotherapy has not yielded positive results. The nuclear factor NRF2 is a transcription factor whose activity upregulates the expression of cell detoxifying enzymes in response to oxidative stress. NRF2 levels are modulated by KEAP1, a sensor of oxidative stress. KEAP1 binds NRF2 and facilitates its ubiquitination and subsequent degradation. Recently, compounds that reversibly disrupt the NRF2-KEAP1 interaction have been described, opening the field to a new era of safer NRF2 activators. This paper describes a set of new, robust and informative biochemical assays that enable the selection and optimization of non-covalent KEAP1 binders. These include a time-resolved fluorescence resonance energy transfer (TR-FRET) primary assay with high modularity and robustness, a surface plasmon resonance (SPR) based KEAP1 direct binding assay that enables the quantification and analysis of full kinetic binding parameters and finally a 1H-15N heteronuclear single quantum coherence (HSQC) NMR assay suited to study the interaction surface of KEAP1 with residue-specific information to validate the interaction of ligands in the KEAP1 binding site.
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Affiliation(s)
| | | | | | | | | | - Licia Tomei
- IRBM Science Park S.p.A., Pomezia, Roma, Italy
| | - Daniel Oscar Cicero
- IRBM Science Park S.p.A., Pomezia, Roma, Italy; Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma "Tor Vergata", Roma, Italy
| | | | | | | | | | | | | | | | | | | | - Larry C Park
- CHDI Management/CHDI Foundation, Los Angeles, CA, USA.
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207
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Abstract
Ubiquitin E3 ligases control every aspect of eukaryotic biology by promoting protein ubiquitination and degradation. At the end of a three-enzyme cascade, ubiquitin ligases mediate the transfer of ubiquitin from an E2 ubiquitin-conjugating enzyme to specific substrate proteins. Early investigations of E3s of the RING (really interesting new gene) and HECT (homologous to the E6AP carboxyl terminus) types shed light on their enzymatic activities, general architectures, and substrate degron-binding modes. Recent studies have provided deeper mechanistic insights into their catalysis, activation, and regulation. In this review, we summarize the current progress in structure-function studies of ubiquitin ligases as well as exciting new discoveries of novel classes of E3s and diverse substrate recognition mechanisms. Our increased understanding of ubiquitin ligase function and regulation has provided the rationale for developing E3-targeting therapeutics for the treatment of human diseases.
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Affiliation(s)
- Ning Zheng
- Howard Hughes Medical Institute and Department of Pharmacology, University of Washington, Seattle, Washington 98195; ,
| | - Nitzan Shabek
- Howard Hughes Medical Institute and Department of Pharmacology, University of Washington, Seattle, Washington 98195; ,
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208
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Lucas X, Ciulli A. Recognition of substrate degrons by E3 ubiquitin ligases and modulation by small-molecule mimicry strategies. Curr Opin Struct Biol 2017; 44:101-110. [DOI: 10.1016/j.sbi.2016.12.015] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 12/12/2016] [Accepted: 12/16/2016] [Indexed: 12/11/2022]
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209
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Sun H, Zhu J, Lin H, Gu K, Feng F. Recent progress in the development of small molecule Nrf2 modulators: a patent review (2012-2016). Expert Opin Ther Pat 2017; 27:763-785. [PMID: 28454500 DOI: 10.1080/13543776.2017.1325464] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
INTRODUCTION The NF-E2-related factor-2 (Nrf2) is a critical transcription factor that regulates the expression of many phase II and antioxidant genes to maintain the homeostasis. It has many biological functions and plays a central role in the cellular defensive machinery. The abnormal regulation of Nrf2 is closely associated with multiple diseases. Areas covered: This article first discusses the molecular regulatory mechanism of Nrf2-antioxidant response element (ARE) signaling. Then patents and publications about Nrf2 activators and inhibitors from 2012-2016 are reviewed. Several case studies are emphasized to introduce the molecular design strategy, especially on Keap1-Nrf2 protein-protein interaction (PPI) inhibitor. Expert opinion: Firstly, new chemotypes of Nrf2 modulators can be designed in a combination of the progress of both covalent modifiers and target selective Keap1-Nrf2 interaction inhibitors. The aim is to balance the activity and toxicity of Nrf2 modulators. Secondly, considering many known Nrf2 activators, such as DMF and SFN, are electrophilic entities with very small molecular weight, we need to update the concept of how to recognize a drug candidate. Finally, per the mechanism of the Nrf2 modulator, compounds with the most active Nrf2 inductivity maybe not the best choice for the design of an ideal chemopreventive agent.
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Affiliation(s)
- Haopeng Sun
- a Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Jie Zhu
- a Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Hongzhi Lin
- a Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Kai Gu
- a Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Feng Feng
- b Key Laboratory of Biomedical Functional Materials, School of Science , China Pharmaceutical University , Nanjing , China
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210
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El Ali Z, Deloménie C, Botton J, Pallardy M, Kerdine-Römer S. Dendritic cells' death induced by contact sensitizers is controlled by Nrf2 and depends on glutathione levels. Toxicol Appl Pharmacol 2017; 322:41-50. [DOI: 10.1016/j.taap.2017.02.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Revised: 01/31/2017] [Accepted: 02/16/2017] [Indexed: 12/17/2022]
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211
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Discovery of a Kelch-like ECH-associated protein 1-inhibitory tetrapeptide and its structural characterization. Biochem Biophys Res Commun 2017; 486:620-625. [PMID: 28315327 DOI: 10.1016/j.bbrc.2017.03.038] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 03/11/2017] [Indexed: 02/02/2023]
Abstract
Keap1 constitutively binds to the transcription factor Nrf2 to promote its degradation, resulting in negative modulation of genes involved in cellular protection against oxidative stress. Keap1 is increasingly recognized as an attractive target for treating diseases involving oxidative stress, including cancer, atherosclerosis, diabetes, arthritis, and neurodegeneration. We used phage-display peptide screening to identify a tetrapeptide showing moderate binding affinity, which inhibits the interaction between Nrf2 and Keap1. The tetrapeptide does not include an ETGE motif, which is a commonly found consensus sequence in known peptidic inhibitors. In addition to affinity parameters, IC50, KD, and thermodynamic parameters, the crystal structure of the complex was determined to elucidate the binding conformation. The binding interactions resemble those of known small-molecule inhibitors as opposed to those of substrates and peptidic inhibitors. Although the tetrapeptide's affinity is not very high, our results may help facilitate the designing of small-molecule inhibitors during lead generation in drug discovery.
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212
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213
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Dinkova-Kostova AT, Kostov RV, Canning P. Keap1, the cysteine-based mammalian intracellular sensor for electrophiles and oxidants. Arch Biochem Biophys 2017; 617:84-93. [PMID: 27497696 PMCID: PMC5339396 DOI: 10.1016/j.abb.2016.08.005] [Citation(s) in RCA: 225] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 07/30/2016] [Accepted: 08/01/2016] [Indexed: 12/19/2022]
Abstract
The Kelch-like ECH associated protein 1 (Keap1) is a component of a Cullin3-based Cullin-RING E3 ubiquitin ligase (CRL) multisubunit protein complex. Within the CRL, homodimeric Keap1 functions as the Cullin3 adaptor, and importantly, it is also the critical component of the E3 ligase that performs the substrate recognition. The best-characterized substrate of Keap1 is transcription factor NF-E2 p45-related factor 2 (Nrf2), which orchestrates an elaborate transcriptional program in response to environmental challenges caused by oxidants, electrophiles and pro-inflammatory agents, allowing adaptation and survival under stress conditions. Keap1 is equipped with reactive cysteine residues that act as sensors for endogenously produced and exogenously encountered small molecules (termed inducers), which have a characteristic chemical signature, reactivity with sulfhydryl groups. Inducers modify the cysteine sensors of Keap1 and impair its ability to target Nrf2 for ubiquitination and degradation. Consequently, Nrf2 accumulates, enters the nucleus and drives the transcription of its target genes, which encode a large network of cytoprotective proteins. Here we summarize the early studies leading to the prediction of the existence of Keap1, followed by the discovery of Keap1 as the main negative regulator of Nrf2. We then describe the available structural information on Keap1, its assembly with Cullin3, and its interaction with Nrf2. We also discuss the multiple cysteine sensors of Keap1 that allow for detection of a wide range of endogenous and environmental inducers, and provide fine-tuning and tight control of the Keap1/Nrf2 stress-sensing response.
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Affiliation(s)
- Albena T Dinkova-Kostova
- Division of Cancer Research, School of Medicine, University of Dundee, Scotland, UK; Department Pharmacology and Molecular Sciences and Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Rumen V Kostov
- Division of Cancer Research, School of Medicine, University of Dundee, Scotland, UK
| | - Peter Canning
- Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
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214
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Zhuang C, Wu Z, Xing C, Miao Z. Small molecules inhibiting Keap1-Nrf2 protein-protein interactions: a novel approach to activate Nrf2 function. MEDCHEMCOMM 2017; 8:286-294. [PMID: 30108745 PMCID: PMC6072482 DOI: 10.1039/c6md00500d] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 11/16/2016] [Indexed: 12/21/2022]
Abstract
Oxidative stress is well recognized to contribute to the cause of a wide range of diseases, such as cancer, diabetes, Alzheimer's disease, arteriosclerosis, and inflammation. The Keap1-Nrf2-ARE pathway plays a critical regulatory role and can protect cells from oxidative stress through activating Nrf2 to induce its downstream phase II enzymes. Nrf2 activation through the covalent inactivation of Keap1 may cause unpredictable side effects. Non-covalent disruption of the Keap1-Nrf2 protein-protein interactions is an alternative strategy for Nrf2 activation, potentially with reduced risk of toxicity. Efforts have been made in recent years to develop peptide- and small molecule-based Keap1-Nrf2 PPI inhibitors via different approaches, including high-throughput screening, target-based virtual screening, structure-based optimization, and fragment-based drug design. This review aims to highlight the recently discovered small-molecule inhibitors as well as their therapeutic potential.
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Affiliation(s)
- Chunlin Zhuang
- School of Pharmacy , Second Military Medical University , 325 Guohe Road , Shanghai 200433 , China .
| | - Zhongli Wu
- School of Pharmacy , Second Military Medical University , 325 Guohe Road , Shanghai 200433 , China .
| | - Chengguo Xing
- Department of Medicinal Chemistry , College of Pharmacy , University of Florida , 1345 Center Dr. , Gainesville , FL 32610 , USA .
| | - Zhenyuan Miao
- School of Pharmacy , Second Military Medical University , 325 Guohe Road , Shanghai 200433 , China .
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215
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Deck LM, Whalen LJ, Hunsaker LA, Royer RE, Vander Jagt DL. Activation of anti-oxidant Nrf2 signaling by substituted trans stilbenes. Bioorg Med Chem 2017; 25:1423-1430. [PMID: 28126440 DOI: 10.1016/j.bmc.2017.01.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 01/02/2017] [Accepted: 01/04/2017] [Indexed: 12/11/2022]
Abstract
Nrf2, which is a member of the cap'n'collar family of transcription factors, is a major regulator of phase II detoxification and anti-oxidant genes as well as anti-inflammatory and neuroprotective genes. The importance of inflammation and oxidative stress in many chronic diseases supports the concept that activation of anti-oxidant Nrf2 signaling may have therapeutic potential. A number of Nrf2 activators have entered into clinical trials. Nrf2 exists in the cytosol in complex with its binding partner Keap1, which is a thiol-rich redox-sensing protein. In response to oxidative and electrophilic stress, select cysteine residues of Keap1 are modified, which locks Keap1 in the Nrf2-Keap1 complex and allows newly synthesized Nrf2 to enter the nucleus. Numerous Nrf2-activating chemicals, including a number of natural products, are electrophiles that modify Keap1, often by Michael addition, leading to activation of Nrf2. One concern with the design of Nrf2 activators that are electrophilic covalent modifiers of Keap1 is the issue of selectivity. In the present study, substituted trans stilbenes were identified as activators of Nrf2. These activators of Nrf2 are not highly electrophilic and therefore are unlikely to activate Nrf2 through covalent modification of Keap1. Dose-response studies demonstrated that a range of substituents on either ring of the trans stilbenes, especially fluorine and methoxy substituents, influenced not only the sensitivity to activation, reflected in EC50 values, but also the extent of activation, which suggests that multiple mechanisms are involved in the activation of Nrf2. The stilbene backbone appears to be a privileged scaffold for development of a new class of Nrf2 activators.
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Affiliation(s)
- Lorraine M Deck
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131, United States
| | - Lisa J Whalen
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131, United States
| | - Lucy A Hunsaker
- Department of Biochemistry and Molecular Biology, University of New Mexico School of Medicine, Albuquerque, NM 87131, United States
| | - Robert E Royer
- Department of Biochemistry and Molecular Biology, University of New Mexico School of Medicine, Albuquerque, NM 87131, United States
| | - David L Vander Jagt
- Department of Biochemistry and Molecular Biology, University of New Mexico School of Medicine, Albuquerque, NM 87131, United States.
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216
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Li L, Liu J, Nie S, Ding L, Wang L, Liu J, Liu W, Zhang T. Direct inhibition of Keap1–Nrf2 interaction by egg-derived peptides DKK and DDW revealed by molecular docking and fluorescence polarization. RSC Adv 2017. [DOI: 10.1039/c7ra04352j] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
DKK and DDW, egg-derived direct inhibitors of the Keap1–Nrf2 interaction, screening by fluorescence polarization assays and cell experiments.
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Affiliation(s)
- Liangyu Li
- Jilin Key Laboratory of Nutrition and Functional Food
- Jilin University
- Changchun 130062
- People's Republic of China
| | - Jingbo Liu
- Jilin Key Laboratory of Nutrition and Functional Food
- Jilin University
- Changchun 130062
- People's Republic of China
| | - Shaoping Nie
- State Key Laboratory Food Science & Technology
- Nanchang University
- Nanchang 330047
- People's Republic of China
| | - Long Ding
- Jilin Key Laboratory of Nutrition and Functional Food
- Jilin University
- Changchun 130062
- People's Republic of China
| | - Liying Wang
- Jilin Key Laboratory of Nutrition and Functional Food
- Jilin University
- Changchun 130062
- People's Republic of China
| | - Jiyun Liu
- Jilin Key Laboratory of Nutrition and Functional Food
- Jilin University
- Changchun 130062
- People's Republic of China
| | - Wenchao Liu
- Jilin Key Laboratory of Nutrition and Functional Food
- Jilin University
- Changchun 130062
- People's Republic of China
| | - Ting Zhang
- Jilin Key Laboratory of Nutrition and Functional Food
- Jilin University
- Changchun 130062
- People's Republic of China
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217
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Siegert TR, Bird M, Kritzer JA. Identifying Loop-Mediated Protein-Protein Interactions Using LoopFinder. Methods Mol Biol 2017; 1561:255-277. [PMID: 28236243 DOI: 10.1007/978-1-4939-6798-8_15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Peptides are an increasingly useful class of molecules, finding unique applications as chemical probes and potential drugs. They are particularly adept at inhibiting protein-protein interactions, which are often difficult to target using small molecules. The identification and rational design of protein-binding epitopes remains a bottleneck in the development of bioactive peptides. One fruitful strategy has been using structured scaffolds to present essential hot spot residues involved in protein-protein recognition, and this process has been greatly advanced by computational tools that can identify hot spot residues. Here we discuss LoopFinder, a program that uses structures from the Protein Data Bank to comprehensively search for protein-protein interactions that are mediated by nonhelical, nonsheet loop structures. We developed LoopFinder to identify these "hot loops" and to assist in the design of cyclic peptides that mimic these important structures. In this article, we provide all key files, outline step-by-step methods for users to conduct independent LoopFinder searches, and provide guidance on additional potential applications for the LoopFinder program.
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Affiliation(s)
- Timothy R Siegert
- Department of Chemistry, Tufts University, 62 Talbot Ave., Medford, MA, 02155, USA
| | - Michael Bird
- Department of Chemistry, Tufts University, 62 Talbot Ave., Medford, MA, 02155, USA
| | - Joshua A Kritzer
- Department of Chemistry, Tufts University, 62 Talbot Ave., Medford, MA, 02155, USA.
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218
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Development of Keap1-interactive small molecules that regulate Nrf2 transcriptional activity. CURRENT OPINION IN TOXICOLOGY 2016. [DOI: 10.1016/j.cotox.2016.08.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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219
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Schumacher FR, Schubert S, Hannus M, Sönnichsen B, Ittrich C, Kreideweiss S, Kurz T, Rippmann JF. RNAi Screen for NRF2 Inducers Identifies Targets That Rescue Primary Lung Epithelial Cells from Cigarette Smoke Induced Radical Stress. PLoS One 2016; 11:e0166352. [PMID: 27832175 PMCID: PMC5104413 DOI: 10.1371/journal.pone.0166352] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 10/27/2016] [Indexed: 12/30/2022] Open
Abstract
Chronic Obstructive Pulmonary Disease (COPD) is a highly prevalent condition characterized by inflammation and progressive obstruction of the airways. At present, there is no treatment that suppresses the chronic inflammation of the disease, and COPD patients often succumb to the condition. Excessive oxidative stress caused by smoke inhalation is a major driving force of the disease. The transcription factor NRF2 is a critical player in the battle against oxidative stress and its function is impaired in COPD. Increasing NRF2 activity may therefore be a viable therapeutic option for COPD treatment. We show that down regulation of KEAP1, a NRF2 inhibitor, protects primary human lung epithelial cells from cigarette-smoke-extract (CSE) induced cell death in an established in vitro model of radical stress. To identify new potential drug targets with a similar effect, we performed a siRNA screen of the ‘druggable’ genome using a NRF2 transcriptional reporter cell line. This screen identified multiple genes that when down regulated increased NRF2 transcriptional activity and provided a survival benefit in the in vitro model. Our results suggest that inhibiting components of the ubiquitin-proteasome system will have the strongest effects on NRF2 transcriptional activity by increasing NRF2 levels. We also find that down regulation of the small GTPase Rab28 or the Estrogen Receptor ESRRA provide a survival benefit. Rab28 knockdown increased NRF2 protein levels, indicating that Rab28 may regulate NRF2 proteolysis. Conversely ESRRA down regulation increased NRF2 transcriptional activity without affecting NRF2 levels, suggesting a proteasome-independent mechanism.
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Affiliation(s)
- Frances-Rose Schumacher
- MRC Protein Phosphorylation and Ubiquitylation Unit, The Sir James Black Center, University of Dundee, Dow Street, Dundee, DD1 5EH, United Kingdom
| | | | | | | | - Carina Ittrich
- Boehringer Ingelheim Pharma GmbH & Co. KG, Research Germany, 8400, Biberach a. d. Riss, Germany
| | - Stefan Kreideweiss
- Boehringer Ingelheim Pharma GmbH & Co. KG, Research Germany, 8400, Biberach a. d. Riss, Germany
| | - Thimo Kurz
- MRC Protein Phosphorylation and Ubiquitylation Unit, The Sir James Black Center, University of Dundee, Dow Street, Dundee, DD1 5EH, United Kingdom
- * E-mail:
| | - Jörg F. Rippmann
- Boehringer Ingelheim Pharma GmbH & Co. KG, Research Germany, 8400, Biberach a. d. Riss, Germany
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220
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Wang L, Peng JB. Phosphorylation of KLHL3 at serine 433 impairs its interaction with the acidic motif of WNK4: a molecular dynamics study. Protein Sci 2016; 26:163-173. [PMID: 27727489 DOI: 10.1002/pro.3063] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 09/09/2016] [Accepted: 10/09/2016] [Indexed: 12/17/2022]
Abstract
Interaction between the acidic motif (AM) of protein kinase WNK4 and the Kelch domain of KLHL3 are involved in the pathogenesis of pseudohypoaldosteronism type II, a hereditary form of hypertension. This interaction is disrupted by some disease-causing mutations in either WNK4 or KLHL3, or by angiotensin II- and insulin-induced phosphorylation of KLHL3 at serine 433, which is also a site frequently mutated in patients. However, the mechanism by which this phosphorylation disrupts the interaction is unclear. In this study, we approached this problem using molecular dynamics simulation with structural, dynamical and energetic analyses. Results from independent simulations indicate that when S433 was phosphorylated, the electrostatic potential became more negative in the AM binding site of KLHL3 and therefore was unfavorable for binding with the negatively charged AM. In addition, the intermolecular hydrogen bond network that kept the AM stable in the binding site of KLHL3 was disrupted, and the forces for the hydrophobic interactions between the AM of WNK4 and KLHL3 were also reduced. As a result, the weakened interactions were no longer capable of holding the AM of WNK4 at its binding site in KLHL3. In conclusion, phosphorylation of KLHL3 at S433 disrupts the hydrogen bonds, hydrophobic and electrostatic interactions between the Kelch domain of KLHL3 and the AM of WNK4. This study provides a key molecular understanding of the KLHL3-mediated regulation of WNK4, which is an integrative regulator of electrolyte homeostasis and blood pressure regulation in the kidney. Significances Statement: WNK4 is an integrative regulator of electrolyte homeostasis, which is important in the blood pressure regulation by the kidney. Interaction between WNK4 and KLHL3 is a key physiological process that is impaired in a hereditary form of hypertension. This study provides substantial new insights into the role of phosphorylation of KLHL3 in regulating the interaction with WNK4, and therefore advances our understanding of molecular pathogenesis of hypertension and the mechanism of blood pressure regulation.
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Affiliation(s)
- Lingyun Wang
- Division of Nephrology, Department of Medicine, Nephrology Research and Training Center, University of Alabama at Birmingham, Birmingham, AL, 35294
| | - Ji-Bin Peng
- Division of Nephrology, Department of Medicine, Nephrology Research and Training Center, University of Alabama at Birmingham, Birmingham, AL, 35294.,Department of Urology, University of Alabama at Birmingham, Birmingham, AL, 35294
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221
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Arora R, Sawney S, Saini V, Steffi C, Tiwari M, Saluja D. Esculetin induces antiproliferative and apoptotic response in pancreatic cancer cells by directly binding to KEAP1. Mol Cancer 2016; 15:64. [PMID: 27756327 PMCID: PMC5069780 DOI: 10.1186/s12943-016-0550-2] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 10/06/2016] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND A handful of studies have exploited antitumor potential of esculetin, a dihydroxy coumarine derivative; the targets to which it binds and the possible downstream mechanism for its cytotoxicity in cancer cells remain to be elucidated. Using pancreatic cancer cell lines as a model system, herein the study was initiated to check the efficacy of esculetin in inhibiting growth of these cancer cells, to decipher mechanism of its action and to predict its direct binding target protein. METHODS The cytotoxicity of esculetin was determined in PANC-1, MIA PaCa-2 and AsPC-1 cell lines; followed by an inspection of intracellular levels of ROS and its associated transcription factor, p65-NF-κB. The interaction between transcription factor, Nrf2 and its regulator KEAP1 was studied in the presence and absence of esculetin. The effect of Nrf2 on gene expression of antioxidant response element pathway was monitored by real time PCR. Thereafter, potential binding target of esculetin was predicted through molecular docking and then confirmed in vitro. RESULTS Esculetin treatment in all three pancreatic cancer cell lines resulted in significant growth inhibition with G1-phase cell cycle arrest and induction of mitochondrial dependent apoptosis through activation of caspases 3, 8 and 9. A notable decrease was observed in intracellular ROS and protein levels of p65-NF-κB in PANC-1 cells on esculetin treatment. Antioxidant response regulator Nrf2 has been reportedly involved in crosstalk with NF-κB. Interaction between Nrf2 and KEAP1 was found to be lost upon esculetin treatment in PANC-1 and MIA Paca-2 cells. Nuclear accumulation of Nrf2 and an upregulation of expression of Nrf2 regulated gene NQO1, observed on esculetin treatment in PANC-1 further supported the activation of Nrf2. To account for the loss of Nrf2-KEAP1 interaction on esculetin treatment, direct binding potential between esculetin and KEAP1 was depicted in silico using molecular docking studies. Pull down assay using esculetin conjugated sepharose beads confirmed the binding between esculetin and KEAP1. CONCLUSIONS We propose that esculetin binds to KEAP1 and inhibits its interaction with Nrf2 in pancreatic cancer cells. This thereby promotes nuclear accumulation of Nrf2 in PANC-1 cells that induces antiproliferative and apoptotic response possibly by attenuating NF-κB.
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Affiliation(s)
- Rashi Arora
- Dr. B.R. Ambedkar Centre for Biomedical Research, University of Delhi, Delhi, 110007 India
| | - Sharad Sawney
- Dr. B.R. Ambedkar Centre for Biomedical Research, University of Delhi, Delhi, 110007 India
| | - Vikas Saini
- Dr. B.R. Ambedkar Centre for Biomedical Research, University of Delhi, Delhi, 110007 India
| | - Chris Steffi
- Dr. B.R. Ambedkar Centre for Biomedical Research, University of Delhi, Delhi, 110007 India
| | - Manisha Tiwari
- Dr. B.R. Ambedkar Centre for Biomedical Research, University of Delhi, Delhi, 110007 India
| | - Daman Saluja
- Dr. B.R. Ambedkar Centre for Biomedical Research, University of Delhi, Delhi, 110007 India
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222
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Jiang ZY, Lu MC, You QD. Discovery and Development of Kelch-like ECH-Associated Protein 1. Nuclear Factor Erythroid 2-Related Factor 2 (KEAP1:NRF2) Protein-Protein Interaction Inhibitors: Achievements, Challenges, and Future Directions. J Med Chem 2016; 59:10837-10858. [PMID: 27690435 DOI: 10.1021/acs.jmedchem.6b00586] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The transcription factor Nrf2 is the primary regulator of the cellular defense system, and enhancing Nrf2 activity has potential usages in various diseases, especially chronic age-related and inflammatory diseases. Recently, directly targeting Keap1-Nrf2 protein-protein interaction (PPI) has been an emerging strategy to selectively and effectively activate Nrf2. This Perspective summarizes the progress in the discovery and development of Keap1-Nrf2 PPI inhibitors, including the Keap1-Nrf2 regulatory mechanisms, biochemical techniques for inhibitor identification, and approaches for identifying peptide and small-molecule inhibitors, as well as discusses privileged structures and future directions for further development of Keap1-Nrf2 PPI inhibitors.
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Affiliation(s)
- Zheng-Yu Jiang
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University , Nanjing 210009, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University , 24 Tongjiaxiang, Nanjing 210009, China
| | - Meng-Chen Lu
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University , Nanjing 210009, China
| | - Qi-Dong You
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University , Nanjing 210009, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University , 24 Tongjiaxiang, Nanjing 210009, China
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223
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Protocol for a Steady-State FRET Assay in Cancer Chemoprevention. Methods Mol Biol 2016; 1379:165-79. [PMID: 26608299 DOI: 10.1007/978-1-4939-3191-0_15] [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: 02/11/2023]
Abstract
Cancer chemoprevention is an important strategy to prevent, reverse, or suppress the development of cancer. One of the target pathways that has emerged in recent years is the Keap1-Nrf2-ARE system that regulates the protection of cells against various carcinogens and their metabolites. Increased concentrations of the redox transcription factor nuclear factor erythroid 2-related factor 2 (Nrf2) induces the activation of antioxidant and phase 2 detoxifying genes. Nrf2 is regulated by substrate adaptor protein Kelch-like ECH-associated protein 1 (Keap1) that can target Nrf2 for ubiquitination and degradation by the proteasome. The interaction between Nrf2 and Keap1 can be disrupted at the protein-protein interface in order to increase Nrf2 activity for potential therapeutic purposes. This chapter describes a protocol for a steady-state fluorescence or Förster resonance energy transfer (FRET) assay to examine the Keap1-Nrf2 protein-protein interaction (PPI), to investigate the effects of Nrf2 mutations on Keap1 binding and finally to identify potential inhibitors of this PPI. In the assay system Keap1 is conjugated to an YFP protein at the N-terminus whereas an Nrf2-derived 16-mer peptide containing a high-affinity "ETGE" motif is conjugated to a CFP protein at the N-terminus.
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224
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Johnson B, Li J, Adhikari J, Edwards MR, Zhang H, Schwarz T, Leung DW, Basler CF, Gross ML, Amarasinghe GK. Dimerization Controls Marburg Virus VP24-dependent Modulation of Host Antioxidative Stress Responses. J Mol Biol 2016; 428:3483-94. [PMID: 27497688 PMCID: PMC5010500 DOI: 10.1016/j.jmb.2016.07.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 07/27/2016] [Accepted: 07/27/2016] [Indexed: 12/13/2022]
Abstract
Marburg virus (MARV), a member of the Filoviridae family that also includes Ebola virus (EBOV), causes lethal hemorrhagic fever with case fatality rates that have exceeded 50% in some outbreaks. Within an infected cell, there are numerous host-viral interactions that contribute to the outcome of infection. Recent studies identified MARV protein 24 (mVP24) as a modulator of the host antioxidative responses, but the molecular mechanism remains unclear. Using a combination of biochemical and mass spectrometry studies, we show that mVP24 is a dimer in solution that directly binds to the Kelch domain of Kelch-like ECH-associated protein 1 (Keap1) to regulate nuclear factor (erythroid-derived 2)-like 2 (Nrf2). This interaction between Keap1 and mVP24 occurs through the Kelch interaction loop (K-Loop) of mVP24 leading to upregulation of antioxidant response element transcription, which is distinct from other Kelch binders that regulate Nrf2 activity. N-terminal truncations disrupt mVP24 dimerization, allowing monomeric mVP24 to bind Kelch with higher affinity and stimulate higher antioxidative stress response element (ARE) reporter activity. Mass spectrometry-based mapping of the interface revealed overlapping binding sites on Kelch for mVP24 and the Nrf2 proteins. Substitution of conserved cysteines, C209 and C210, to alanine in the mVP24 K-Loop abrogates Kelch binding and ARE activation. Our studies identify a shift in the monomer-dimer equilibrium of MARV VP24, driven by its interaction with Keap1 Kelch domain, as a critical determinant that modulates host responses to pathogenic Marburg viral infections.
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Affiliation(s)
- Britney Johnson
- Department of Pathology and Immunology, Washington University School of Medicine in St Louis, St Louis, MO 63110, USA
| | - Jing Li
- Department of Chemistry, Box 1134, Washington University, One Brookings Drive, St. Louis, Mo, 63130, USA
| | - Jagat Adhikari
- Department of Chemistry, Box 1134, Washington University, One Brookings Drive, St. Louis, Mo, 63130, USA
| | - Megan R Edwards
- Department of Pathology and Immunology, Washington University School of Medicine in St Louis, St Louis, MO 63110, USA; Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303, USA
| | - Hao Zhang
- Department of Chemistry, Box 1134, Washington University, One Brookings Drive, St. Louis, Mo, 63130, USA
| | - Toni Schwarz
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Daisy W Leung
- Department of Pathology and Immunology, Washington University School of Medicine in St Louis, St Louis, MO 63110, USA
| | - Christopher F Basler
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Michael L Gross
- Department of Chemistry, Box 1134, Washington University, One Brookings Drive, St. Louis, Mo, 63130, USA.
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine in St Louis, St Louis, MO 63110, USA.
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225
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Cullin3-KLHL15 ubiquitin ligase mediates CtIP protein turnover to fine-tune DNA-end resection. Nat Commun 2016; 7:12628. [PMID: 27561354 PMCID: PMC5007465 DOI: 10.1038/ncomms12628] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 07/19/2016] [Indexed: 12/16/2022] Open
Abstract
Human CtIP is a decisive factor in DNA double-strand break repair pathway choice by enabling DNA-end resection, the first step that differentiates homologous recombination (HR) from non-homologous end-joining (NHEJ). To coordinate appropriate and timely execution of DNA-end resection, CtIP function is tightly controlled by multiple protein-protein interactions and post-translational modifications. Here, we identify the Cullin3 E3 ligase substrate adaptor Kelch-like protein 15 (KLHL15) as a new interaction partner of CtIP and show that KLHL15 promotes CtIP protein turnover via the ubiquitin-proteasome pathway. A tripeptide motif (FRY) conserved across vertebrate CtIP proteins is essential for KLHL15-binding; its mutation blocks KLHL15-dependent CtIP ubiquitination and degradation. Consequently, DNA-end resection is strongly attenuated in cells overexpressing KLHL15 but amplified in cells either expressing a CtIP-FRY mutant or lacking KLHL15, thus impacting the balance between HR and NHEJ. Collectively, our findings underline the key importance and high complexity of CtIP modulation for genome integrity.
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226
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Kim K, Park JM, Kim NJ, Kim SJ, Moon H, An H, Lee J, Park HJ, Surh YJ, Suh YG. Identification and Structural Analysis of New Nrf2 Activators by Mechanism-Based Chemical Transformation of 15-Deoxy-Δ12, 14-PGJ2. Chembiochem 2016; 17:1900-1904. [DOI: 10.1002/cbic.201600165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Indexed: 01/05/2023]
Affiliation(s)
- Kyeojin Kim
- College of Pharmacy; Seoul National University; 1 Gwanak-ro Gwanak-gu Seoul 151-742 Republic of Korea
| | - Jong-Min Park
- CHA Cancer Prevention Research Center; CHA University School of Medicine; Seoul 135-081 Republic of Korea
| | - Nam-Jung Kim
- Department of Pharmacy; College of Pharmacy; Kyung Hee University; 26 Kyungheedae-ro Dongdaemun-gu Seoul 130-701 Republic of Korea
| | - Su-Jung Kim
- Tumor Microenvironment Global Core Research Center; College of Pharmacy; Seoul National University; 1 Gwanak-ro Gwanak-gu Seoul 151-742 Republic of Korea
| | - Hyunyoung Moon
- College of Pharmacy; Seoul National University; 1 Gwanak-ro Gwanak-gu Seoul 151-742 Republic of Korea
| | - Hongchan An
- College of Pharmacy; Seoul National University; 1 Gwanak-ro Gwanak-gu Seoul 151-742 Republic of Korea
| | - Jeeyeon Lee
- College of Pharmacy; Seoul National University; 1 Gwanak-ro Gwanak-gu Seoul 151-742 Republic of Korea
| | - Hyun-Ju Park
- School of Pharmacy; Sungkyunkwan University; Suwon 440-746 Republic of Korea
| | - Young-Joon Surh
- Tumor Microenvironment Global Core Research Center; College of Pharmacy; Seoul National University; 1 Gwanak-ro Gwanak-gu Seoul 151-742 Republic of Korea
| | - Young-Ger Suh
- College of Pharmacy; Seoul National University; 1 Gwanak-ro Gwanak-gu Seoul 151-742 Republic of Korea
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227
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Molecular and cellular basis for the unique functioning of Nrf1, an indispensable transcription factor for maintaining cell homoeostasis and organ integrity. Biochem J 2016; 473:961-1000. [PMID: 27060105 DOI: 10.1042/bj20151182] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 01/26/2016] [Indexed: 12/30/2022]
Abstract
The consensuscis-regulatory AP-1 (activator protein-1)-like AREs (antioxidant-response elements) and/or EpREs (electrophile-response elements) allow for differential recruitment of Nrf1 [NF-E2 (nuclear factor-erythroid 2)-related factor 1], Nrf2 and Nrf3, together with each of their heterodimeric partners (e.g. sMaf, c-Jun, JunD or c-Fos), to regulate different sets of cognate genes. Among them, NF-E2 p45 and Nrf3 are subject to tissue-specific expression in haemopoietic and placental cell lineages respectively. By contrast, Nrf1 and Nrf2 are two important transcription factors expressed ubiquitously in various vertebrate tissues and hence may elicit putative combinational or competitive functions. Nevertheless, they have de facto distinct biological activities because knockout of their genes in mice leads to distinguishable phenotypes. Of note, Nrf2 is dispensable during development and growth, albeit it is accepted as a master regulator of antioxidant, detoxification and cytoprotective genes against cellular stress. Relative to the water-soluble Nrf2, less attention has hitherto been drawn to the membrane-bound Nrf1, even though it has been shown to be indispensable for embryonic development and organ integrity. The biological discrepancy between Nrf1 and Nrf2 is determined by differences in both their primary structures and topovectorial subcellular locations, in which they are subjected to distinct post-translational processing so as to mediate differential expression of ARE-driven cytoprotective genes. In the present review, we focus on the molecular and cellular basis for Nrf1 and its isoforms, which together exert its essential functions for maintaining cellular homoeostasis, normal organ development and growth during life processes. Conversely, dysfunction of Nrf1 results in spontaneous development of non-alcoholic steatohepatitis, hepatoma, diabetes and neurodegenerative diseases in animal models.
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228
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Niu B, Scott AD, Sengupta S, Bailey MH, Batra P, Ning J, Wyczalkowski MA, Liang WW, Zhang Q, McLellan MD, Sun SQ, Tripathi P, Lou C, Ye K, Mashl RJ, Wallis J, Wendl MC, Chen F, Ding L. Protein-structure-guided discovery of functional mutations across 19 cancer types. Nat Genet 2016; 48:827-37. [PMID: 27294619 PMCID: PMC5315576 DOI: 10.1038/ng.3586] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 05/13/2016] [Indexed: 02/07/2023]
Abstract
Local concentrations of mutations are well known in human cancers. However, their three-dimensional spatial relationships in the encoded protein have yet to be systematically explored. We developed a computational tool, HotSpot3D, to identify such spatial hotspots (clusters) and to interpret the potential function of variants within them. We applied HotSpot3D to >4,400 TCGA tumors across 19 cancer types, discovering >6,000 intra- and intermolecular clusters, some of which showed tumor and/or tissue specificity. In addition, we identified 369 rare mutations in genes including TP53, PTEN, VHL, EGFR, and FBXW7 and 99 medium-recurrence mutations in genes such as RUNX1, MTOR, CA3, PI3, and PTPN11, all mapping within clusters having potential functional implications. As a proof of concept, we validated our predictions in EGFR using high-throughput phosphorylation data and cell-line-based experimental evaluation. Finally, mutation-drug cluster and network analysis predicted over 800 promising candidates for druggable mutations, raising new possibilities for designing personalized treatments for patients carrying specific mutations.
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Affiliation(s)
- Beifang Niu
- McDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USA
| | - Adam D. Scott
- McDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USA
- Division of Oncology, Department of Medicine, Washington University, St. Louis, Missouri 63108, USA
| | - Sohini Sengupta
- McDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USA
- Division of Oncology, Department of Medicine, Washington University, St. Louis, Missouri 63108, USA
| | - Matthew H. Bailey
- McDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USA
- Division of Oncology, Department of Medicine, Washington University, St. Louis, Missouri 63108, USA
| | - Prag Batra
- McDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USA
| | - Jie Ning
- McDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USA
- Division of Nephrology, Department of Medicine, Washington University, St. Louis, Missouri 63108, USA
| | - Matthew A. Wyczalkowski
- McDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USA
- Division of Oncology, Department of Medicine, Washington University, St. Louis, Missouri 63108, USA
| | - Wen-Wei Liang
- McDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USA
- Division of Oncology, Department of Medicine, Washington University, St. Louis, Missouri 63108, USA
| | - Qunyuan Zhang
- McDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USA
- Department of Genetics, Washington University, St. Louis, Missouri 63108, USA
| | - Michael D. McLellan
- McDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USA
| | - Sam Q. Sun
- McDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USA
- Division of Oncology, Department of Medicine, Washington University, St. Louis, Missouri 63108, USA
| | - Piyush Tripathi
- Division of Nephrology, Department of Medicine, Washington University, St. Louis, Missouri 63108, USA
| | - Carolyn Lou
- McDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USA
- Division of Oncology, Department of Medicine, Washington University, St. Louis, Missouri 63108, USA
| | - Kai Ye
- McDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USA
- Department of Genetics, Washington University, St. Louis, Missouri 63108, USA
| | - R. Jay Mashl
- McDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USA
- Division of Oncology, Department of Medicine, Washington University, St. Louis, Missouri 63108, USA
| | - John Wallis
- McDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USA
| | - Michael C. Wendl
- McDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USA
- Division of Oncology, Department of Medicine, Washington University, St. Louis, Missouri 63108, USA
- Department of Genetics, Washington University, St. Louis, Missouri 63108, USA
- Department of Mathematics, Washington University, St. Louis, Missouri 63108, USA
| | - Feng Chen
- Division of Nephrology, Department of Medicine, Washington University, St. Louis, Missouri 63108, USA
- Siteman Cancer Center, Washington University, St. Louis, Missouri 63108, USA
- Department of Cell Biology and Physiology, Washington University, St. Louis, Missouri 63108, USA
| | - Li Ding
- McDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USA
- Division of Oncology, Department of Medicine, Washington University, St. Louis, Missouri 63108, USA
- Division of Nephrology, Department of Medicine, Washington University, St. Louis, Missouri 63108, USA
- Siteman Cancer Center, Washington University, St. Louis, Missouri 63108, USA
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229
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Bhakkiyalakshmi E, Dineshkumar K, Karthik S, Sireesh D, Hopper W, Paulmurugan R, Ramkumar KM. Pterostilbene-mediated Nrf2 activation: Mechanistic insights on Keap1:Nrf2 interface. Bioorg Med Chem 2016; 24:3378-86. [DOI: 10.1016/j.bmc.2016.05.011] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 05/07/2016] [Accepted: 05/10/2016] [Indexed: 01/18/2023]
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230
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Lu M, Zhou HS, You QD, Jiang Z. Design, Synthesis, and Initial Evaluation of Affinity-Based Small-Molecule Probes for Fluorescent Visualization and Specific Detection of Keap1. J Med Chem 2016; 59:7305-10. [DOI: 10.1021/acs.jmedchem.6b00775] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Mengchen Lu
- State
Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of
Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
| | - Hai-shan Zhou
- State
Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of
Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
| | - Qi-Dong You
- State
Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of
Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department
of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Zhengyu Jiang
- State
Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of
Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department
of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
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231
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Structural mapping of Kelch13 mutations associated with artemisinin resistance in malaria. ACTA ACUST UNITED AC 2016; 17:51-6. [DOI: 10.1007/s10969-016-9205-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 07/07/2016] [Indexed: 10/21/2022]
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232
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Obuobi S, Karatayev S, Chai CLL, Ee PLR, Mátyus P. The role of modulation of antioxidant enzyme systems in the treatment of neurodegenerative diseases. J Enzyme Inhib Med Chem 2016; 31:194-204. [PMID: 27389167 DOI: 10.1080/14756366.2016.1205047] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Oxidative stress is a much-appreciated phenomenon associated with the progression of neurodegenerative diseases (NDDs) due to imbalances in redox homeostasis. The poor correlations between the in vitro benefits and clinical trials of direct radical scavengers have prompted research into indirect antioxidant enzymes such as Nrf2. Activation of Nrf2 leads to the upregulation of a myriad of cytoprotective and antioxidant enzymes/proteins. Traditionally, early Nrf2-activators were studied as chemoprotective agents. There is a consequential lack of clinical trials testing Nrf2 activation in NDDs. However, there is abundant evidence of their utility in pre-clinical studies. Herein, we review the endogenous Nrf2 regulatory pathway and avenues for targeting this pathway. Furthermore, we provide updated information on pre-clinical studies for natural and synthetic Nrf2 activators. On the basis of our findings, we posit that successful therapeutics for NDDs rely on the design of potent synthetic Nrf2 activators with a careful combination of other neuroprotective activities.
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Affiliation(s)
- Sybil Obuobi
- a Department of Pharmacy , National University of Singapore , Singapore
| | - Sanzhar Karatayev
- a Department of Pharmacy , National University of Singapore , Singapore
| | | | - Pui Lai Rachel Ee
- a Department of Pharmacy , National University of Singapore , Singapore
| | - Peter Mátyus
- b Department of Organic Chemistry , Semmelweis University , Budapest , Hungary , and.,c Bionics Innovation Center Nonprofit Ltd , Budapest , Hungary
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233
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Lebovitz CB, Robertson AG, Goya R, Jones SJ, Morin RD, Marra MA, Gorski SM. Cross-cancer profiling of molecular alterations within the human autophagy interaction network. Autophagy 2016. [PMID: 26208877 PMCID: PMC4590660 DOI: 10.1080/15548627.2015.1067362] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Aberrant activation or disruption of autophagy promotes tumorigenesis in various preclinical models of cancer, but whether the autophagy pathway is a target for recurrent molecular alteration in human cancer patient samples is unknown. To address this outstanding question, we surveyed 211 human autophagy-associated genes for tumor-related alterations to DNA sequence and RNA expression levels and examined their association with patient survival outcomes in multiple cancer types with sequence data from The Cancer Genome Atlas consortium. We found 3 (RB1CC1/FIP200, ULK4, WDR45/WIPI4) and one (ATG7) core autophagy genes to be under positive selection for somatic mutations in endometrial carcinoma and clear cell renal carcinoma, respectively, while 29 autophagy regulators and pathway interactors, including previously identified KEAP1, NFE2L2, and MTOR, were significantly mutated in 6 of the 11 cancer types examined. Gene expression analyses revealed that GABARAPL1 and MAP1LC3C/LC3C transcripts were less abundant in breast cancer and non-small cell lung cancers than in matched normal tissue controls; ATG4D transcripts were increased in lung squamous cell carcinoma, as were ATG16L2 transcripts in kidney cancer. Unsupervised clustering of autophagy-associated mRNA levels in tumors stratified patient overall survival in 3 of 9 cancer types (acute myeloid leukemia, clear cell renal carcinoma, and head and neck cancer). These analyses provide the first comprehensive resource of recurrently altered autophagy-associated genes in human tumors, and highlight cancer types and subtypes where perturbed autophagy may be relevant to patient overall survival.
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Affiliation(s)
- Chandra B Lebovitz
- a The Genome Sciences Centre; BC Cancer Agency ; Vancouver, BC Canada.,b Department of Molecular Biology and Biochemistry ; Simon Fraser University ; Burnaby , BC Canada
| | | | - Rodrigo Goya
- a The Genome Sciences Centre; BC Cancer Agency ; Vancouver, BC Canada.,c Centre for High-Throughput Biology; University of British Columbia ; Vancouver , BC Canada
| | - Steven J Jones
- a The Genome Sciences Centre; BC Cancer Agency ; Vancouver, BC Canada.,b Department of Molecular Biology and Biochemistry ; Simon Fraser University ; Burnaby , BC Canada.,d Department of Medical Genetics ; University of British Columbia ; Vancouver , BC Canada
| | - Ryan D Morin
- a The Genome Sciences Centre; BC Cancer Agency ; Vancouver, BC Canada.,b Department of Molecular Biology and Biochemistry ; Simon Fraser University ; Burnaby , BC Canada
| | - Marco A Marra
- a The Genome Sciences Centre; BC Cancer Agency ; Vancouver, BC Canada.,d Department of Medical Genetics ; University of British Columbia ; Vancouver , BC Canada
| | - Sharon M Gorski
- a The Genome Sciences Centre; BC Cancer Agency ; Vancouver, BC Canada.,b Department of Molecular Biology and Biochemistry ; Simon Fraser University ; Burnaby , BC Canada
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234
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Heyninck K, Sabbe L, Chirumamilla CS, Szarc vel Szic K, Vander Veken P, Lemmens KJ, Lahtela-Kakkonen M, Naulaerts S, Op de Beeck K, Laukens K, Van Camp G, Weseler AR, Bast A, Haenen GR, Haegeman G, Vanden Berghe W. Withaferin A induces heme oxygenase (HO-1) expression in endothelial cells via activation of the Keap1/Nrf2 pathway. Biochem Pharmacol 2016; 109:48-61. [DOI: 10.1016/j.bcp.2016.03.026] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 03/31/2016] [Indexed: 01/06/2023]
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235
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Lu MC, Ji JA, Jiang ZY, You QD. The Keap1-Nrf2-ARE Pathway As a Potential Preventive and Therapeutic Target: An Update. Med Res Rev 2016; 36:924-63. [PMID: 27192495 DOI: 10.1002/med.21396] [Citation(s) in RCA: 535] [Impact Index Per Article: 66.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Revised: 04/12/2016] [Accepted: 04/14/2016] [Indexed: 12/12/2022]
Abstract
The Keap1-Nrf2-ARE ((Kelch-like ECH-Associating protein 1) nuclear factor erythroid 2 related factor 2-antioxidant response element) pathway is one of the most important defense mechanisms against oxidative and/or electrophilic stresses, and it is closely associated with inflammatory diseases, including cancer, neurodegenerative diseases, cardiovascular diseases, and aging. In recent years, progress has been made in strategies aimed at modulating the Keap1-Nrf2-ARE pathway. The Nrf2 activator DMF (Dimethylfumarates) has been approved by the FDA as a new first-line oral drug to treat patients with relapsing forms of multiple sclerosis, while a phase 3 study of another promising candidate, CDDO-Me, was terminated for safety reasons. Directly inhibiting Keap1-Nrf2 protein-protein interactions as a novel Nrf2-modulating strategy has many advantages over using electrophilic Nrf2 activators. The development of Keap1-Nrf2 protein-protein interaction inhibitors has become a topic of intense research, and potent inhibitors of this target have been identified. In addition, inhibiting Nrf2 activity has attracted an increasing amount of attention because it may provide an alternative cancer therapy. This review summarizes the molecular mechanisms and biological functions of the Keap1-Nrf2-ARE system. The main focus of this review is on recent progress in studies of agents that target the Keap1-Nrf2-ARE pathway and the therapeutic applications of such agents.
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Affiliation(s)
- Meng-Chen Lu
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China.,Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China
| | - Jian-Ai Ji
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China.,Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China
| | - Zheng-Yu Jiang
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China.,Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Qi-Dong You
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China.,Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China
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236
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Carvalho AN, Marques C, Guedes RC, Castro-Caldas M, Rodrigues E, van Horssen J, Gama MJ. S-Glutathionylation of Keap1: a new role for glutathioneS-transferase pi in neuronal protection. FEBS Lett 2016; 590:1455-66. [DOI: 10.1002/1873-3468.12177] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 04/01/2016] [Accepted: 04/11/2016] [Indexed: 01/23/2023]
Affiliation(s)
- Andreia Neves Carvalho
- Instituto de Investigação do Medicamento (iMed.ULisboa); Faculty of Pharmacy; Universidade de Lisboa; Portugal
| | - Carla Marques
- Centre of Ophthalmology and Vision Sciences; Institute of Biomedical Imaging and Life Sciences (IBILI); Faculty of Medicine; University of Coimbra; Portugal
| | - Rita C. Guedes
- Instituto de Investigação do Medicamento (iMed.ULisboa); Faculty of Pharmacy; Universidade de Lisboa; Portugal
- Department of Pharmaceutical Chemistry and Therapeutics; Faculty of Pharmacy; University of Lisbon; Portugal
| | - Margarida Castro-Caldas
- Instituto de Investigação do Medicamento (iMed.ULisboa); Faculty of Pharmacy; Universidade de Lisboa; Portugal
- Departamento de Ciências da Vida; Faculdade de Ciências e Tecnologia; Universidade NOVA de Lisboa; Caparica Portugal
| | - Elsa Rodrigues
- Instituto de Investigação do Medicamento (iMed.ULisboa); Faculty of Pharmacy; Universidade de Lisboa; Portugal
- Department of Biochemistry and Human Biology; Faculty of Pharmacy; University of Lisbon; Portugal
| | - Jack van Horssen
- Department of Molecular Cell Biology and Immunology; VU University Medical Center Amsterdam; The Netherlands
| | - Maria João Gama
- Instituto de Investigação do Medicamento (iMed.ULisboa); Faculty of Pharmacy; Universidade de Lisboa; Portugal
- Department of Biochemistry and Human Biology; Faculty of Pharmacy; University of Lisbon; Portugal
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237
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Davies TG, Wixted WE, Coyle JE, Griffiths-Jones C, Hearn K, McMenamin R, Norton D, Rich SJ, Richardson C, Saxty G, Willems HMG, Woolford AJA, Cottom JE, Kou JP, Yonchuk JG, Feldser HG, Sanchez Y, Foley JP, Bolognese BJ, Logan G, Podolin PL, Yan H, Callahan JF, Heightman TD, Kerns JK. Monoacidic Inhibitors of the Kelch-like ECH-Associated Protein 1: Nuclear Factor Erythroid 2-Related Factor 2 (KEAP1:NRF2) Protein–Protein Interaction with High Cell Potency Identified by Fragment-Based Discovery. J Med Chem 2016; 59:3991-4006. [DOI: 10.1021/acs.jmedchem.6b00228] [Citation(s) in RCA: 170] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Thomas G. Davies
- Astex Pharmaceuticals, 436 Cambridge
Science Park, Cambridge CB4 0QA, U.K
| | - William E. Wixted
- GlaxoSmithKline
Pharmaceuticals, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Joseph E. Coyle
- Astex Pharmaceuticals, 436 Cambridge
Science Park, Cambridge CB4 0QA, U.K
| | | | - Keisha Hearn
- Astex Pharmaceuticals, 436 Cambridge
Science Park, Cambridge CB4 0QA, U.K
| | - Rachel McMenamin
- Astex Pharmaceuticals, 436 Cambridge
Science Park, Cambridge CB4 0QA, U.K
| | - David Norton
- Astex Pharmaceuticals, 436 Cambridge
Science Park, Cambridge CB4 0QA, U.K
| | - Sharna J. Rich
- Astex Pharmaceuticals, 436 Cambridge
Science Park, Cambridge CB4 0QA, U.K
| | | | - Gordon Saxty
- Astex Pharmaceuticals, 436 Cambridge
Science Park, Cambridge CB4 0QA, U.K
| | | | | | - Joshua E. Cottom
- GlaxoSmithKline
Pharmaceuticals, 1250 South Collegeville
Road, Collegeville, Pennsylvania 19426, United States
| | - Jen-Pyng Kou
- GlaxoSmithKline
Pharmaceuticals, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - John G. Yonchuk
- GlaxoSmithKline
Pharmaceuticals, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Heidi G. Feldser
- GlaxoSmithKline
Pharmaceuticals, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Yolanda Sanchez
- GlaxoSmithKline
Pharmaceuticals, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Joseph P. Foley
- GlaxoSmithKline
Pharmaceuticals, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Brian J. Bolognese
- GlaxoSmithKline
Pharmaceuticals, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Gregory Logan
- GlaxoSmithKline
Pharmaceuticals, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Patricia L. Podolin
- GlaxoSmithKline
Pharmaceuticals, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Hongxing Yan
- GlaxoSmithKline
Pharmaceuticals, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - James F. Callahan
- GlaxoSmithKline
Pharmaceuticals, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Tom D. Heightman
- Astex Pharmaceuticals, 436 Cambridge
Science Park, Cambridge CB4 0QA, U.K
| | - Jeffrey K. Kerns
- GlaxoSmithKline
Pharmaceuticals, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
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238
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Scott DE, Bayly AR, Abell C, Skidmore J. Small molecules, big targets: drug discovery faces the protein–protein interaction challenge. Nat Rev Drug Discov 2016; 15:533-50. [DOI: 10.1038/nrd.2016.29] [Citation(s) in RCA: 625] [Impact Index Per Article: 78.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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239
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Wong MHL, Bryan HK, Copple IM, Jenkins RE, Chiu PH, Bibby J, Berry NG, Kitteringham NR, Goldring CE, O'Neill PM, Park BK. Design and Synthesis of Irreversible Analogues of Bardoxolone Methyl for the Identification of Pharmacologically Relevant Targets and Interaction Sites. J Med Chem 2016; 59:2396-409. [PMID: 26908173 DOI: 10.1021/acs.jmedchem.5b01292] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Semisynthetic triterpenoids such as bardoxolone methyl (methyl-2-cyano 3,12-dioxooleano-1,9-dien-28-oate; CDDO-Me) (4) are potent inducers of antioxidant and anti-inflammatory signaling pathways, including those regulated by the transcription factor Nrf2. However, the reversible nature of the interaction between triterpenoids and thiols has hindered attempts to identify pharmacologically relevant targets and characterize the sites of interaction. Here, we report a shortened synthesis and SAR profiling of 4, enabling the design of analogues that react irreversibly with model thiols, as well as the model protein glutathione S-transferase P1, in vitro. We show that one of these analogues, CDDO-epoxide (13), is comparable to 4 in terms of cytotoxicity and potency toward Nrf2 in rat hepatoma cells and stably modifies specific cysteine residues (namely, Cys-257, -273, -288, -434, -489, and -613) within Keap1, the major repressor of Nrf2, both in vitro and in living cells. Supported by molecular modeling, these data demonstrate the value of 13 for identifying site(s) of interaction with pharmacologically relevant targets and informing the continuing development of triterpenoids as novel drug candidates.
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Affiliation(s)
- Michael H L Wong
- Department of Chemistry, University of Liverpool , L69 7ZD Liverpool, U.K
- MRC Centre for Drug Safety Science, Department of Molecular and Clinical Pharmacology, University of Liverpool , L69 3GE Liverpool, U.K
| | - Holly K Bryan
- MRC Centre for Drug Safety Science, Department of Molecular and Clinical Pharmacology, University of Liverpool , L69 3GE Liverpool, U.K
| | - Ian M Copple
- MRC Centre for Drug Safety Science, Department of Molecular and Clinical Pharmacology, University of Liverpool , L69 3GE Liverpool, U.K
| | - Rosalind E Jenkins
- MRC Centre for Drug Safety Science, Department of Molecular and Clinical Pharmacology, University of Liverpool , L69 3GE Liverpool, U.K
| | - Pak Him Chiu
- MRC Centre for Drug Safety Science, Department of Molecular and Clinical Pharmacology, University of Liverpool , L69 3GE Liverpool, U.K
| | - Jaclyn Bibby
- Department of Chemistry, University of Liverpool , L69 7ZD Liverpool, U.K
| | - Neil G Berry
- Department of Chemistry, University of Liverpool , L69 7ZD Liverpool, U.K
| | - Neil R Kitteringham
- MRC Centre for Drug Safety Science, Department of Molecular and Clinical Pharmacology, University of Liverpool , L69 3GE Liverpool, U.K
| | - Christopher E Goldring
- MRC Centre for Drug Safety Science, Department of Molecular and Clinical Pharmacology, University of Liverpool , L69 3GE Liverpool, U.K
| | - Paul M O'Neill
- Department of Chemistry, University of Liverpool , L69 7ZD Liverpool, U.K
| | - B Kevin Park
- MRC Centre for Drug Safety Science, Department of Molecular and Clinical Pharmacology, University of Liverpool , L69 3GE Liverpool, U.K
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240
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Li XY, Liu Y, Jiang WD, Jiang J, Wu P, Zhao J, Kuang SY, Tang L, Tang WN, Zhang YA, Zhou XQ, Feng L. Co- and Post-Treatment with Lysine Protects Primary Fish Enterocytes against Cu-Induced Oxidative Damage. PLoS One 2016; 11:e0147408. [PMID: 26812682 PMCID: PMC4727818 DOI: 10.1371/journal.pone.0147408] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 01/04/2016] [Indexed: 01/24/2023] Open
Abstract
The aim of the work was primarily to explore the protective activity pathways of lysine against oxidative damage in fish in vivo and in enterocytes in vitro. First, grass carp were fed diets containing six graded levels of lysine (7.1-19.6 g kg-1 diet) for 56 days. Second, the enterocytes were treated with different concentrations of lysine (0-300 mg/L in media) prior to (pre-treatment), along with (co-treatment) or following (post-treatment) with 6 mg/L of Cu for 24 h. The results indicated that lysine improved grass carp growth performance. Meanwhile, lysine ameliorated lipid and protein oxidation by elevating the gene expression and activity of antioxidant enzymes (superoxide dismutase (SOD), glutathioneperoxidase (GPx), glutathione-S-transferase (GST) and reductase (GR)), and nuclear factor erythroid 2-related factor 2 (Nrf2) mRNA levels in fish intestine. The in vitro studies showed that co- and post-treatment with lysine conferred significant protection against Cu-induced oxidative damage in fish primary enterocytes as measured by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) OD values, along with alkaline phosphatase (ALP) and lactate dehydrogenase activities, and the depletion of protein carbonyl (PC), malondialdehyde (MDA) and 8-hydroxydeoxyguanosine contents. Moreover, lysine co-treatment decreased the activities and mRNA level of cellular SOD, GPx, GST and GR compared with the Cu-only exposed group. Gene expression of the signalling molecule Nrf2 showed the same pattern as that of SOD activity, whereas Kelch-like ECH-associated protein 1b (Keap1b) followed the opposite trend, indicating that co-treatment with lysine induced antioxidant enzymes that protected against oxidative stress through Nrf2 pathway. In addition, post-treatment with lysine increased proteasomal activity and blocked the Cu-stimulated increase in mRNA levels of GST and associated catalase (CAT) and GST activities (P<0.01 and P<0.001). GR activity and gene expression, and glutathione (GSH) content followed an opposite trend to GST activity (P<0.05). Thus, post-treatment of lysine elevated protein and DNA repair abilities and ameliorated the cellular redox state of enterocytes. The overall results suggest that lysine plays a significant role in the protection of fish intestine in vivo and in vitro through the induction of key antioxidant protection.
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Affiliation(s)
- Xue-Yin Li
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
- Fish Nutrition and Safety Production University Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yang Liu
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
- Fish Nutrition and Safety Production University Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Wei-Dan Jiang
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
- Fish Nutrition and Safety Production University Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jun Jiang
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
- Fish Nutrition and Safety Production University Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Pei Wu
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
- Fish Nutrition and Safety Production University Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Juan Zhao
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
- Fish Nutrition and Safety Production University Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Sheng-Yao Kuang
- Animal Nutrition Institute, Sichuan Academy of Animal Science, Chengdu, 610066, Sichuan, China
| | - Ling Tang
- Animal Nutrition Institute, Sichuan Academy of Animal Science, Chengdu, 610066, Sichuan, China
| | - Wu-Neng Tang
- Animal Nutrition Institute, Sichuan Academy of Animal Science, Chengdu, 610066, Sichuan, China
| | - Yong-An Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Xiao-Qiu Zhou
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
- Fish Nutrition and Safety Production University Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Lin Feng
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
- Fish Nutrition and Safety Production University Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Sichuan Agricultural University, Chengdu, Sichuan, China
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241
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Chen A, Feldman M, Vershinin Z, Levy D. SETD6 is a negative regulator of oxidative stress response. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1859:420-7. [PMID: 26780326 DOI: 10.1016/j.bbagrm.2016.01.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 12/01/2015] [Accepted: 01/04/2016] [Indexed: 12/18/2022]
Abstract
The protein methyltransferase SETD6 is a key regulator of proliferation and inflammatory processes. However, the role of SETD6 in the regulation of additional cell signaling pathways has not been well studied. Here we show that SETD6 is a negative regulator of the oxidative stress response. Depletion of SETD6 from cells results in elevated Nrf2 levels and a significant increase in Nrf2 antioxidant target gene expression. Using proteomic tools, we uncovered a novel interaction between SETD6 and the oxidative stress sensor DJ1, a protein required for Nrf2-dependent transcription of antioxidant target genes. We show that SETD6 binds DJ1 both in-vitro and in cells but does not methylate DJ1. Under basal conditions, SETD6 and DJ1 are associated at chromatin. Through this interaction, SETD6 inhibits DJ1 activity, which in turn leads to the repression of Nrf2-dependent transcription. In response to oxidative stress, the transcription of Nrf2 antioxidant genes increases. We here show that under this condition, SETD6 mRNA and protein levels are reduced, leading to elevation in Nrf2 expression level and to a weaken interaction between SETD6 and DJ1 at chromatin. Taken together, these findings demonstrate that SETD6 negatively regulates the Nrf2-mediated oxidative stress response through a physical and catalytically independent interaction with DJ1 at chromatin.
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Affiliation(s)
- Ayelet Chen
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Israel; National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be'er Sheva 84105, Israel
| | - Michal Feldman
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Israel; National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be'er Sheva 84105, Israel
| | - Zlata Vershinin
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Israel; National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be'er Sheva 84105, Israel
| | - Dan Levy
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Israel; National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be'er Sheva 84105, Israel.
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242
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Lu MC, Yuan ZW, Jiang YL, Chen ZY, You QD, Jiang ZY. A systematic molecular dynamics approach to the study of peptide Keap1–Nrf2 protein–protein interaction inhibitors and its application to p62 peptides. MOLECULAR BIOSYSTEMS 2016; 12:1378-87. [DOI: 10.1039/c6mb00030d] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Protein–protein interactions (PPIs) as drug targets have been gaining growing interest, though developing drug-like small molecule PPI inhibitors remains challenging.
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Affiliation(s)
- Meng-Chen Lu
- State Key Laboratory of Natural Medicines
- China Pharmaceutical University
- Nanjing 210009
- China
- Jiangsu Key Laboratory of Drug Design and Optimization
| | - Zhen-Wei Yuan
- State Key Laboratory of Natural Medicines
- China Pharmaceutical University
- Nanjing 210009
- China
- Jiangsu Key Laboratory of Drug Design and Optimization
| | - Yong-Lin Jiang
- State Key Laboratory of Natural Medicines
- China Pharmaceutical University
- Nanjing 210009
- China
- Jiangsu Key Laboratory of Drug Design and Optimization
| | - Zhi-Yun Chen
- State Key Laboratory of Natural Medicines
- China Pharmaceutical University
- Nanjing 210009
- China
- Jiangsu Key Laboratory of Drug Design and Optimization
| | - Qi-Dong You
- State Key Laboratory of Natural Medicines
- China Pharmaceutical University
- Nanjing 210009
- China
- Jiangsu Key Laboratory of Drug Design and Optimization
| | - Zheng-Yu Jiang
- State Key Laboratory of Natural Medicines
- China Pharmaceutical University
- Nanjing 210009
- China
- Jiangsu Key Laboratory of Drug Design and Optimization
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243
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Do TN, Choy WY, Karttunen M. Binding of Disordered Peptides to Kelch: Insights from Enhanced Sampling Simulations. J Chem Theory Comput 2015; 12:395-404. [PMID: 26636721 DOI: 10.1021/acs.jctc.5b00868] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Keap1 protein plays an essential role in regulating cellular oxidative stress response and is a crucial binding hub for multiple proteins, several of which are intrinsically disordered proteins (IDP). Among Kelch's IDP binding partners, NRF2 and PTMA are the two most interesting cases. They share a highly similar binding motif; however, NRF2 binds to Kelch with a binding affinity of approximately 100-fold higher than that of PTMA. In this study, we perform an exhaustive sampling composed of 6 μs well-tempered metadynamics and 2 μs unbiased molecular dynamics (MD) simulations aiming at characterizing the binding mechanisms and structural properties of these two peptides. Our results agree with previous experimental observations that PTMA is remarkably more disordered than NRF2 in both the free and bound states. This explains PTMA's lower binding affinity. Our extensive sampling also provides valuable insights into the vast conformational ensembles of both NRF2 and PTMA, supports the hypothesis of coupled folding-binding, and confirms the essential role of linear motifs in IDP binding.
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Affiliation(s)
- Trang Nhu Do
- Department of Chemistry and Waterloo Institute for Nanotechnology, University of Waterloo , 200 University Avenue West, Waterloo, ON, Canada N2L 3G1
| | - Wing-Yiu Choy
- Department of Biochemistry, University of Western Ontario , 1151 Richmond Street, London, ON, Canada N6A 3K7
| | - Mikko Karttunen
- Department of Mathematics and Computer Science & Institute for Complex Molecular Systems, Eindhoven University of Technology , P.O. Box 513, MetaForum, 5600 MB, Eindhoven, The Netherlands
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244
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Do TN, Choy WY, Karttunen M. Accelerating the Conformational Sampling of Intrinsically Disordered Proteins. J Chem Theory Comput 2015; 10:5081-94. [PMID: 26584388 DOI: 10.1021/ct5004803] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Intrinsically disordered proteins (IDPs) are a class of proteins lacking a well-defined secondary structure. Instead, they are able to attain multiple conformations, bind to multiple targets, and respond to changes in their surroundings. Functionally, IDPs have been associated with molecular recognition, cell regulation, and signal transduction. The dynamic conformational ensemble of IDPs is highly environmental and binding partner dependent, rendering the characterization of IDPs extremely challenging. Here, we compare the sampling efficiencies of conventional molecular dynamics (MD), well-tempered metadynamics (WT-META), and bias-exchange metadynamics (BE-META). The total simulation time was over 10 μs, and a 20-mer peptide derived from the Neh2 domain of the Nuclear factor erythroid 2-related factor 2 (Nrf2) protein was simulated. BE-META, with a neutral replica and seven biased replicas employing a set of seven relevant collective variables (CVs), provided the most reliable and efficient sampling. Finally, we propose a free-energy reconstruction method based on the probability distribution of the secondary structure contents. This postprocessing analysis confirms the presence of not only the β-hairpin conformation of the free Neh2 peptide but also its rare bound-state-like conformation, both of that have been experimentally observed. In addition, our simulations also predict other possible conformations to be verified with future experiments.
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Affiliation(s)
- Trang Nhu Do
- Department of Chemistry and Waterloo Institute for Nanotechnology, University of Waterloo , 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Wing-Yiu Choy
- Department of Biochemistry, University of Western Ontario , 1151 Richmond Street, London, Ontario N6A 3K7, Canada
| | - Mikko Karttunen
- Department of Chemistry and Waterloo Institute for Nanotechnology, University of Waterloo , 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
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245
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Nasiri HR, Linge S, Ullmann D. Thermodynamic profiling of inhibitors of Nrf2:Keap1 interactions. Bioorg Med Chem Lett 2015; 26:526-529. [PMID: 26653613 DOI: 10.1016/j.bmcl.2015.11.082] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 11/20/2015] [Accepted: 11/21/2015] [Indexed: 12/31/2022]
Abstract
Keap1 binds to the transcription factor Nrf2 and negatively modulates the expression of genes involved in cellular protection against oxidative stress. Small molecules have been discovered to inhibit the Nrf2:Keap1 interactions and act as antagonists of Keap1. The affinities of these small molecules are not very high and need further improvement in follow up hit-to-lead programs. In addition to the affinity parameters Ki, Kd, and IC50 thermodynamic parameters provide useful information for the selection and optimization of these hit molecules at the early stage of the lead discovery process. In this letter a tracer displacement assay was used to determine the thermodynamic signature of some of the known inhibitors of the Nrf2:Keap1 interaction. An optimized assay protocol is presented, which can be applied to other small molecules in hit-to-lead programs in a medium throughput manner.
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Affiliation(s)
- Hamid R Nasiri
- Evotec AG, Manfred Eigen Campus, Essener Bogen 7, D-22419 Hamburg, Germany.
| | - Sandra Linge
- Evotec AG, Manfred Eigen Campus, Essener Bogen 7, D-22419 Hamburg, Germany
| | - Dirk Ullmann
- Evotec AG, Manfred Eigen Campus, Essener Bogen 7, D-22419 Hamburg, Germany.
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246
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Canning P, Sorrell FJ, Bullock AN. Structural basis of Keap1 interactions with Nrf2. Free Radic Biol Med 2015; 88:101-107. [PMID: 26057936 PMCID: PMC4668279 DOI: 10.1016/j.freeradbiomed.2015.05.034] [Citation(s) in RCA: 384] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 05/29/2015] [Accepted: 05/29/2015] [Indexed: 12/11/2022]
Abstract
Keap1 is a highly redox-sensitive member of the BTB-Kelch family that assembles with the Cul3 protein to form a Cullin-RING E3 ligase complex for the degradation of Nrf2. Oxidative stress disables Keap1, allowing Nrf2 protein levels to accumulate for the transactivation of critical stress response genes. Consequently, the Keap1-Nrf2 system is extensively pursued for the development of protein-protein interaction inhibitors that will stabilize Nrf2 for therapeutic effect in conditions of neurodegeneration, inflammation, and cancer. Here we review current progress toward the structure determination of Keap1 and its protein complexes with Cul3, Nrf2 substrate, and small-molecule antagonists. Together the available structures establish a rational three-dimensional model to explain the two-site binding of Nrf2 as well as its efficient ubiquitination.
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Affiliation(s)
- Peter Canning
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Oxford OX3 7DQ, UK
| | - Fiona J Sorrell
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Oxford OX3 7DQ, UK
| | - Alex N Bullock
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Oxford OX3 7DQ, UK.
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247
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Cho HY, Marzec J, Kleeberger SR. Functional polymorphisms in Nrf2: implications for human disease. Free Radic Biol Med 2015; 88:362-372. [PMID: 26117318 PMCID: PMC6779133 DOI: 10.1016/j.freeradbiomed.2015.06.012] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Revised: 06/09/2015] [Accepted: 06/10/2015] [Indexed: 12/18/2022]
Abstract
Nuclear factor (erythroid derived)-2 like 2 (NFE2L2), also known as nuclear factor erythroid 2 (NF-E2)-related factor 2 (Nrf2), is a ubiquitous transcription factor essential for protecting cells and tissues from oxidative stress-induced injury. Positional cloning and studies with Nrf2 knockout mice have identified important roles for this transcription factor in disease phenotypes for many organ systems. Studies have also characterized the means through which human Nrf2 is regulated and the mechanisms of interaction with antioxidant response elements (ARE) in promoters of effector genes. Moreover, single nucleotide polymorphisms (SNPs) in Nrf2 have been identified and evaluated for effects on gene expression and function, and translational investigations have sought to determine whether loss of function SNPs associate with disease progression. In this review, we present 1) an overview of the human Nrf2 gene and protein domain, 2) identification of genetic mutations in Nrf2 and associations of the mutations with multiple diseases, and 3) the role of somatic mutations in Nrf2 in diseases, primarily various cancers.
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Affiliation(s)
- Hye-Youn Cho
- Inflammation, Immunity, and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Jacqui Marzec
- Inflammation, Immunity, and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Steven R Kleeberger
- Inflammation, Immunity, and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA.
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248
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Gacesa R, Dunlap WC, Long PF. Bioinformatics analyses provide insight into distant homology of the Keap1-Nrf2 pathway. Free Radic Biol Med 2015; 88:373-380. [PMID: 26117326 DOI: 10.1016/j.freeradbiomed.2015.06.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 06/03/2015] [Accepted: 06/06/2015] [Indexed: 12/25/2022]
Abstract
An essential requirement for the evolution of early eukaryotic life was the development of effective means to protect against metabolic oxidative stress and exposure to environmental toxicants. In present-day mammals, the master transcription factor Nrf2 regulates basal level homeostasis and inducible expression of numerous detoxifying and antioxidant genes. To examine early evolution of the Keap1-Nrf2 pathway, we present bioinformatics analyses of distant homology of mammalian Keap1 and Nrf2 proteins across the Kingdoms of Life. Software written for this analysis is made freely available on-line. Furthermore, utilizing protein modeling and virtual screening methods, we demonstrate potential for Nrf2 activation by competitive inhibition of its binding to Keap1, specifically by UV-protective fungal mycosporines and marine mycosporine-like amino acids (MAAs). We contend that coevolution of Nrf2-activating secondary metabolites by fungi and other extant microbiota may provide prospective compound leads for the design of new therapeutics to target activation of the human Keap1-Nrf2 pathway for treating degenerative diseases of ageing.
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Affiliation(s)
- Ranko Gacesa
- Institute of Pharmaceutical Science, King's College London, 150 Stamford Street, London SE1 9NH, UK
| | - Walter C Dunlap
- Institute of Pharmaceutical Science, King's College London, 150 Stamford Street, London SE1 9NH, UK
| | - Paul F Long
- Institute of Pharmaceutical Science, King's College London, 150 Stamford Street, London SE1 9NH, UK; Department of Chemistry, King's College London, 150 Stamford Street, London SE1 9NH, UK.
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249
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Jain AD, Potteti H, Richardson BG, Kingsley L, Luciano JP, Ryuzoji AF, Lee H, Krunic A, Mesecar AD, Reddy SP, Moore TW. Probing the structural requirements of non-electrophilic naphthalene-based Nrf2 activators. Eur J Med Chem 2015; 103:252-68. [PMID: 26363505 PMCID: PMC4600463 DOI: 10.1016/j.ejmech.2015.08.049] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 08/22/2015] [Accepted: 08/25/2015] [Indexed: 12/31/2022]
Abstract
Activation of the transcription factor Nrf2 has been posited to be a promising therapeutic strategy in a number of inflammatory and oxidative stress diseases due to its regulation of detoxifying enzymes. In this work, we have developed a comprehensive structure-activity relationship around a known, naphthalene-based non-electrophilic activator of Nrf2, and we report highly potent non-electrophilic activators of Nrf2. Computational docking analysis of a subset of the compound series demonstrates the importance of water molecule displacement for affinity, and the X-ray structure of di-amide 12e supports the computational analysis. One of the best compounds, acid 16b, has an IC50 of 61 nM in a fluorescence anisotropy assay and a Kd of 120 nM in a surface plasmon resonance assay. Additionally, we demonstrate that the ethyl ester of 16b is an efficacious inducer of Nrf2 target genes, exhibiting ex vivo efficacy similar to the well-known electrophilic activator, sulforaphane.
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Affiliation(s)
- Atul D Jain
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Haranatha Potteti
- Department of Pediatrics, College of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Benjamin G Richardson
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Laura Kingsley
- Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Julia P Luciano
- Department of Biological Sciences Purdue University, West Lafayette, IN 47907, USA
| | - Aya F Ryuzoji
- Department of Biological Sciences Purdue University, West Lafayette, IN 47907, USA
| | - Hyun Lee
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Aleksej Krunic
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Andrew D Mesecar
- Department of Biological Sciences Purdue University, West Lafayette, IN 47907, USA; Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Sekhar P Reddy
- Department of Pediatrics, College of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA; University of Illinois Cancer Center, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Terry W Moore
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, USA; University of Illinois Cancer Center, University of Illinois at Chicago, Chicago, IL 60612, USA.
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250
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Guntas G, Lewis SM, Mulvaney KM, Cloer EW, Tripathy A, Lane TR, Major MB, Kuhlman B. Engineering a genetically encoded competitive inhibitor of the KEAP1-NRF2 interaction via structure-based design and phage display. Protein Eng Des Sel 2015; 29:1-9. [PMID: 26489878 DOI: 10.1093/protein/gzv055] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 09/24/2015] [Indexed: 12/31/2022] Open
Abstract
In its basal state, KEAP1 binds the transcription factor NRF2 (Kd = 5 nM) and promotes its degradation by ubiquitylation. Changes in the redox environment lead to modification of key cysteines within KEAP1, resulting in NRF2 protein accumulation and the transcription of genes important for restoring the cellular redox state. Using phage display and a computational loop grafting protocol, we engineered a monobody (R1) that is a potent competitive inhibitor of the KEAP1-NRF2 interaction. R1 bound to KEAP1 with a Kd of 300 pM and in human cells freed NRF2 from KEAP1 resulting in activation of the NRF2 promoter. Unlike cysteine-reactive small molecules that lack protein specificity, R1 is a genetically encoded, reversible inhibitor designed specifically for KEAP1. R1 should prove useful for studying the role of the KEAP1-NRF2 interaction in several disease states. The structure-based phage display strategy employed here is a general approach for engineering high-affinity binders that compete with naturally occurring interactions.
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Affiliation(s)
| | | | - Kathleen M Mulvaney
- Department of Cell Biology and Physiology Lineberger Comprehensive Cancer Center, University of North Carolina, 120 Mason Farm Road, Genetic Medicine Building 3010, Chapel Hill, NC 27599-7260, USA
| | - Erica W Cloer
- Department of Cell Biology and Physiology Lineberger Comprehensive Cancer Center, University of North Carolina, 120 Mason Farm Road, Genetic Medicine Building 3010, Chapel Hill, NC 27599-7260, USA
| | | | | | - Michael B Major
- Department of Cell Biology and Physiology Lineberger Comprehensive Cancer Center, University of North Carolina, 120 Mason Farm Road, Genetic Medicine Building 3010, Chapel Hill, NC 27599-7260, USA
| | - Brian Kuhlman
- Department of Cell Biology and Physiology Lineberger Comprehensive Cancer Center, University of North Carolina, 120 Mason Farm Road, Genetic Medicine Building 3010, Chapel Hill, NC 27599-7260, USA
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