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Chu Z, Zhu L, Zhou Y, Yang F, Hu Z, Luo Y, Li W, Luo F. Targeting Nrf2 by bioactive peptides alleviate inflammation: expanding the role of gut microbiota and metabolites. Crit Rev Food Sci Nutr 2024:1-20. [PMID: 38881345 DOI: 10.1080/10408398.2024.2367570] [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: 06/18/2024]
Abstract
Inflammation is a complex process that usually refers to the general response of the body to the harmful stimuli of various pathogens, tissue damage, or exogenous pollutants. Nuclear factor erythroid 2-related factor 2 (Nrf2) is a transcription factor that regulates cellular defense against oxidative damage and toxicity by expressing genes related to oxidative stress response and drug detoxification. In addition to its antioxidant properties, Nrf2 is involved in many other important physiological processes, including inflammation and metabolism. Nrf2 can bind the promoters of antioxidant genes and upregulates their expressions, which alleviate oxidation-induced inflammation. Nrf2 has been shown to upregulate heme oxygenase-1 expression, which promotes NF-κB activation and is closely related with inflammation. Nrf2, as a key factor in antioxidant response, is closely related to the expressions of pro-inflammatory factors, NF-κB pathway and cell metabolism. Bioactive peptides come from a wide range of sources and have many biological functions. Increasing evidence indicates that bioactive peptides have potential anti-inflammatory activities. This article summarized the sources, absorption and utilization of bioactive peptides and their role in alleviating inflammation via Nrf2 pathway. Bioactive peptides can also regulate gut microbiota and alter metabolites, which regulates the Nrf2 pathway through novel pathway and supplement the anti-inflammatory mechanisms of bioactive peptides. This review provides a reference for further study on the anti-inflammatory effect of bioactive peptides and the development and utilization of functional foods.
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Affiliation(s)
- Zhongxing Chu
- Hunan Key Laboratory of Grain-oil Deep Process and Quality Control, Hunan Key Laboratory of Forestry Edible Resources Safety and Processing, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Lingfeng Zhu
- Hunan Agricultural Product Processing Institute, Hunan Academy of Agricultural Sciences, Changsha, Hunan, China
| | - Yaping Zhou
- Hunan Key Laboratory of Grain-oil Deep Process and Quality Control, Hunan Key Laboratory of Forestry Edible Resources Safety and Processing, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Feiyan Yang
- Hunan Key Laboratory of Grain-oil Deep Process and Quality Control, Hunan Key Laboratory of Forestry Edible Resources Safety and Processing, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Zuomin Hu
- Hunan Key Laboratory of Grain-oil Deep Process and Quality Control, Hunan Key Laboratory of Forestry Edible Resources Safety and Processing, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Yi Luo
- Department of Clinic Medicine, Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Wen Li
- Hunan Key Laboratory of Grain-oil Deep Process and Quality Control, Hunan Key Laboratory of Forestry Edible Resources Safety and Processing, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Feijun Luo
- Hunan Key Laboratory of Grain-oil Deep Process and Quality Control, Hunan Key Laboratory of Forestry Edible Resources Safety and Processing, Central South University of Forestry and Technology, Changsha, Hunan, China
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2
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Carrow KP, Hamilton HL, Hopps MP, Li Y, Qiao B, Payne NC, Thompson MP, Zhang X, Magassa A, Fattah M, Agarwal S, Vincent MP, Buyanova M, Bertin PA, Mazitschek R, Olvera de la Cruz M, Johnson DA, Johnson JA, Gianneschi NC. Inhibiting the Keap1/Nrf2 Protein-Protein Interaction with Protein-Like Polymers. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2311467. [PMID: 38241649 DOI: 10.1002/adma.202311467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/11/2024] [Indexed: 01/21/2024]
Abstract
Successful and selective inhibition of the cytosolic protein-protein interaction (PPI) between nuclear factor erythroid 2-related factor 2 (Nrf2) and Kelch-like ECH-associating protein 1 (Keap1) can enhance the antioxidant response, with the potential for a therapeutic effect in a range of settings including in neurodegenerative disease (ND). Small molecule inhibitors have been developed, yet many have off-target effects, or are otherwise limited by poor cellular permeability. Peptide-based strategies have also been attempted to enhance specificity, yet face challenges due to susceptibility to degradation and lack of cellular penetration. Herein, these barriers are overcome utilizing a polymer-based proteomimetics. The protein-like polymer (PLP) consists of a synthetic, lipophilic polymer backbone displaying water soluble Keap1-binding peptides on each monomer unit forming a brush polymer architecture. The PLPs are capable of engaging Keap1 and displacing the cellular protective transcription factor Nrf2, which then translocates to the nucleus, activating the antioxidant response element (ARE). PLPs exhibit increased Keap1 binding affinity by several orders of magnitude compared to free peptides, maintain serum stability, are cell-penetrant, and selectively activate the ARE pathway in cells, including in primary cortical neuronal cultures. Keap1/Nrf2-inhibitory PLPs have the potential to impact the treatment of disease states associated with dysregulation of oxidative stress, such as NDs.
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Affiliation(s)
- Kendal P Carrow
- Department of Biomedical Engineering, McCormick School of Engineering, Medical Scientist Training Program, Feinberg School of Medicine, International Institute for Nanotechnology, Northwestern University, Evanston, 60208, IL, USA
| | - Haylee L Hamilton
- School of Pharmacy, University of Wisconsin, Madison, 57305, WI, USA
| | - Madeline P Hopps
- International Institute for Nanotechnology, Department of Chemistry, Chemistry of Life Processes Institute, Northwestern University, Evanston, 60208, IL, USA
| | - Yang Li
- Department of Chemical and Biological Engineering, McCormick School of Engineering, Northwestern University, Evanston, 60208, IL, USA
| | - Baofu Qiao
- Department of Natural Sciences, Baruch College, City University of New York, New York, 10010, NY, USA
| | - N Connor Payne
- Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, 02138, MA, USA
| | - Matthew P Thompson
- International Institute for Nanotechnology, Department of Chemistry, Chemistry of Life Processes Institute, Northwestern University, Evanston, 60208, IL, USA
| | - Xiaoyu Zhang
- International Institute for Nanotechnology, Department of Chemistry, Chemistry of Life Processes Institute, Northwestern University, Evanston, 60208, IL, USA
| | - Assa Magassa
- International Institute for Nanotechnology, Department of Chemistry, Chemistry of Life Processes Institute, Northwestern University, Evanston, 60208, IL, USA
| | - Mara Fattah
- International Institute for Nanotechnology, Department of Chemistry, Chemistry of Life Processes Institute, Northwestern University, Evanston, 60208, IL, USA
| | - Shivangi Agarwal
- Grove Biopharma, Inc, 1375 W. Fulton St., Ste. 650, Chicago, 60558, IL, USA
| | - Michael P Vincent
- Grove Biopharma, Inc, 1375 W. Fulton St., Ste. 650, Chicago, 60558, IL, USA
| | - Marina Buyanova
- Grove Biopharma, Inc, 1375 W. Fulton St., Ste. 650, Chicago, 60558, IL, USA
| | - Paul A Bertin
- Grove Biopharma, Inc, 1375 W. Fulton St., Ste. 650, Chicago, 60558, IL, USA
| | - Ralph Mazitschek
- Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, 02142, MA, USA
- Harvard T.H. Chan School of Public Health, Boston, 02115, MA, USA
| | - Monica Olvera de la Cruz
- Department of Materials Science & Engineering, Robert R. McCormick School of Engineering and Applied Science, Center for Computation and Theory of Soft Materials, Northwestern University, Evanston, 60208, IL, USA
| | - Delinda A Johnson
- School of Pharmacy, University of Wisconsin, Madison, 57305, WI, USA
| | - Jeffrey A Johnson
- School of Pharmacy, University of Wisconsin, Madison, 57305, WI, USA
| | - Nathan C Gianneschi
- Departments of Chemistry, Materials Science & Engineering, Biomedical Engineering, Pharmacology, Simpson Querrey Institute, Chemistry of Life Processes Institute, Lurie Cancer Center, International Institute for Nanotechnology, Northwestern University, Evanston, 60208, IL, USA
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Iegre J, Krajcovicova S, Gunnarsson A, Wissler L, Käck H, Luchniak A, Tångefjord S, Narjes F, Spring DR. A cell-active cyclic peptide targeting the Nrf2/Keap1 protein-protein interaction. Chem Sci 2023; 14:10800-10805. [PMID: 37829032 PMCID: PMC10566475 DOI: 10.1039/d3sc04083f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 09/19/2023] [Indexed: 10/14/2023] Open
Abstract
The disruption of the protein-protein interaction (PPI) between Nrf2 and Keap1 is an attractive strategy to counteract the oxidative stress that characterises a variety of severe diseases. Peptides represent a complementary approach to small molecules for the inhibition of this therapeutically important PPI. However, due to their polar nature and the negative net charge required for binding to Keap1, the peptides reported to date exhibit either mid-micromolar activity or are inactive in cells. Herein, we present a two-component peptide stapling strategy to rapidly access a variety of constrained and functionalised peptides that target the Nrf2/Keap1 PPI. The most promising peptide, P8-H containing a fatty acid tag, binds to Keap1 with nanomolar affinity and is effective at inducing transcription of ARE genes in a human lung epithelial cell line at sub-micromolar concentration. Furthermore, crystallography of the peptide in complex with Keap1 yielded a high resolution X-ray structure, adding to the toolbox of structures available to develop cell-permeable peptidomimetic inhibitors.
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Affiliation(s)
- Jessica Iegre
- Yusuf Hamied Department of Chemistry Lensfield Road CB2 1EW Cambridge UK
| | - Sona Krajcovicova
- Yusuf Hamied Department of Chemistry Lensfield Road CB2 1EW Cambridge UK
- Department of Organic Chemistry, Palacky University Olomouc Tr. 17. Listopadu 12 77900 Olomouc Czech Republic
| | - Anders Gunnarsson
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca Pepparedsleden 1 43183 Gothenburg Sweden
| | - Lisa Wissler
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca Pepparedsleden 1 43183 Gothenburg Sweden
| | - Helena Käck
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca Pepparedsleden 1 43183 Gothenburg Sweden
| | - Anna Luchniak
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca Pepparedsleden 1 43183 Gothenburg Sweden
| | - Stefan Tångefjord
- BioScience, Research & Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca Pepparedsleden 1 43183 Gothenburg Sweden
| | - Frank Narjes
- Medicinal Chemistry, Research & Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca Pepparedsleden 1 43183 Gothenburg Sweden
| | - David R Spring
- Yusuf Hamied Department of Chemistry Lensfield Road CB2 1EW Cambridge UK
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Bai X, Bian Z, Zhang M. Targeting the Nrf2 signaling pathway using phytochemical ingredients: A novel therapeutic road map to combat neurodegenerative diseases. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2023; 109:154582. [PMID: 36610130 DOI: 10.1016/j.phymed.2022.154582] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 11/11/2022] [Accepted: 11/29/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Nuclear factor erythroid 2-related factor 2 (Nrf2) is a classical nuclear transcription factor that regulates the system's anti-oxidative stress response. The activation of Nrf2 induces the expression of antioxidant proteins and improves the system's anti-oxidative stress ability. Accumulating evidence suggests that Nrf2-centered signaling pathways may be a key pharmacological target for the treatment of neurodegenerative diseases (NDDs). However, phytochemicals as new therapeutic agents against NDDs have not been clearly delineated. PURPOSE To review the therapeutic effects of phytochemical ingredients on NDDs by activating Nrf2 and reducing oxidative stress injury. METHODS A comprehensive search of published articles was performed using various literature databases including PubMed, Google Scholar, and China National Knowledge Infrastructure. The search terms included "Nrf2", "phytochemical ingredients", "natural bioactive agents", "neurodegenerative diseases", "Antioxidant", "Alzheimer's disease", "Parkinson's disease", "Huntington's disease", "amyotrophic lateral sclerosis" "multiple sclerosis", "toxicity", and combinations of these keywords. A total of 769 preclinical studies were retrieved until August 2022, and we included 39 of these articless on phytochemistry, pharmacology, toxicology and other fields. RESULTS Numerous in vivo and in vitro studies showed that phytochemical ingredients could act as an Nrf2 activator in the treatment of NDDs through the antioxidant defense mechanism. These phytochemical ingredients, such as salidroside, naringenin, resveratrol, sesaminol, ellagic acid, ginsenoside Re, tanshinone I, sulforaphane, curcumin, naringin, tetramethylpyrazine, withametelin, magnolol, piperine, and myricetin, had the potential to improve Nrf2 signaling, thereby combatting NDDs. CONCLUSION As Nrf2 activators, phytochemical ingredients may provide a novel potential strategy for the treatment of NDDs. Here, we reviewed the interaction between phytochemical ingredients, Nrf2, and its antioxidant damaging pathway in NDDs and explored the advantages of phytochemical ingredients in anti-oxidative stress, which provides a reliable basis for improving the treatment of NDDs. However, further clinical trials are needed to determine the safety and efficacy of Nrf2 activators for NDDs.
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Affiliation(s)
- Xue Bai
- Department of Gerontology and Geriatrics, Shengjing Hospital of China Medical University, 36 Sanhao Street, Heping District, 110004, Shenyang, Liaoning, PR China
| | - Zhigang Bian
- Department of Otolaryngology Head and Neck Surgery, Shengjing Hospital of China Medical University, 36 Sanhao Street, Heping District, 110004, Shenyang, Liaoning, PR China
| | - Meng Zhang
- Department of Gerontology and Geriatrics, Shengjing Hospital of China Medical University, 36 Sanhao Street, Heping District, 110004, Shenyang, Liaoning, PR China.
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Crisman E, Duarte P, Dauden E, Cuadrado A, Rodríguez-Franco MI, López MG, León R. KEAP1-NRF2 protein-protein interaction inhibitors: Design, pharmacological properties and therapeutic potential. Med Res Rev 2023; 43:237-287. [PMID: 36086898 PMCID: PMC10087726 DOI: 10.1002/med.21925] [Citation(s) in RCA: 47] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 06/27/2022] [Accepted: 08/18/2022] [Indexed: 02/04/2023]
Abstract
The transcription factor nuclear factor erythroid 2-related factor 2 (NRF2) is considered the master regulator of the phase II antioxidant response. It controls a plethora of cytoprotective genes related to oxidative stress, inflammation, and protein homeostasis, among other processes. Activation of these pathways has been described in numerous pathologies including cancer, cardiovascular, respiratory, renal, digestive, metabolic, autoimmune, and neurodegenerative diseases. Considering the increasing interest of discovering novel NRF2 activators due to its clinical application, initial efforts were devoted to the development of electrophilic drugs able to induce NRF2 nuclear accumulation by targeting its natural repressor protein Kelch-like ECH-associated protein 1 (KEAP1) through covalent modifications on cysteine residues. However, off-target effects of these drugs prompted the development of an innovative strategy, the search of KEAP1-NRF2 protein-protein interaction (PPI) inhibitors. These innovative activators are proposed to target NRF2 in a more selective way, leading to potentially improved drugs with the application for a variety of diseases that are currently under investigation. In this review, we summarize known KEAP1-NRF2 PPI inhibitors to date and the bases of their design highlighting the most important features of their respective interactions. We also discuss the preclinical pharmacological properties described for the most promising compounds.
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Affiliation(s)
- Enrique Crisman
- Instituto de Química Médica, Consejo Superior de Investigaciones Científicas (IQM-CSIC), Madrid, Spain.,Instituto de Investigación Sanitaria La Princesa, Hospital Universitario de la Princesa, Madrid, Spain.,Instituto Teófilo Hernando y Departamento de Farmacología y Terapéutica, Facultad de Medicina, Universidad Autónoma de Madrid, Madrid, Spain
| | - Pablo Duarte
- Instituto de Química Médica, Consejo Superior de Investigaciones Científicas (IQM-CSIC), Madrid, Spain.,Instituto Teófilo Hernando y Departamento de Farmacología y Terapéutica, Facultad de Medicina, Universidad Autónoma de Madrid, Madrid, Spain
| | - Esteban Dauden
- Instituto Teófilo Hernando y Departamento de Farmacología y Terapéutica, Facultad de Medicina, Universidad Autónoma de Madrid, Madrid, Spain
| | - Antonio Cuadrado
- Departmento de Bioquímica, Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Instituto de Investigación Sanitaria La Paz (IdiPaz), Instituto de Investigaciones Biomédicas 'Alberto Sols' UAM-CSIC, Facultad de Medicina, Universidad Autónoma de Madrid, Madrid, Spain
| | | | - Manuela G López
- Instituto de Investigación Sanitaria La Princesa, Hospital Universitario de la Princesa, Madrid, Spain.,Instituto Teófilo Hernando y Departamento de Farmacología y Terapéutica, Facultad de Medicina, Universidad Autónoma de Madrid, Madrid, Spain
| | - Rafael León
- Instituto de Química Médica, Consejo Superior de Investigaciones Científicas (IQM-CSIC), Madrid, Spain
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Ulasov AV, Rosenkranz AA, Georgiev GP, Sobolev AS. Nrf2/Keap1/ARE signaling: Towards specific regulation. Life Sci 2022; 291:120111. [PMID: 34732330 PMCID: PMC8557391 DOI: 10.1016/j.lfs.2021.120111] [Citation(s) in RCA: 146] [Impact Index Per Article: 73.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/22/2021] [Accepted: 10/27/2021] [Indexed: 02/06/2023]
Abstract
The Nrf2 transcription factor governs the expression of hundreds genes involved in cell defense against oxidative stress, the hallmark of numerous diseases such as neurodegenerative, cardiovascular, some viral pathologies, diabetes and others. The main route for Nrf2 activity regulation is via interactions with the Keap1 protein. Under the normoxia the Keap1 binds the Nrf2 and targets it to the proteasomal degradation, while the Keap1 is regenerated. Upon oxidative stress the interactions between Nrf2 and Keap1 are interrupted and the Nrf2 activates the transcription of the protective genes. Currently, the Nrf2 system activation is considered as a powerful cytoprotective strategy for treatment of different pathologies, which pathogenesis relies on oxidative stress including viral diseases of pivotal importance such as COVID-19. The implementation of this strategy is accomplished mainly through the inactivation of the Keap1 "guardian" function. Two approaches are now developing: the Keap1 modification via electrophilic agents, which leads to the Nrf2 release, and direct interruption of the Nrf2:Keap1 protein-protein interactions (PPI). Because of theirs chemical structure, the Nrf2 electrophilic inducers could non-specifically interact with others cellular proteins leading to undesired effects. Whereas the non-electrophilic inhibitors of the Nrf2:Keap1 PPI could be more specific, thereby widening the therapeutic window.
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Affiliation(s)
- Alexey V Ulasov
- Department of Molecular Genetics of Intracellular Transport, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia.
| | - Andrey A Rosenkranz
- Department of Molecular Genetics of Intracellular Transport, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia; Faculty of Biology, Moscow State University, 1-12 Leninskiye Gory St., 119234 Moscow, Russia
| | - Georgii P Georgiev
- Department of Molecular Genetics of Intracellular Transport, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia
| | - Alexander S Sobolev
- Department of Molecular Genetics of Intracellular Transport, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia; Faculty of Biology, Moscow State University, 1-12 Leninskiye Gory St., 119234 Moscow, Russia
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7
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Ershov PV, Mezentsev YV, Ivanov AS. Interfacial Peptides as Affinity Modulating Agents of Protein-Protein Interactions. Biomolecules 2022; 12:106. [PMID: 35053254 PMCID: PMC8773757 DOI: 10.3390/biom12010106] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/06/2022] [Accepted: 01/06/2022] [Indexed: 12/25/2022] Open
Abstract
The identification of disease-related protein-protein interactions (PPIs) creates objective conditions for their pharmacological modulation. The contact area (interfaces) of the vast majority of PPIs has some features, such as geometrical and biochemical complementarities, "hot spots", as well as an extremely low mutation rate that give us key knowledge to influence these PPIs. Exogenous regulation of PPIs is aimed at both inhibiting the assembly and/or destabilization of protein complexes. Often, the design of such modulators is associated with some specific problems in targeted delivery, cell penetration and proteolytic stability, as well as selective binding to cellular targets. Recent progress in interfacial peptide design has been achieved in solving all these difficulties and has provided a good efficiency in preclinical models (in vitro and in vivo). The most promising peptide-containing therapeutic formulations are under investigation in clinical trials. In this review, we update the current state-of-the-art in the field of interfacial peptides as potent modulators of a number of disease-related PPIs. Over the past years, the scientific interest has been focused on following clinically significant heterodimeric PPIs MDM2/p53, PD-1/PD-L1, HIF/HIF, NRF2/KEAP1, RbAp48/MTA1, HSP90/CDC37, BIRC5/CRM1, BIRC5/XIAP, YAP/TAZ-TEAD, TWEAK/FN14, Bcl-2/Bax, YY1/AKT, CD40/CD40L and MINT2/APP.
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Affiliation(s)
- Pavel V. Ershov
- Institute of Biomedical Chemistry, 119121 Moscow, Russia; (Y.V.M.); (A.S.I.)
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8
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Benz C, Ali M, Krystkowiak I, Simonetti L, Sayadi A, Mihalic F, Kliche J, Andersson E, Jemth P, Davey NE, Ivarsson Y. Proteome-scale mapping of binding sites in the unstructured regions of the human proteome. Mol Syst Biol 2022; 18:e10584. [PMID: 35044719 PMCID: PMC8769072 DOI: 10.15252/msb.202110584] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 12/21/2021] [Accepted: 12/22/2021] [Indexed: 12/18/2022] Open
Abstract
Specific protein-protein interactions are central to all processes that underlie cell physiology. Numerous studies have together identified hundreds of thousands of human protein-protein interactions. However, many interactions remain to be discovered, and low affinity, conditional, and cell type-specific interactions are likely to be disproportionately underrepresented. Here, we describe an optimized proteomic peptide-phage display library that tiles all disordered regions of the human proteome and allows the screening of ~ 1,000,000 overlapping peptides in a single binding assay. We define guidelines for processing, filtering, and ranking the results and provide PepTools, a toolkit to annotate the identified hits. We uncovered >2,000 interaction pairs for 35 known short linear motif (SLiM)-binding domains and confirmed the quality of the produced data by complementary biophysical or cell-based assays. Finally, we show how the amino acid resolution-binding site information can be used to pinpoint functionally important disease mutations and phosphorylation events in intrinsically disordered regions of the proteome. The optimized human disorderome library paired with PepTools represents a powerful pipeline for unbiased proteome-wide discovery of SLiM-based interactions.
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Affiliation(s)
- Caroline Benz
- Department of Chemistry ‐ BMCUppsala UniversityUppsalaSweden
| | - Muhammad Ali
- Department of Chemistry ‐ BMCUppsala UniversityUppsalaSweden
| | | | | | - Ahmed Sayadi
- Department of Chemistry ‐ BMCUppsala UniversityUppsalaSweden
| | - Filip Mihalic
- Department of Medical Biochemistry and MicrobiologyUppsala UniversityUppsalaSweden
| | - Johanna Kliche
- Department of Chemistry ‐ BMCUppsala UniversityUppsalaSweden
| | - Eva Andersson
- Department of Medical Biochemistry and MicrobiologyUppsala UniversityUppsalaSweden
| | - Per Jemth
- Department of Medical Biochemistry and MicrobiologyUppsala UniversityUppsalaSweden
| | - Norman E Davey
- Division of Cancer BiologyThe Institute of Cancer ResearchLondonUK
| | - Ylva Ivarsson
- Department of Chemistry ‐ BMCUppsala UniversityUppsalaSweden
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9
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Ren Y, Wu S, Chen S, Burdette JE, Cheng X, Kinghorn AD. Interaction of (+)-Strebloside and Its Derivatives with Na +/K +-ATPase and Other Targets. Molecules 2021; 26:5675. [PMID: 34577146 PMCID: PMC8467840 DOI: 10.3390/molecules26185675] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 09/08/2021] [Accepted: 09/14/2021] [Indexed: 01/09/2023] Open
Abstract
Docking profiles for (+)-strebloside, a cytotoxic cardiac glycoside identified from Streblus asper, and some of its derivatives and Na+/K+-ATPase have been investigated. In addition, binding between (+)-strebloside and its aglycone, strophanthidin, and several of their other molecular targets, including FIH-1, HDAC, KEAP1 and MDM2 (negative regulators of Nrf2 and p53, respectively), NF-κB, and PI3K and Akt1, have been inspected and compared with those for digoxin and its aglycone, digoxigenin. The results showed that (+)-strebloside, digoxin, and their aglycones bind to KEAP1 and MDM2, while (+)-strebloside, strophanthidin, and digoxigenin dock to the active pocket of PI3K, and (+)-strebloside and digoxin interact with FIH-1. Thus, these cardiac glycosides could directly target HIF-1, Nrf2, and p53 protein-protein interactions, Na+/K+-ATPase, and PI3K to mediate their antitumor activity. Overall, (+)-strebloside seems more promising than digoxin for the development of potential anticancer agents.
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Affiliation(s)
- Yulin Ren
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA; (Y.R.); (S.W.); (S.C.)
| | - Sijin Wu
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA; (Y.R.); (S.W.); (S.C.)
| | - Sijie Chen
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA; (Y.R.); (S.W.); (S.C.)
| | - Joanna E. Burdette
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, USA;
| | - Xiaolin Cheng
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA; (Y.R.); (S.W.); (S.C.)
| | - A. Douglas Kinghorn
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA; (Y.R.); (S.W.); (S.C.)
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10
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Alexa A, Ember O, Szabó I, Mo'ath Y, Póti ÁL, Reményi A, Bánóczi Z. Peptide Based Inhibitors of Protein Binding to the Mitogen-Activated Protein Kinase Docking Groove. Front Mol Biosci 2021; 8:690429. [PMID: 34277705 PMCID: PMC8281026 DOI: 10.3389/fmolb.2021.690429] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 06/18/2021] [Indexed: 11/21/2022] Open
Abstract
Mitogen-activated protein kinases (MAPK) are important regulatory units in cells and they take part in the regulation of many cellular functions such as cell division, differentiation or apoptosis. All MAPKs have a shallow docking groove that interacts with linear binding motifs of their substrate proteins and their regulatory proteins such as kinases, phosphatases, scaffolds. Inhibition of these protein–protein interactions may reduce or abolish the activity of the targeted kinase. Based on the wide range of their biological activity, this kind of inhibition can be useful in the treatment of many disorders like tumors, inflammation or undesired cell apoptosis. In this study a linear binding motif from the RHDF1 protein—a 15 amino acids long peptide—was selected for optimization to increase its cellular uptake but retaining its low micromolar binding affinity. First, we synthesized an octaarginine conjugate that showed efficient cellular uptake. Next, we set out to reduce the size of this construct. We were able to decrease the length of the original peptide, and to increase its cellular uptake with specific chemical modifications. These new constructs bound better to ERK2 and p38 kinases than the original peptide and they showed markedly increased cellular uptake. The new octaarginine conjugate and one of the minimized bicyclic derivatives could inhibit the phosphorylation of intracellular ERK or p38. However, the modulation of MAPK phosphorylation levels by these cell-penetrating peptides were complex, despite that in biochemical assays they all inhibited MAPK-substrate binding as well as phosphorylation. The optimized peptides depending on the applied concentration caused an expected decrease, but also some unexpected increase in MAPK phosphorylation patterns in the cell. This possibly reflects the complexity of MAPK docking groove mediated protein–protein interactions including bone fide MAPK clients such activator kinases, deactivating phosphatases or regulatory scaffolds. Thus, our findings with optimized cell-penetrating “inhibitory” peptides highlight the opportunities but also the pitfalls of docking peptide based MAPK activity regulation and call for a better quantitative understanding of MAPK mediated protein–protein interactions in cells.
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Affiliation(s)
- Anita Alexa
- Biomolecular Interactions Laboratory, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
| | - Orsolya Ember
- Biomolecular Interactions Laboratory, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary.,Department of Organic Chemistry, Institute of Chemistry, Eötvös Loránd University, Budapest, Hungary
| | - Ildikó Szabó
- MTA-ELTE Research Group of Peptide Chemistry, Eötvös Loránd Research Network (ELKH), Eötvös L. University, Budapest, Hungary
| | - Yousef Mo'ath
- Department of Organic Chemistry, Institute of Chemistry, Eötvös Loránd University, Budapest, Hungary
| | - Ádám L Póti
- Biomolecular Interactions Laboratory, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
| | - Attila Reményi
- Biomolecular Interactions Laboratory, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
| | - Zoltán Bánóczi
- Department of Organic Chemistry, Institute of Chemistry, Eötvös Loránd University, Budapest, Hungary
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Madden SK, Itzhaki LS. Exploring the binding of rationally engineered tandem-repeat proteins to E3 ubiquitin ligase Keap1. Protein Eng Des Sel 2021; 34:gzab027. [PMID: 34882773 PMCID: PMC8660007 DOI: 10.1093/protein/gzab027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 09/06/2021] [Accepted: 10/04/2021] [Indexed: 11/12/2022] Open
Abstract
The process of displaying functional peptides by 'grafting' them onto loops of a stable protein scaffold can be used to impart binding affinity for a target, but it can be difficult to predict the affinity of the grafted peptide and the effect of grafting on scaffold stability. In this study, we show that a series of peptides that bind to the E3 ubiquitin ligase Keap1 can be grafted into the inter-repeat loop of a consensus-designed tetratricopeptide repeat (CTPR) protein resulting in proteins with high stability. We found that these CTPR-grafted peptides had similar affinities to their free peptide counterparts and achieved a low nanomolar range. This result is likely due to a good structural match between the inter-repeat loop of the CTPR and the Keap1-binding peptide. The grafting process led to the discovery of a new Keap1-binding peptide, Ac-LDPETGELL-NH2, with low nanomolar affinity for Keap1, highlighting the potential of the repeat-protein class for application in peptide display.
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Affiliation(s)
- Sarah K Madden
- Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD, UK
| | - Laura S Itzhaki
- Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD, UK
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12
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González-Muñiz R, Bonache MÁ, Pérez de Vega MJ. Modulating Protein-Protein Interactions by Cyclic and Macrocyclic Peptides. Prominent Strategies and Examples. Molecules 2021; 26:445. [PMID: 33467010 PMCID: PMC7830901 DOI: 10.3390/molecules26020445] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/11/2021] [Accepted: 01/13/2021] [Indexed: 12/11/2022] Open
Abstract
Cyclic and macrocyclic peptides constitute advanced molecules for modulating protein-protein interactions (PPIs). Although still peptide derivatives, they are metabolically more stable than linear counterparts, and should have a lower degree of flexibility, with more defined secondary structure conformations that can be adapted to imitate protein interfaces. In this review, we analyze recent progress on the main methods to access cyclic/macrocyclic peptide derivatives, with emphasis in a few selected examples designed to interfere within PPIs. These types of peptides can be from natural origin, or prepared by biochemical or synthetic methodologies, and their design could be aided by computational approaches. Some advances to facilitate the permeability of these quite big molecules by conjugation with cell penetrating peptides, and the incorporation of β-amino acid and peptoid structures to improve metabolic stability, are also commented. It is predicted that this field of research could have an important future mission, running in parallel to the discovery of new, relevant PPIs involved in pathological processes.
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Affiliation(s)
- Rosario González-Muñiz
- Instituto de Química Médica (IQM-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain; (M.Á.B.); (M.J.P.d.V.)
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