1
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Andlovic B, Valenti D, Centorrino F, Picarazzi F, Hristeva S, Hiltmann M, Wolf A, Cantrelle FX, Mori M, Landrieu I, Levy LM, Klebl B, Tzalis D, Genski T, Eickhoff J, Ottmann C. Fragment-Based Interrogation of the 14-3-3/TAZ Protein-Protein Interaction. Biochemistry 2024; 63:2196-2206. [PMID: 39172504 PMCID: PMC11375770 DOI: 10.1021/acs.biochem.4c00248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
The identification of chemical starting points for the development of molecular glues is challenging. Here, we employed fragment screening and identified an allosteric stabilizer of the complex between 14-3-3 and a TAZ-derived peptide. The fragment binds preferentially to the 14-3-3/TAZ peptide complex and shows moderate stabilization in differential scanning fluorimetry and microscale thermophoresis. The binding site of the fragment was predicted by molecular dynamics calculations to be distant from the 14-3-3/TAZ peptide interface, located between helices 8 and 9 of the 14-3-3 protein. This site was confirmed by nuclear magnetic resonance and X-ray protein crystallography, revealing the first example of an allosteric stabilizer for 14-3-3 protein-protein interactions.
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Affiliation(s)
- Blaž Andlovic
- Lead Discovery Center GmbH, Otto-Hahn-Str. 15, 44227 Dortmund, Germany
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
| | - Dario Valenti
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
- Taros Chemicals GmbH & Co. KG, Emil-Figge-Straße 76a, 44227 Dortmund, Germany
| | - Federica Centorrino
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
| | - Francesca Picarazzi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Stanimira Hristeva
- Taros Chemicals GmbH & Co. KG, Emil-Figge-Straße 76a, 44227 Dortmund, Germany
| | | | - Alexander Wolf
- Lead Discovery Center GmbH, Otto-Hahn-Str. 15, 44227 Dortmund, Germany
| | - François-Xavier Cantrelle
- CNRS EMR9002 Integrative Structural Biology, University of Lille, F-59000 Lille, France
- University of Lille, Inserm, Institut Pasteur de Lille, U1167─RID-AGE─Risk Factors and Molecular Determinants of Aging-Related Diseases, F-59000 Lille, France
| | - Mattia Mori
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Isabelle Landrieu
- CNRS EMR9002 Integrative Structural Biology, University of Lille, F-59000 Lille, France
- University of Lille, Inserm, Institut Pasteur de Lille, U1167─RID-AGE─Risk Factors and Molecular Determinants of Aging-Related Diseases, F-59000 Lille, France
| | - Laura M Levy
- Taros Chemicals GmbH & Co. KG, Emil-Figge-Straße 76a, 44227 Dortmund, Germany
| | - Bert Klebl
- Lead Discovery Center GmbH, Otto-Hahn-Str. 15, 44227 Dortmund, Germany
| | - Dimitrios Tzalis
- Taros Chemicals GmbH & Co. KG, Emil-Figge-Straße 76a, 44227 Dortmund, Germany
| | - Thorsten Genski
- Taros Chemicals GmbH & Co. KG, Emil-Figge-Straße 76a, 44227 Dortmund, Germany
| | - Jan Eickhoff
- Lead Discovery Center GmbH, Otto-Hahn-Str. 15, 44227 Dortmund, Germany
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
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2
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Somsen BA, Cossar PJ, Arkin MR, Brunsveld L, Ottmann C. 14-3-3 Protein-Protein Interactions: From Mechanistic Understanding to Their Small-Molecule Stabilization. Chembiochem 2024; 25:e202400214. [PMID: 38738787 DOI: 10.1002/cbic.202400214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 05/11/2024] [Accepted: 05/13/2024] [Indexed: 05/14/2024]
Abstract
Protein-protein interactions (PPIs) are of utmost importance for maintenance of cellular homeostasis. Herein, a central role can be found for 14-3-3 proteins. These hub-proteins are known to bind hundreds of interaction partners, thereby regulating their activity, localization, and/or stabilization. Due to their ability to bind a large variety of client proteins, studies of 14-3-3 protein complexes flourished over the last decades, aiming to gain greater molecular understanding of these complexes and their role in health and disease. Because of their crucial role within the cell, 14-3-3 protein complexes are recognized as highly interesting therapeutic targets, encouraging the discovery of small molecule modulators of these PPIs. We discuss various examples of 14-3-3-mediated regulation of its binding partners on a mechanistic level, highlighting the versatile and multi-functional role of 14-3-3 within the cell. Furthermore, an overview is given on the development of stabilizers of 14-3-3 protein complexes, from initially used natural products to fragment-based approaches. These studies show the potential of 14-3-3 PPI stabilizers as novel agents in drug discovery and as tool compounds to gain greater molecular understanding of the role of 14-3-3-based protein regulation.
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Affiliation(s)
- Bente A Somsen
- Department of Biomedical Engineering and Institute for Complex Molecular Systems, Laboratory of Chemical Biology, Eindhoven University of Technology, P.O. Box 513, MB Eindhoven, 5600, Eindhoven, The Netherlands
| | - Peter J Cossar
- Department of Biomedical Engineering and Institute for Complex Molecular Systems, Laboratory of Chemical Biology, Eindhoven University of Technology, P.O. Box 513, MB Eindhoven, 5600, Eindhoven, The Netherlands
| | - Michelle R Arkin
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center (SMDC), University of California, San Francisco, California, 94143, United States
| | - Luc Brunsveld
- Department of Biomedical Engineering and Institute for Complex Molecular Systems, Laboratory of Chemical Biology, Eindhoven University of Technology, P.O. Box 513, MB Eindhoven, 5600, Eindhoven, The Netherlands
| | - Christian Ottmann
- Department of Biomedical Engineering and Institute for Complex Molecular Systems, Laboratory of Chemical Biology, Eindhoven University of Technology, P.O. Box 513, MB Eindhoven, 5600, Eindhoven, The Netherlands
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3
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Kapitonova AA, Perfilova KV, Cooley RB, Sluchanko NN. Phosphorylation Code of Human Nucleophosmin Includes Four Cryptic Sites for Hierarchical Binding of 14-3-3 Proteins. J Mol Biol 2024; 436:168592. [PMID: 38702038 DOI: 10.1016/j.jmb.2024.168592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/18/2024] [Accepted: 04/27/2024] [Indexed: 05/06/2024]
Abstract
Nucleophosmin (NPM1) is the 46th most abundant human protein with many functions whose dysregulation leads to various cancers. Pentameric NPM1 resides in the nucleolus but can also shuttle to the cytosol. NPM1 is regulated by multisite phosphorylation, yet molecular consequences of site-specific NPM1 phosphorylation remain elusive. Here we identify four 14-3-3 protein binding sites in NPM1 concealed within its oligomerization and α-helical C-terminal domains that are found phosphorylated in vivo. By combining mutagenesis, in-cell phosphorylation and PermaPhos technology for site-directed incorporation of a non-hydrolyzable phosphoserine mimic, we show how phosphorylation promotes NPM1 monomerization and partial unfolding, to recruit 14-3-3 dimers with low-micromolar affinity. Using fluorescence anisotropy we quantified pairwise interactions of all seven human 14-3-3 isoforms with four recombinant NPM1 phosphopeptides and assessed their druggability by fusicoccin. This revealed a complex hierarchy of 14-3-3 affinities toward the primary (S48, S293) and secondary (S106, S260) sites, differentially modulated by the small molecule. As three of these 14-3-3 binding phosphosites in NPM1 reside within signal sequences, this work suggests a mechanism of NPM1 regulation by which NPM1 phosphorylation can promote 14-3-3 binding to affect NPM1 shuttling between cell compartments. It also provides further evidence that phosphorylation-induced structural rearrangements of globular proteins serve to expose otherwise cryptic 14-3-3-binding sites that are important for cellular function.
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Affiliation(s)
- Anna A Kapitonova
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Kristina V Perfilova
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Richard B Cooley
- GCE4All Center, Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia.
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4
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Kapitonova AA, Perfilova KV, Cooley RB, Sluchanko NN. Phosphorylation code of human nucleophosmin includes four cryptic sites for hierarchical binding of 14-3-3 proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.13.580064. [PMID: 38405961 PMCID: PMC10888825 DOI: 10.1101/2024.02.13.580064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Nucleophosmin (NPM1) is the 46th most abundant human protein with many functions whose dysregulation leads to various cancers. Pentameric NPM1 resides in the nucleolus but can also shuttle to the cytosol. NPM1 is regulated by multisite phosphorylation, yet molecular consequences of site-specific NPM1 phosphorylation remain elusive. Here we identify four 14-3-3 protein binding sites in NPM1 concealed within its oligomerization and α-helical C-terminal domains that are found phosphorylated in vivo. By combining mutagenesis, in-cell phosphorylation and PermaPhos technology for site-directed incorporation of a non-hydrolyzable phosphoserine mimic, we show how phosphorylation promotes NPM1 monomerization and partial unfolding, to recruit 14-3-3 dimers with low-micromolar affinity. Using fluorescence anisotropy we quantified pairwise interactions of all seven human 14-3-3 isoforms with four recombinant NPM1 phosphopeptides and assessed their druggability by fusicoccin. This revealed a complex hierarchy of 14-3-3 affinities toward the primary (S48, S293) and secondary (S106, S260) sites, differentially modulated by the small molecule. As three of these 14-3-3 binding phospho-sites in NPM1 reside within signal sequences, this work highlights a key mechanism of NPM1 regulation by which NPM1 phosphorylation promotes 14-3-3 binding to control nucleocytoplasmic shuttling. It also provides further evidence that phosphorylation-induced structural rearrangements of globular proteins serve to expose otherwise cryptic 14-3-3-binding sites that are important for cellular function.
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Affiliation(s)
- Anna A. Kapitonova
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Kristina V. Perfilova
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Richard B. Cooley
- GCE4All Center, Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, 97331, USA
| | - Nikolai N. Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
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5
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Ward JA, Romartinez-Alonso B, Kay DF, Bellamy-Carter J, Thurairajah B, Basran J, Kwon H, Leney AC, Macip S, Roversi P, Muskett FW, Doveston RG. Characterizing the protein-protein interaction between MDM2 and 14-3-3σ; proof of concept for small molecule stabilization. J Biol Chem 2024; 300:105651. [PMID: 38237679 PMCID: PMC10864208 DOI: 10.1016/j.jbc.2024.105651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/01/2023] [Accepted: 01/01/2024] [Indexed: 02/10/2024] Open
Abstract
Mouse Double Minute 2 (MDM2) is a key negative regulator of the tumor suppressor protein p53. MDM2 overexpression occurs in many types of cancer and results in the suppression of WT p53. The 14-3-3 family of adaptor proteins are known to bind MDM2 and the 14-3-3σ isoform controls MDM2 cellular localization and stability to inhibit its activity. Therefore, small molecule stabilization of the 14-3-3σ/MDM2 protein-protein interaction (PPI) is a potential therapeutic strategy for the treatment of cancer. Here, we provide a detailed biophysical and structural characterization of the phosphorylation-dependent interaction between 14-3-3σ and peptides that mimic the 14-3-3 binding motifs within MDM2. The data show that di-phosphorylation of MDM2 at S166 and S186 is essential for high affinity 14-3-3 binding and that the binary complex formed involves one MDM2 di-phosphorylated peptide bound to a dimer of 14-3-3σ. However, the two phosphorylation sites do not simultaneously interact so as to bridge the 14-3-3 dimer in a 'multivalent' fashion. Instead, the two phosphorylated MDM2 motifs 'rock' between the two binding grooves of the dimer, which is unusual in the context of 14-3-3 proteins. In addition, we show that the 14-3-3σ-MDM2 interaction is amenable to small molecule stabilization. The natural product fusicoccin A forms a ternary complex with a 14-3-3σ dimer and an MDM2 di-phosphorylated peptide resulting in the stabilization of the 14-3-3σ/MDM2 PPI. This work serves as a proof-of-concept of the drugability of the 14-3-3/MDM2 PPI and paves the way toward the development of more selective and efficacious small molecule stabilizers.
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Affiliation(s)
- Jake A Ward
- Leicester Institute for Structural and Chemical Biology, University of Leicester, Leicester, UK; Mechanisms of Cancer and Aging Laboratory, Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Beatriz Romartinez-Alonso
- Leicester Institute for Structural and Chemical Biology, University of Leicester, Leicester, UK; Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Danielle F Kay
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
| | | | - Bethany Thurairajah
- Leicester Institute for Structural and Chemical Biology, University of Leicester, Leicester, UK; School of Chemistry, University of Leicester, Leicester, UK
| | - Jaswir Basran
- Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Hanna Kwon
- Leicester Institute for Structural and Chemical Biology, University of Leicester, Leicester, UK; Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Aneika C Leney
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Salvador Macip
- Mechanisms of Cancer and Aging Laboratory, Department of Molecular and Cell Biology, University of Leicester, Leicester, UK; FoodLab, Faculty of Health Sciences, Universitat Oberta de Catalunya, Barcelona, Spain; Josep Carreras Leukaemia Research Institute, Ctra de Can Ruti, Camí de les Escoles, s/n, Badalona, Barcelona, Spain
| | - Pietro Roversi
- Leicester Institute for Structural and Chemical Biology, University of Leicester, Leicester, UK; Institute of Agricultural Biology and Biotechnology, C.N.R., Unit of Milan, Milano, Italy
| | - Frederick W Muskett
- Leicester Institute for Structural and Chemical Biology, University of Leicester, Leicester, UK; Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Richard G Doveston
- Leicester Institute for Structural and Chemical Biology, University of Leicester, Leicester, UK; School of Chemistry, University of Leicester, Leicester, UK.
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6
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Jiang W, Jiang Y, Luo Y, Qiao W, Yang T. Facilitating the development of molecular glues: Opportunities from serendipity and rational design. Eur J Med Chem 2024; 263:115950. [PMID: 37984298 DOI: 10.1016/j.ejmech.2023.115950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 11/09/2023] [Accepted: 11/09/2023] [Indexed: 11/22/2023]
Abstract
Molecular glues can specifically induce interactions between two or more proteins to modulate biological functions and have been proven to be a powerful therapeutic modality in drug discovery. It plays a variety of vital roles in several biological processes, such as complex stabilization, interactome modulation and transporter inhibition, thus enabling challenging therapeutic targets to be druggable. Most known molecular glues were identified serendipitously, such as IMiDs, auxin, and rapamycin. In recent years, more rational strategies were explored with the development of chemical biology and a deep understanding of the interaction between molecular glues and proteins, which led to the rational discovery of several molecular glues. Thus, in this review, we aim to highlight the discovery strategies of molecular glues from three aspects: serendipitous discovery, screening methods and rational design principles. We expect that this review will provide a reasonable reference and insights for the discovery of molecular glues.
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Affiliation(s)
- Weiqing Jiang
- Laboratory of Human Diseases and Immunotherapies, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China; Institute of Immunology and Inflammation, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yunhan Jiang
- Laboratory of Human Diseases and Immunotherapies, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China; Institute of Immunology and Inflammation, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, China; Cardiovascular Surgery Research Laboratory, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Youfu Luo
- Laboratory of Human Diseases and Immunotherapies, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Wenliang Qiao
- Lung Cancer Center, Laboratory of Lung Cancer, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Tao Yang
- Laboratory of Human Diseases and Immunotherapies, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China; Institute of Immunology and Inflammation, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, China.
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7
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Wu Q, Centorrino F, Guillory X, Wolter M, Ottmann C, Cossar PJ, Brunsveld L. Discovery of 14-3-3 PPI Stabilizers by Extension of an Amidine-Substituted Thiophene Fragment. Chembiochem 2024; 25:e202300636. [PMID: 37902676 DOI: 10.1002/cbic.202300636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 10/29/2023] [Accepted: 10/30/2023] [Indexed: 10/31/2023]
Abstract
Protein-protein interaction (PPI) modulation is a promising approach in drug discovery with the potential to expand the 'druggable' proteome and develop new therapeutic strategies. While there have been significant advancements in methodologies for developing PPI inhibitors, there is a relative scarcity of literature describing the 'bottom-up' development of PPI stabilizers (Molecular Glues). The hub protein 14-3-3 and its interactome provide an excellent platform for exploring conceptual approaches to PPI modulation, including evolution of chemical matter for Molecular Glues. In this study, we employed a fragment extension strategy to discover stabilizers for the complex of 14-3-3 protein and an Estrogen Receptor alpha-derived peptide (ERα). A focused library of analogues derived from an amidine-substituted thiophene fragment enhanced the affinity of the 14-3-3/ERα complex up to 6.2-fold. Structure-activity relationship (SAR) analysis underscored the importance of the newly added, aromatic side chain with a certain degree of rigidity. X-ray structural analysis revealed a unique intermolecular π-π stacking binding mode of the most active analogues, resulting in the simultaneous binding of two molecules to the PPI binding pocket. Notably, analogue 11 displayed selective stabilization of the 14-3-3/ERα complex.
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Affiliation(s)
- Qi Wu
- Laboratory of Chemical Biology, Department of Biomedical Engineering and, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Federica Centorrino
- Laboratory of Chemical Biology, Department of Biomedical Engineering and, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Xavier Guillory
- Laboratory of Chemical Biology, Department of Biomedical Engineering and, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Madita Wolter
- Laboratory of Chemical Biology, Department of Biomedical Engineering and, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering and, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Peter J Cossar
- Laboratory of Chemical Biology, Department of Biomedical Engineering and, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering and, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
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8
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Konstantinidou M, Visser EJ, Vandenboorn E, Chen S, Jaishankar P, Overmans M, Dutta S, Neitz RJ, Renslo AR, Ottmann C, Brunsveld L, Arkin MR. Structure-Based Optimization of Covalent, Small-Molecule Stabilizers of the 14-3-3σ/ERα Protein-Protein Interaction from Nonselective Fragments. J Am Chem Soc 2023; 145:20328-20343. [PMID: 37676236 PMCID: PMC10515640 DOI: 10.1021/jacs.3c05161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Indexed: 09/08/2023]
Abstract
The stabilization of protein-protein interactions (PPIs) has emerged as a promising strategy in chemical biology and drug discovery. The identification of suitable starting points for stabilizing native PPIs and their subsequent elaboration into selective and potent molecular glues lacks structure-guided optimization strategies. We have previously identified a disulfide fragment that stabilized the hub protein 14-3-3σ bound to several of its clients, including ERα and C-RAF. Here, we show the structure-based optimization of the nonselective fragment toward selective and highly potent small-molecule stabilizers of the 14-3-3σ/ERα complex. The more elaborated molecular glues, for example, show no stabilization of 14-3-3σ/C-RAF up to 150 μM compound. Orthogonal biophysical assays, including mass spectrometry and fluorescence anisotropy, were used to establish structure-activity relationships. The binding modes of 37 compounds were elucidated with X-ray crystallography, which further assisted the concomitant structure-guided optimization. By targeting specific amino acids in the 14-3-3σ/ERα interface and locking the conformation with a spirocycle, the optimized covalent stabilizer 181 achieved potency, cooperativity, and selectivity similar to the natural product Fusicoccin-A. This case study showcases the value of addressing the structure, kinetics, and cooperativity for molecular glue development.
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Affiliation(s)
- Markella Konstantinidou
- Department
of Pharmaceutical Chemistry and Small Molecule Discovery Center (SMDC), University of California, San Francisco, California 94143, United States
| | - Emira J. Visser
- Laboratory
of Chemical Biology, Department of Biomedical Engineering and Institute
for Complex Molecular Systems (ICMS), Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Edmee Vandenboorn
- Laboratory
of Chemical Biology, Department of Biomedical Engineering and Institute
for Complex Molecular Systems (ICMS), Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Sheng Chen
- Department
of Pharmaceutical Chemistry and Small Molecule Discovery Center (SMDC), University of California, San Francisco, California 94143, United States
| | - Priyadarshini Jaishankar
- Department
of Pharmaceutical Chemistry and Small Molecule Discovery Center (SMDC), University of California, San Francisco, California 94143, United States
| | - Maurits Overmans
- Laboratory
of Chemical Biology, Department of Biomedical Engineering and Institute
for Complex Molecular Systems (ICMS), Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Shubhankar Dutta
- Department
of Pharmaceutical Chemistry and Small Molecule Discovery Center (SMDC), University of California, San Francisco, California 94143, United States
| | - R. Jeffrey Neitz
- Department
of Pharmaceutical Chemistry and Small Molecule Discovery Center (SMDC), University of California, San Francisco, California 94143, United States
| | - Adam R. Renslo
- Department
of Pharmaceutical Chemistry and Small Molecule Discovery Center (SMDC), University of California, San Francisco, California 94143, United States
| | - Christian Ottmann
- Laboratory
of Chemical Biology, Department of Biomedical Engineering and Institute
for Complex Molecular Systems (ICMS), Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Luc Brunsveld
- Laboratory
of Chemical Biology, Department of Biomedical Engineering and Institute
for Complex Molecular Systems (ICMS), Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Michelle R. Arkin
- Department
of Pharmaceutical Chemistry and Small Molecule Discovery Center (SMDC), University of California, San Francisco, California 94143, United States
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9
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Murabito A, Bhatt J, Ghigo A. It Takes Two to Tango! Protein-Protein Interactions behind cAMP-Mediated CFTR Regulation. Int J Mol Sci 2023; 24:10538. [PMID: 37445715 DOI: 10.3390/ijms241310538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/16/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
Over the last fifteen years, with the approval of the first molecular treatments, a breakthrough era has begun for patients with cystic fibrosis (CF), the rare genetic disease caused by mutations in the gene encoding the cystic fibrosis transmembrane conductance regulator (CFTR). These molecules, known as CFTR modulators, have led to unprecedented improvements in the lung function and quality of life of most CF patients. However, the efficacy of these drugs is still suboptimal, and the clinical response is highly variable even among individuals bearing the same mutation. Furthermore, not all patients carrying rare CFTR mutations are eligible for CFTR modulator therapies, indicating the need for alternative and/or add-on therapeutic approaches. Because the second messenger 3',5'-cyclic adenosine monophosphate (cAMP) represents the primary trigger for CFTR activation and a major regulator of different steps of the life cycle of the channel, there is growing interest in devising ways to fine-tune the cAMP signaling pathway for therapeutic purposes. This review article summarizes current knowledge regarding the role of cAMP signalosomes, i.e., multiprotein complexes bringing together key enzymes of the cAMP pathway, in the regulation of CFTR function, and discusses how modulating this signaling cascade could be leveraged for therapeutic intervention in CF.
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Affiliation(s)
- Alessandra Murabito
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Torino, 10126 Torino, Italy
| | - Janki Bhatt
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Torino, 10126 Torino, Italy
- Kither Biotech S.r.l., 10126 Torino, Italy
| | - Alessandra Ghigo
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Torino, 10126 Torino, Italy
- Kither Biotech S.r.l., 10126 Torino, Italy
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10
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Vinueza-Gavilanes R, Bravo-González JJ, Basurco L, Boncristiani C, Fernández-Irigoyen J, Santamaría E, Marcilla I, Pérez-Mediavilla A, Luquin MR, Vales A, González-Aseguinolaza G, Aymerich MS, Aragón T, Arrasate M. Stabilization of 14-3-3 protein-protein interactions with Fusicoccin-A decreases alpha-synuclein dependent cell-autonomous death in neuronal and mouse models. Neurobiol Dis 2023:106166. [PMID: 37245833 DOI: 10.1016/j.nbd.2023.106166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 05/19/2023] [Accepted: 05/21/2023] [Indexed: 05/30/2023] Open
Abstract
Synucleinopathies are a group of neurodegenerative diseases without effective treatment characterized by the abnormal aggregation of alpha-synuclein (aSyn) protein. Changes in levels or in the amino acid sequence of aSyn (by duplication/triplication of the aSyn gene or point mutations in the encoding region) cause familial cases of synucleinopathies. However, the specific molecular mechanisms of aSyn-dependent toxicity remain unclear. Increased aSyn protein levels or pathological mutations may favor abnormal protein-protein interactions (PPIs) that could either promote neuronal death or belong to a coping response program against neurotoxicity. Therefore, the identification and modulation of aSyn-dependent PPIs can provide new therapeutic targets for these diseases. To identify aSyn-dependent PPIs we performed a proximity biotinylation assay based on the promiscuous biotinylase BioID2. When expressed as a fusion protein, BioID2 biotinylates by proximity stable and transient interacting partners, allowing their identification by streptavidin affinity purification and mass spectrometry. The aSyn interactome was analyzed using BioID2-tagged wild-type (WT) and pathological mutant E46K aSyn versions in HEK293 cells. We found the 14-3-3 epsilon isoform as a common protein interactor for WT and E46K aSyn. 14-3-3 epsilon correlates with aSyn protein levels in brain regions of a transgenic mouse model overexpressing WT human aSyn. Using a neuronal model in which aSyn cell-autonomous toxicity is quantitatively scored by longitudinal survival analysis, we found that stabilization of 14-3-3 protein-proteins interactions with Fusicoccin-A (FC-A) decreases aSyn-dependent toxicity. Furthermore, FC-A treatment protects dopaminergic neuronal somas in the substantia nigra of a Parkinson's disease mouse model. Based on these results, we propose that the stabilization of 14-3-3 epsilon interaction with aSyn might reduce aSyn toxicity, and highlight FC-A as a potential therapeutic compound for synucleinopathies.
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Affiliation(s)
- Rodrigo Vinueza-Gavilanes
- Gene Therapy and Regulation of Gene Expression Program, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain.
| | - Jorge Juan Bravo-González
- Gene Therapy and Regulation of Gene Expression Program, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain.
| | - Leyre Basurco
- Gene Therapy and Regulation of Gene Expression Program, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain; Biochemistry and Genetics Department, School of Sciences, University of Navarra, Pamplona, Spain.
| | | | - Joaquín Fernández-Irigoyen
- Proteored-Institute of Health Carlos III (ISCIII), Clinical Neuroproteomics Unit, Navarrabiomed, Navarra Health Department, Public University of Navarra, Pamplona, Spain; IdiSNA (Navarra Institute for Health Research), Pamplona, Spain.
| | - Enrique Santamaría
- Proteored-Institute of Health Carlos III (ISCIII), Clinical Neuroproteomics Unit, Navarrabiomed, Navarra Health Department, Public University of Navarra, Pamplona, Spain; IdiSNA (Navarra Institute for Health Research), Pamplona, Spain.
| | - Irene Marcilla
- Gene Therapy and Regulation of Gene Expression Program, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain; IdiSNA (Navarra Institute for Health Research), Pamplona, Spain.
| | - Alberto Pérez-Mediavilla
- Gene Therapy and Regulation of Gene Expression Program, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain; Biochemistry and Genetics Department, School of Sciences, University of Navarra, Pamplona, Spain; IdiSNA (Navarra Institute for Health Research), Pamplona, Spain.
| | - María Rosario Luquin
- Department of Neurology, Clínica Universidad de Navarra, University of Navarra, Pamplona, Spain; IdiSNA (Navarra Institute for Health Research), Pamplona, Spain.
| | - Africa Vales
- Gene Therapy and Regulation of Gene Expression Program, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain; IdiSNA (Navarra Institute for Health Research), Pamplona, Spain.
| | - Gloria González-Aseguinolaza
- Gene Therapy and Regulation of Gene Expression Program, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain; IdiSNA (Navarra Institute for Health Research), Pamplona, Spain.
| | - María Soledad Aymerich
- Gene Therapy and Regulation of Gene Expression Program, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain; Biochemistry and Genetics Department, School of Sciences, University of Navarra, Pamplona, Spain; IdiSNA (Navarra Institute for Health Research), Pamplona, Spain.
| | - Tomás Aragón
- Gene Therapy and Regulation of Gene Expression Program, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain; IdiSNA (Navarra Institute for Health Research), Pamplona, Spain.
| | - Montserrat Arrasate
- Gene Therapy and Regulation of Gene Expression Program, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain; Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, Pamplona, Spain; IdiSNA (Navarra Institute for Health Research), Pamplona, Spain.
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11
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Somsen BA, Sijbesma E, Leysen S, Honzejkova K, Visser EJ, Cossar PJ, Obšil T, Brunsveld L, Ottmann C. Molecular basis and dual ligand regulation of tetrameric Estrogen Receptor α/14-3-3ζ protein complex. J Biol Chem 2023:104855. [PMID: 37224961 PMCID: PMC10302166 DOI: 10.1016/j.jbc.2023.104855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 05/26/2023] Open
Abstract
Therapeutic strategies targeting Nuclear Receptors (NRs) beyond their endogenous ligand binding pocket have gained significant scientific interest, driven by a need to circumvent problems associated with drug resistance and pharmacological profile. The hub protein 14-3-3 is an endogenous regulator of various NRs, providing a novel entry point for small molecule modulation of NR activity. Exemplified, 14-3-3 binding to the C-terminal F-domain of the Estrogen Receptor alpha (ERα), and small molecule stabilization of the ERα/14-3-3ζ protein complex by the natural product Fusicoccin A (FC-A), was demonstrated to downregulate ERα-mediated breast cancer proliferation. This presents a novel drug discovery approach to target ERα, however, structural and mechanistic insights into ERα/14-3-3 complex formation are lacking. Here, we provide an in-depth molecular understanding of the ERα/14-3-3ζ complex by isolating 14-3-3ζ in complex with an ERα protein construct comprising its Ligand Binding Domain (LBD) and phosphorylated F-domain. Bacterial co-expression and co-purification of the ERα/14-3-3ζ complex, followed by extensive biophysical and structural characterization, revealed a tetrameric complex between the ERα homodimer and the 14-3-3ζ homodimer. 14-3-3ζ binding to ERα, and ERα/14-3-3ζ complex stabilization by FC-A, appeared to be orthogonal to ERα endogenous agonist (E2) binding, E2-induced conformational changes, and cofactor recruitment. Similarly, the ERα antagonist 4-hydroxytamoxifen inhibited cofactor recruitment to the ERα LBD while ERα was bound to 14-3-3ζ. Furthermore, stabilization of the ERα/14-3-3ζ protein complex by FC-A was not influenced by the disease-associated and 4-hydroxytamoxifen resistant ERα-Y537S mutant. Together, these molecular and mechanistic insights provide direction for targeting ERα via the ERα/14-3-3 complex as an alternative drug discovery approach.
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Affiliation(s)
- Bente A Somsen
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB Eindhoven, The Netherlands
| | - Eline Sijbesma
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB Eindhoven, The Netherlands
| | - Seppe Leysen
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB Eindhoven, The Netherlands
| | - Karolina Honzejkova
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Emira J Visser
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB Eindhoven, The Netherlands
| | - Peter J Cossar
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB Eindhoven, The Netherlands
| | - Tomáš Obšil
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB Eindhoven, The Netherlands.
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB Eindhoven, The Netherlands.
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12
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Lau R, Hann MM, Ottmann C. Crystal structure and ligandability of the 14-3-3/pyrin interface. Biochem Biophys Res Commun 2023; 651:1-7. [PMID: 36774661 DOI: 10.1016/j.bbrc.2023.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/02/2023] [Accepted: 02/03/2023] [Indexed: 02/05/2023]
Abstract
Overactivation of Pyrin is the cause of the inflammatory diseases Mediterranean Fever and Pyrin-associated autoinflammation with neutrophilic dermatosis (PAAND). Binding of 14-3-3 proteins reduces the pro-inflammatory activity of Pyrin, hence small molecules that stabilize the Pyrin/14-3-3 complex could convey an anti-inflammatory effect. We have solved the atomic resolution crystal structures of phosphorylated peptides derived from PyrinpS208 and PyrinpS242 - the two principle 14-3-3 binding sites in Pyrin - in complex with 14-3-3 and analyzed the ligandability of these protein-peptide interfaces by crystal-based fragment soaking. The complex between 14-3-3 and PyrinpS242 appears to be much more amenable for small-molecule binding than that of 14-3-3/PyrinpS208. Consequently, only for the 14-3-3/PyrinpS242 complex could we find an interface-binding fragment, validating protein crystallography and fragment soaking as a method to evaluate the ligandability of protein surfaces.
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Affiliation(s)
- Roxanne Lau
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Den Dolech 2, 5612 AZ, Eindhoven, the Netherlands
| | | | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Den Dolech 2, 5612 AZ, Eindhoven, the Netherlands.
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13
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Thurairajah B, Hudson AJ, Doveston RG. Contemporary biophysical approaches for studying 14-3-3 protein-protein interactions. Front Mol Biosci 2022; 9:1043673. [PMID: 36425654 PMCID: PMC9679655 DOI: 10.3389/fmolb.2022.1043673] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 10/24/2022] [Indexed: 06/28/2024] Open
Abstract
14-3-3 proteins are a family of regulatory hubs that function through a vast network of protein-protein interactions. Their dysfunction or dysregulation is implicated in a wide range of diseases, and thus they are attractive drug targets, especially for molecular glues that promote protein-protein interactions for therapeutic intervention. However, an incomplete understanding of the molecular mechanisms that underpin 14-3-3 function hampers progress in drug design and development. Biophysical methodologies are an essential element of the 14-3-3 analytical toolbox, but in many cases have not been fully exploited. Here, we present a contemporary review of the predominant biophysical techniques used to study 14-3-3 protein-protein interactions, with a focus on examples that address key questions and challenges in the 14-3-3 field.
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Affiliation(s)
| | | | - Richard G. Doveston
- Leicester Institute for Structural and Chemical Biology and School of Chemistry, University of Leicester, Leicester, United Kingdom
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14
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Structure-activity-relationship study of semi-synthetically modified fusicoccins on their stabilization effect for 14-3-3-phospholigand interactions. Bioorg Med Chem 2022; 73:117020. [DOI: 10.1016/j.bmc.2022.117020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/12/2022] [Accepted: 09/13/2022] [Indexed: 11/19/2022]
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15
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Obsilova V, Obsil T. Structural insights into the functional roles of 14-3-3 proteins. Front Mol Biosci 2022; 9:1016071. [PMID: 36188227 PMCID: PMC9523730 DOI: 10.3389/fmolb.2022.1016071] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/02/2022] [Indexed: 12/02/2022] Open
Abstract
Signal transduction cascades efficiently transmit chemical and/or physical signals from the extracellular environment to intracellular compartments, thereby eliciting an appropriate cellular response. Most often, these signaling processes are mediated by specific protein-protein interactions involving hundreds of different receptors, enzymes, transcription factors, and signaling, adaptor and scaffolding proteins. Among them, 14-3-3 proteins are a family of highly conserved scaffolding molecules expressed in all eukaryotes, where they modulate the function of other proteins, primarily in a phosphorylation-dependent manner. Through these binding interactions, 14-3-3 proteins participate in key cellular processes, such as cell-cycle control, apoptosis, signal transduction, energy metabolism, and protein trafficking. To date, several hundreds of 14-3-3 binding partners have been identified, including protein kinases, phosphatases, receptors and transcription factors, which have been implicated in the onset of various diseases. As such, 14-3-3 proteins are promising targets for pharmaceutical interventions. However, despite intensive research into their protein-protein interactions, our understanding of the molecular mechanisms whereby 14-3-3 proteins regulate the functions of their binding partners remains insufficient. This review article provides an overview of the current state of the art of the molecular mechanisms whereby 14-3-3 proteins regulate their binding partners, focusing on recent structural studies of 14-3-3 protein complexes.
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Affiliation(s)
- Veronika Obsilova
- Institute of Physiology of the Czech Academy of Sciences, Laboratory of Structural Biology of Signaling Proteins, Division BIOCEV, Vestec, Czechia
- *Correspondence: Veronika Obsilova, ; Tomas Obsil,
| | - Tomas Obsil
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Prague, Czechia
- *Correspondence: Veronika Obsilova, ; Tomas Obsil,
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16
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Srdanović S, Wolter M, Trinh CH, Ottmann C, Warriner SL, Wilson AJ. Understanding the interaction of 14-3-3 proteins with hDMX and hDM2: a structural and biophysical study. FEBS J 2022; 289:5341-5358. [PMID: 35286747 PMCID: PMC9541495 DOI: 10.1111/febs.16433] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/11/2022] [Accepted: 03/11/2022] [Indexed: 01/06/2023]
Abstract
p53 plays a critical role in regulating diverse biological processes: DNA repair, cell cycle arrest, apoptosis and senescence. The p53 pathway has therefore served as the focus of multiple drug-discovery efforts. p53 is negatively regulated by hDMX and hDM2; prior studies have identified 14-3-3 proteins as hDMX and hDM2 client proteins. 14-3-3 proteins are adaptor proteins that modulate localization, degradation and interactions of their targets in response to phosphorylation. Thus, 14-3-3 proteins may indirectly modulate the interaction between hDMX or hDM2 and p53 and represent potential targets for modulation of the p53 pathway. In this manuscript, we report on the biophysical and structural characterization of peptide/protein interactions that are representative of the interaction between 14-3-3 and hDMX or hDM2. The data establish that proximal phosphosites spaced ~20-25 residues apart in both hDMX and hDM2 co-operate to facilitate high-affinity 14-3-3 binding and provide structural insight that can be utilized in future stabilizer/inhibitor discovery efforts.
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Affiliation(s)
- Sonja Srdanović
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsUK,School of ChemistryUniversity of LeedsUK
| | - Madita Wolter
- Laboratory of Chemical BiologyDepartment of Biomedical EngineeringTechnische Universiteit EindhovenThe Netherlands,Institute for Complex Molecular SystemsTechnische Universiteit EindhovenThe Netherlands
| | - Chi H. Trinh
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsUK,School of Molecular and Cellular BiologyUniversity of LeedsUK
| | - Christian Ottmann
- Laboratory of Chemical BiologyDepartment of Biomedical EngineeringTechnische Universiteit EindhovenThe Netherlands,Institute for Complex Molecular SystemsTechnische Universiteit EindhovenThe Netherlands
| | - Stuart L. Warriner
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsUK,School of ChemistryUniversity of LeedsUK
| | - Andrew J. Wilson
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsUK,School of ChemistryUniversity of LeedsUK
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17
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Stevers LM, Wolter M, Carlile GW, Macdonald D, Richard L, Gielkens F, Hanrahan JW, Thomas DY, Chakka SK, Peterson ML, Thomas H, Brunsveld L, Ottmann C. Macrocycle-stabilization of its interaction with 14-3-3 increases plasma membrane localization and activity of CFTR. Nat Commun 2022; 13:3586. [PMID: 35739107 PMCID: PMC9226124 DOI: 10.1038/s41467-022-31206-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 06/07/2022] [Indexed: 11/09/2022] Open
Abstract
Impaired activity of the chloride channel CFTR is the cause of cystic fibrosis. 14-3-3 proteins have been shown to stabilize CFTR and increase its biogenesis and activity. Here, we report the identification and mechanism of action of a macrocycle stabilizing the 14-3-3/CFTR complex. This molecule rescues plasma membrane localization and chloride transport of F508del-CFTR and works additively with the CFTR pharmacological chaperone corrector lumacaftor (VX-809) and the triple combination Trikafta®. This macrocycle is a useful tool to study the CFTR/14-3-3 interaction and the potential of molecular glues in cystic fibrosis therapeutics.
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Affiliation(s)
- Loes M Stevers
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Madita Wolter
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Graeme W Carlile
- Cystic Fibrosis Translational Research Centre, Department of Biochemistry and Physiology, McGill University, Montreal, QC, Canada
| | - Dwight Macdonald
- Cyclenium Pharma Inc., 7171 rue Frederick Banting, Montreal, Quebec, Canada
| | - Luc Richard
- Cyclenium Pharma Inc., 7171 rue Frederick Banting, Montreal, Quebec, Canada
| | - Frank Gielkens
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - John W Hanrahan
- Cystic Fibrosis Translational Research Centre, Department of Biochemistry and Physiology, McGill University, Montreal, QC, Canada
| | - David Y Thomas
- Cystic Fibrosis Translational Research Centre, Department of Biochemistry and Physiology, McGill University, Montreal, QC, Canada
| | - Sai Kumar Chakka
- Cyclenium Pharma Inc., 7171 rue Frederick Banting, Montreal, Quebec, Canada
| | - Mark L Peterson
- Cyclenium Pharma Inc., 7171 rue Frederick Banting, Montreal, Quebec, Canada
| | - Helmut Thomas
- Cyclenium Pharma Inc., 7171 rue Frederick Banting, Montreal, Quebec, Canada
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands.
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18
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Soini L, Leysen S, Davis J, Ottmann C. Molecular glues to stabilise protein-protein interactions. Curr Opin Chem Biol 2022; 69:102169. [PMID: 35749929 DOI: 10.1016/j.cbpa.2022.102169] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 04/21/2022] [Accepted: 05/11/2022] [Indexed: 11/27/2022]
Abstract
Targeting protein-protein interactions (PPIs) has become a common approach to tackle various diseases whose pathobiology is driven by their mis-regulation in important signalling pathways. Modulating PPIs has tremendous untapped therapeutic potential and different approaches can be used to modulate PPIs. Initially, therapeutic effects were mostly sought by inhibiting PPIs. However, by gaining insight in the mode of action of certain therapeutic compounds, it became clear that stabilising (i.e. enhancing) PPIs can also be useful. The latter strategy is recently gaining a lot of attention, as stabilising physiologic, or even inducing novel interactions of a target protein with E3 ubiquitin ligases forms the basis of the targeted protein degradation (TPD) approach. An emerging additional example for drug discovery based on PPI stabilisation are the 14-3-3 proteins, a family of regulatory proteins, which engages in many protein-protein interactions, some of which might become therapeutical targets.
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Affiliation(s)
- Lorenzo Soini
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, the Netherlands; Department of Structural Biology and Biophysics, UCB Biopharma UK, Slough, UK
| | - Seppe Leysen
- Department of Structural Biology and Biophysics, UCB Biopharma UK, Slough, UK
| | - Jeremy Davis
- Department of Chemistry, UCB Biopharma UK, Slough, UK.
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, the Netherlands.
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19
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Lankford C, Houtman J, Baker SA. Identification of HCN1 as a 14-3-3 client. PLoS One 2022; 17:e0268335. [PMID: 35679272 PMCID: PMC9182292 DOI: 10.1371/journal.pone.0268335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 04/28/2022] [Indexed: 11/19/2022] Open
Abstract
Hyperpolarization activated cyclic nucleotide-gated channel 1 (HCN1) is expressed throughout the nervous system and is critical for regulating neuronal excitability, with mutations being associated with multiple forms of epilepsy. Adaptive modulation of HCN1 has been observed, as has pathogenic dysregulation. While the mechanisms underlying this modulation remain incompletely understood, regulation of HCN1 has been shown to include phosphorylation. A candidate phosphorylation-dependent regulator of HCN1 channels is 14-3-3. We used bioinformatics to identify three potential 14-3-3 binding sites in HCN1. We confirmed that 14-3-3 could pull down HCN1 from multiple tissue sources and used HEK293 cells to detail the interaction. Two sites in the intrinsically disordered C-terminus of HCN1 were necessary and sufficient for a phosphorylation-dependent interaction with 14-3-3. The same region of HCN1 containing the 14-3-3 binding peptides is required for phosphorylation-independent protein degradation. We propose a model in which phosphorylation of mouse S810 and S867 (human S789 and S846) recruits 14-3-3 to inhibit a yet unidentified factor signaling for protein degradation, thus increasing the half-life of HCN1.
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Affiliation(s)
- Colten Lankford
- Department of Biochemistry and Molecular Biology, University of Iowa, Iowa City, Iowa, United States of America
| | - Jon Houtman
- Department of Microbiology and Immunology, University of Iowa, Iowa City, Iowa, United States of America
| | - Sheila A. Baker
- Department of Biochemistry and Molecular Biology, University of Iowa, Iowa City, Iowa, United States of America
- * E-mail:
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Abstract
AbstractThe druggable genome is limited by structural features that can be targeted by small molecules in disease-relevant proteins. While orthosteric and allosteric protein modulators have been well studied, they are limited to antagonistic/agonistic functions. This approach to protein modulation leaves many disease-relevant proteins as undruggable targets. Recently, protein-protein interaction modulation has emerged as a promising therapeutic field for previously undruggable protein targets. Molecular glues and heterobifunctional degraders such as PROTACs can facilitate protein interactions and bring the proteasome into proximity to induce targeted protein degradation. In this review, we discuss the function and rational design of molecular glues, heterobifunctional degraders, and hydrophobic tag degraders. We also review historic and novel molecular glues and targets and discuss the challenges and opportunities in this new therapeutic field.
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21
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T. S. S, Dalvi S, Venkatraman P, Vemparala S. Structural insights on the effects of mutation of a charged binding pocket residue on phosphopeptide binding to 14‐3‐3ζ protein. Proteins 2022; 90:1179-1189. [DOI: 10.1002/prot.26300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 12/25/2021] [Accepted: 12/29/2021] [Indexed: 10/19/2022]
Affiliation(s)
- Sreevidya T. S.
- The Institute of Mathematical Sciences Chennai India
- Homi Bhabha National Institute Mumbai India
| | - Somavally Dalvi
- Protein Interactome Lab for Structural and Functional Biology Advanced Centre for Treatment, Research and Education in Cancer Navi Mumbai India
| | - Prasanna Venkatraman
- Homi Bhabha National Institute Mumbai India
- Protein Interactome Lab for Structural and Functional Biology Advanced Centre for Treatment, Research and Education in Cancer Navi Mumbai India
| | - Satyavani Vemparala
- The Institute of Mathematical Sciences Chennai India
- Homi Bhabha National Institute Mumbai India
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22
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Tang R, Chen P, Wang Z, Wang L, Hao H, Hou T, Sun H. Characterizing the stabilization effects of stabilizers in protein-protein systems with end-point binding free energy calculations. Brief Bioinform 2022; 23:6565618. [PMID: 35395683 DOI: 10.1093/bib/bbac127] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/10/2022] [Accepted: 03/15/2022] [Indexed: 02/06/2023] Open
Abstract
Drug design targeting protein-protein interactions (PPIs) associated with the development of diseases has been one of the most important therapeutic strategies. Besides interrupting the PPIs with PPI inhibitors/blockers, increasing evidence shows that stabilizing the interaction between two interacting proteins may also benefit the therapy, such as the development of various types of molecular glues/stabilizers that mostly work by stabilizing the two interacting proteins to regulate the downstream biological effects. However, characterizing the stabilization effect of a stabilizer is usually hard or too complicated for traditional experiments since it involves ternary interactions [protein-protein-stabilizer (PPS) interaction]. Thus, developing reliable computational strategies will facilitate the discovery/design of molecular glues or PPI stabilizers. Here, by fully analyzing the energetic features of the binary interactions in the PPS ternary complex, we systematically investigated the performance of molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) and molecular mechanics generalized Born surface area (MM/GBSA) methods on characterizing the stabilization effects of stabilizers in 14-3-3 systems. The results show that both MM/PBSA and MM/GBSA are powerful tools in distinguishing the stabilizers from the decoys (with area under the curves of 0.90-0.93 for all tested cases) and are reasonable for ranking protein-peptide interactions in the presence or absence of stabilizers as well (with the average Pearson correlation coefficient of ~0.6 at a relatively high dielectric constant for both methods). Moreover, to give a detailed picture of the stabilization effects, the stabilization mechanism is also analyzed from the structural and energetic points of view for individual systems containing strong or weak stabilizers. This study demonstrates a potential strategy to accelerate the discovery of PPI stabilizers.
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Affiliation(s)
- Rongfan Tang
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, Jiangsu, P. R. China
| | - Pengcheng Chen
- Institute of Big Data and Artificial Intelligence in Medicine, School of Electronics and Information Engineering, Taizhou University, Taizhou 318000, Zhejiang, P. R. China
| | - Zhe Wang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China
| | - Lingling Wang
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, Jiangsu, P. R. China
| | - Haiping Hao
- State Key Laboratory of Natural Medicines, Key Lab of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, 210009 Nanjing, China
| | - Tingjun Hou
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China
| | - Huiyong Sun
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, Jiangsu, P. R. China
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23
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Abstract
The 14-3-3 family proteins are vital scaffold proteins that ubiquitously expressed in various tissues. They interact with numerous protein targets and mediate many cellular signaling pathways. The 14-3-3 binding motifs are often embedded in intrinsically disordered regions which are closely associated with liquid-liquid phase separation (LLPS). In the past ten years, LLPS has been observed for a variety of proteins and biological processes, indicating that LLPS plays a fundamental role in the formation of membraneless organelles and cellular condensates. While extensive investigations have been performed on 14-3-3 proteins, its involvement in LLPS is overlooked. To date, 14-3-3 proteins have not been reported to undergo LLPS alone or regulate LLPS of their binding partners. To reveal the potential involvement of 14-3-3 proteins in LLPS, in this review, we summarized the LLPS propensity of 14-3-3 binding partners and found that about one half of them may undergo LLPS spontaneously. We further analyzed the phase separation behavior of representative 14-3-3 binders and discussed how 14-3-3 proteins may be involved. By modulating the conformation and valence of interactions and recruiting other molecules, we speculate that 14-3-3 proteins can efficiently regulate the functions of their targets in the context of LLPS. Considering the critical roles of 14-3-3 proteins, there is an urgent need for investigating the involvement of 14-3-3 proteins in the phase separation process of their targets and the underling mechanisms.
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24
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Fragment-based exploration of the 14-3-3/Amot-p130 interface. Curr Res Struct Biol 2022; 4:21-28. [PMID: 35036934 PMCID: PMC8743172 DOI: 10.1016/j.crstbi.2021.12.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 12/06/2021] [Accepted: 12/20/2021] [Indexed: 02/06/2023] Open
Abstract
The modulation of protein-protein interactions (PPIs) has developed into a well-established field of drug discovery. Despite the advances achieved in the field, many PPIs are still deemed as ‘undruggable’ targets and the design of PPIs stabilizers remains a significant challenge. The application of fragment-based methods for the identification of drug leads and to evaluate the ‘tractability’ of the desired protein target has seen a remarkable development in recent years. In this study, we explore the molecular characteristics of the 14-3-3/Amot-p130 PPI and the conceptual possibility of targeting this interface using X-ray crystallography fragment-based screening. We report the first structural elucidation of the 14-3-3 binding motif of Amot-p130 and the characterization of the binding mode and affinities involved. We made use of fragments to probe the ‘ligandability’ of the 14-3-3/Amot-p130 composite binding pocket. Here we disclose initial hits with promising stabilizing activity and an early-stage selectivity toward the Amot-p130 motifs over other representatives 14-3-3 partners. Our findings highlight the potential of using fragments to characterize and explore proteins' surfaces and might provide a starting point toward the development of small molecules capable of acting as molecular glues. Phosphorylation of Ser 175 mediates binding of Amot-p130 to 14-3-3. The crystal structure of the 14-3-3σΔC/Amot-p130 peptide complex describes the interface. A fragment-based exploration of the interface assesses ‘ligandability’. Fragments binding at the 14-3-3/Amot-p130 interface display an initial stabilizing activity.
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Key Words
- 14-3-3 /protein-protein interactions stabilizers
- AIP4, Atrophin-1 interacting protein 4
- Amot, Angiomotin
- Amot-p130
- AmotL1/2, Angiomotin-like 1/2
- FBDD, Fragment-based drug discovery
- FP, Fluorescence polarization
- Fragment-based drug discovery
- Lats 1/2, Large tumor suppressor 1/2
- Ligandability
- MST, Microscale thermophoresis
- PPI, Protein-protein interaction
- PTMs, post-translational modifications
- X-ray crystallography
- YAP1, Yes-associated protein 1
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25
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Nietert MM, Vinhoven L, Auer F, Hafkemeyer S, Stanke F. Comprehensive Analysis of Chemical Structures That Have Been Tested as CFTR Activating Substances in a Publicly Available Database CandActCFTR. Front Pharmacol 2021; 12:689205. [PMID: 34955819 PMCID: PMC8692862 DOI: 10.3389/fphar.2021.689205] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 11/08/2021] [Indexed: 01/02/2023] Open
Abstract
Background: Cystic fibrosis (CF) is a genetic disease caused by mutations in CFTR, which encodes a chloride and bicarbonate transporter expressed in exocrine epithelia throughout the body. Recently, some therapeutics became available that directly target dysfunctional CFTR, yet research for more effective substances is ongoing. The database CandActCFTR aims to provide detailed and comprehensive information on candidate therapeutics for the activation of CFTR-mediated ion conductance aiding systems-biology approaches to identify substances that will synergistically activate CFTR-mediated ion conductance based on published data. Results: Until 10/2020, we derived data from 108 publications on 3,109 CFTR-relevant substances via the literature database PubMed and further 666 substances via ChEMBL; only 19 substances were shared between these sources. One hundred and forty-five molecules do not have a corresponding entry in PubChem or ChemSpider, which indicates that there currently is no single comprehensive database on chemical substances in the public domain. Apart from basic data on all compounds, we have visualized the chemical space derived from their chemical descriptors via a principal component analysis annotated for CFTR-relevant biological categories. Our online query tools enable the search for most similar compounds and provide the relevant annotations in a structured way. The integration of the KNIME software environment in the back-end facilitates a fast and user-friendly maintenance of the provided data sets and a quick extension with new functionalities, e.g., new analysis routines. CandActBase automatically integrates information from other online sources, such as synonyms from PubChem and provides links to other resources like ChEMBL or the source publications. Conclusion: CandActCFTR aims to establish a database model of candidate cystic fibrosis therapeutics for the activation of CFTR-mediated ion conductance to merge data from publicly available sources. Using CandActBase, our strategy to represent data from several internet resources in a merged and organized form can also be applied to other use cases. For substances tested as CFTR activating compounds, the search function allows users to check if a specific compound or a closely related substance was already tested in the CF field. The acquired information on tested substances will assist in the identification of the most promising candidates for future therapeutics.
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Affiliation(s)
- Manuel Manfred Nietert
- Department of Medical Bioinformatics, University Medical Center Göttingen, Göttingen, Germany.,CIDAS Campus Institute Data Science, Georg-August-University, Göttingen, Germany
| | - Liza Vinhoven
- Department of Medical Bioinformatics, University Medical Center Göttingen, Göttingen, Germany
| | - Florian Auer
- Institute for Informatics, University of Augsburg, Augsburg, Germany
| | | | - Frauke Stanke
- German Center for Lung Research (DZL), Partner Site BREATH, Hannover, Germany.,Clinic for Pediatric Pneumology, Allergology, and Neonatology, Hannover Medical School, Hannover, Germany
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26
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Yokoi N, Fukata Y, Okatsu K, Yamagata A, Liu Y, Sanbo M, Miyazaki Y, Goto T, Abe M, Kassai H, Sakimura K, Meijer D, Hirabayashi M, Fukai S, Fukata M. 14-3-3 proteins stabilize LGI1-ADAM22 levels to regulate seizure thresholds in mice. Cell Rep 2021; 37:110107. [PMID: 34910912 DOI: 10.1016/j.celrep.2021.110107] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 10/08/2021] [Accepted: 11/16/2021] [Indexed: 01/17/2023] Open
Abstract
What percentage of the protein function is required to prevent disease symptoms is a fundamental question in genetic disorders. Decreased transsynaptic LGI1-ADAM22 protein complexes, because of their mutations or autoantibodies, cause epilepsy and amnesia. However, it remains unclear how LGI1-ADAM22 levels are regulated and how much LGI1-ADAM22 function is required. Here, by genetic and structural analysis, we demonstrate that quantitative dual phosphorylation of ADAM22 by protein kinase A (PKA) mediates high-affinity binding of ADAM22 to dimerized 14-3-3. This interaction protects LGI1-ADAM22 from endocytosis-dependent degradation. Accordingly, forskolin-induced PKA activation increases ADAM22 levels. Leveraging a series of ADAM22 and LGI1 hypomorphic mice, we find that ∼50% of LGI1 and ∼10% of ADAM22 levels are sufficient to prevent lethal epilepsy. Furthermore, ADAM22 function is required in excitatory and inhibitory neurons. These results suggest strategies to increase LGI1-ADAM22 complexes over the required levels by targeting PKA or 14-3-3 for epilepsy treatment.
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Affiliation(s)
- Norihiko Yokoi
- Division of Membrane Physiology, Department of Molecular and Cellular Physiology, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan; Department of Physiological Sciences, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan
| | - Yuko Fukata
- Division of Membrane Physiology, Department of Molecular and Cellular Physiology, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan; Department of Physiological Sciences, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan.
| | - Kei Okatsu
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Atsushi Yamagata
- RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa 230-0045, Japan
| | - Yan Liu
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Makoto Sanbo
- Center for Genetic Analysis of Behavior, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
| | - Yuri Miyazaki
- Division of Membrane Physiology, Department of Molecular and Cellular Physiology, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan; Department of Physiological Sciences, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan
| | - Teppei Goto
- Center for Genetic Analysis of Behavior, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
| | - Manabu Abe
- Department of Animal Model Development, Brain Research Institute, Niigata University, Niigata 951-8585, Japan
| | - Hidetoshi Kassai
- Laboratory of Animal Resources, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Kenji Sakimura
- Department of Animal Model Development, Brain Research Institute, Niigata University, Niigata 951-8585, Japan
| | - Dies Meijer
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Masumi Hirabayashi
- Department of Physiological Sciences, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan; Center for Genetic Analysis of Behavior, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
| | - Shuya Fukai
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Masaki Fukata
- Division of Membrane Physiology, Department of Molecular and Cellular Physiology, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan; Department of Physiological Sciences, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan.
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27
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Ecsédi P, Gógl G, Nyitray L. Studying the Structures of Relaxed and Fuzzy Interactions: The Diverse World of S100 Complexes. Front Mol Biosci 2021; 8:749052. [PMID: 34708078 PMCID: PMC8542695 DOI: 10.3389/fmolb.2021.749052] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/06/2021] [Indexed: 01/04/2023] Open
Abstract
S100 proteins are small, dimeric, Ca2+-binding proteins of considerable interest due to their associations with cancer and rheumatic and neurodegenerative diseases. They control the functions of numerous proteins by forming protein–protein complexes with them. Several of these complexes were found to display “fuzzy” properties. Examining these highly flexible interactions, however, is a difficult task, especially from a structural biology point of view. Here, we summarize the available in vitro techniques that can be deployed to obtain structural information about these dynamic complexes. We also review the current state of knowledge about the structures of S100 complexes, focusing on their often-asymmetric nature.
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Affiliation(s)
- Péter Ecsédi
- Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
| | - Gergő Gógl
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Université de Strasbourg, Illkirch, France
| | - László Nyitray
- Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
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28
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Falcicchio M, Ward JA, Chothia SY, Basran J, Mohindra A, Macip S, Roversi P, Doveston RG. Cooperative stabilisation of 14-3-3σ protein-protein interactions via covalent protein modification. Chem Sci 2021; 12:12985-12992. [PMID: 34745529 PMCID: PMC8513901 DOI: 10.1039/d1sc02120f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 09/05/2021] [Indexed: 12/19/2022] Open
Abstract
14-3-3 proteins are an important family of hub proteins that play important roles in many cellular processes via a large network of interactions with partner proteins. Many of these protein-protein interactions (PPI) are implicated in human diseases such as cancer and neurodegeneration. The stabilisation of selected 14-3-3 PPIs using drug-like 'molecular glues' is a novel therapeutic strategy with high potential. However, the examples reported to date have a number of drawbacks in terms of selectivity and potency. Here, we report that WR-1065, the active species of the approved drug amifostine, covalently modifies 14-3-3σ at an isoform-unique cysteine residue, Cys38. This modification leads to isoform-specific stabilisation of two 14-3-3σ PPIs in a manner that is cooperative with a well characterised molecular glue, fusicoccin A. Our findings reveal a novel stabilisation mechanism for 14-3-3σ, an isoform with particular involvement in cancer pathways. This mechanism can be exploited to harness the enhanced potency conveyed by covalent drug molecules and dual ligand cooperativity. This is demonstrated in two cancer cell lines whereby the cooperative behaviour of fusicoccin A and WR-1065 leads to enhanced efficacy for inducing cell death and attenuating cell growth.
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Affiliation(s)
- Marta Falcicchio
- Leicester Institute for Structural and Chemical Biology, University of Leicester University Road Leicester LE1 7RH UK .,School of Chemistry, University of Leicester University Road Leicester LE1 7RH UK
| | - Jake A Ward
- Leicester Institute for Structural and Chemical Biology, University of Leicester University Road Leicester LE1 7RH UK .,Mechanisms of Cancer and Aging Laboratory, Department of Molecular and Cell Biology, University of Leicester University Road Leicester LE1 7RH UK
| | - Sara Y Chothia
- Leicester Institute for Structural and Chemical Biology, University of Leicester University Road Leicester LE1 7RH UK .,School of Chemistry, University of Leicester University Road Leicester LE1 7RH UK
| | - Jaswir Basran
- Department of Molecular and Cell Biology, University of Leicester University Road Leicester LE1 7RH UK
| | - Alisha Mohindra
- Leicester Institute for Structural and Chemical Biology, University of Leicester University Road Leicester LE1 7RH UK .,School of Chemistry, University of Leicester University Road Leicester LE1 7RH UK
| | - Salvador Macip
- Mechanisms of Cancer and Aging Laboratory, Department of Molecular and Cell Biology, University of Leicester University Road Leicester LE1 7RH UK.,FoodLab, Faculty of Health Sciences, Universitat Oberta de Catalunya Barcelona Spain
| | - Pietro Roversi
- Leicester Institute for Structural and Chemical Biology, University of Leicester University Road Leicester LE1 7RH UK .,Department of Molecular and Cell Biology, University of Leicester University Road Leicester LE1 7RH UK.,Institute of Agricultural Biology and Biotechnology, IBBA-CNR Unit of Milano Via Bassini 15 I-20133 Milan Italy
| | - Richard G Doveston
- Leicester Institute for Structural and Chemical Biology, University of Leicester University Road Leicester LE1 7RH UK .,School of Chemistry, University of Leicester University Road Leicester LE1 7RH UK
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29
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Soini L, Redhead M, Westwood M, Leysen S, Davis J, Ottmann C. Identification of molecular glues of the SLP76/14-3-3 protein-protein interaction. RSC Med Chem 2021; 12:1555-1564. [PMID: 34667951 PMCID: PMC8459327 DOI: 10.1039/d1md00172h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/01/2021] [Indexed: 12/12/2022] Open
Abstract
The stabilisation of protein-protein interactions (PPIs) through molecular glues is a novel and promising approach in drug discovery. In stark contrast to research in protein-protein inhibition the field of stabilisation remains underdeveloped with comparatively few examples of small-molecule stabilisers of PPIs reported to date. At the same time identifying molecular glues has received recent sustained interest, especially in the fields of targeted protein degradation and 14-3-3 PPIs. The hub-protein 14-3-3 has a broad interactome with more than 500 known protein partners which presents a great opportunity for therapeutic intervention. In this study we have developed an HTRF assay suitable for HTS of the 14-3-3/SLP76 PPI and have completed a proof of concept screen against a chemically diverse library of 20 K molecules. The adaptor protein SLP76 has been reported to interact with 14-3-3 proteins downstream of the TCR playing an important role in mediating its own proteasomal degradation. We believe that stabilisation of this PPI could be exploited to potentiate degradation of SLP76 and therefore inhibit TCR signalling. This would represent an interesting alternative to other approaches in the field of targeted protein degradation. Here we disclose 16 novel stabilisers of the 14-3-3/SLP76 PPI across multiple different chemotypes. Based on the early results presented here we would recommend this approach to find molecular glues with broad applicability in the field of 14-3-3 PPIs.
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Affiliation(s)
- Lorenzo Soini
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology Eindhoven The Netherlands .,Department of Chemistry, UCB Celltech Slough UK
| | - Martin Redhead
- Exscientia Ltd, Schrodinger Building, Oxford Science Park Oxford OX44GE UK
| | - Marta Westwood
- Structural Biology, Discovery, Charles River, Chesterford Research Park UK
| | - Seppe Leysen
- Department of Structural Biology and Biophysics, UCB Celltech Slough UK
| | | | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology Eindhoven The Netherlands
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30
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Pathways to Parkinson's disease: a spotlight on 14-3-3 proteins. NPJ Parkinsons Dis 2021; 7:85. [PMID: 34548498 PMCID: PMC8455551 DOI: 10.1038/s41531-021-00230-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 07/23/2021] [Indexed: 02/08/2023] Open
Abstract
14-3-3s represent a family of highly conserved 30 kDa acidic proteins. 14-3-3s recognize and bind specific phospho-sequences on client partners and operate as molecular hubs to regulate their activity, localization, folding, degradation, and protein-protein interactions. 14-3-3s are also associated with the pathogenesis of several diseases, among which Parkinson's disease (PD). 14-3-3s are found within Lewy bodies (LBs) in PD patients, and their neuroprotective effects have been demonstrated in several animal models of PD. Notably, 14-3-3s interact with some of the major proteins known to be involved in the pathogenesis of PD. Here we first provide a detailed overview of the molecular composition and structural features of 14-3-3s, laying significant emphasis on their peculiar target-binding mechanisms. We then briefly describe the implication of 14-3-3s in the central nervous system and focus on their interaction with LRRK2, α-Synuclein, and Parkin, three of the major players in PD onset and progression. We finally discuss how different types of small molecules may interfere with 14-3-3s interactome, thus representing a valid strategy in the future of drug discovery.
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31
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The Surprising Story of Fusicoccin: A Wilt-Inducing Phytotoxin, a Tool in Plant Physiology and a 14-3-3-Targeted Drug. Biomolecules 2021; 11:biom11091393. [PMID: 34572605 PMCID: PMC8470340 DOI: 10.3390/biom11091393] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 09/07/2021] [Accepted: 09/15/2021] [Indexed: 12/13/2022] Open
Abstract
Fusicoccin is the α glucoside of a carbotricyclic diterpene, produced by the fungus Phomopsis amygdali (previously classified as Fusicoccum amygdali), the causal agent of almond and peach canker disease. A great interest in this molecule started when it was discovered that it brought about an irreversible stomata opening of higher plants, thereby inducing the wilting of their leaves. Since then, several studies were carried out to elucidate its biological activity, biosynthesis, structure, structure-activity relationships and mode of action. After sixty years of research and more than 1800 published articles, FC is still the most studied phytotoxin and one of the few whose mechanism of action has been elucidated in detail. The ability of FC to stimulate several fundamental plant processes depends on its ability to activate the plasma membrane H+-ATPase, induced by eliciting the association of 14-3-3 proteins, a class of regulatory molecules widespread in eukaryotes. This discovery renewed interest in FC and prompted more recent studies aimed to ascertain the ability of the toxin to influence the interaction between 14-3-3 proteins and their numerous client proteins in animals, involved in the regulation of basic cellular processes and in the etiology of different diseases, including cancer. This review covers the different aspects of FC research partially treated in different previous reviews, starting from its discovery in 1964, with the aim to outline the extraordinary pathway which led this very uncommon diterpenoid to evolve from a phytotoxin into a tool in plant physiology and eventually into a 14-3-3-targeted drug.
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32
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Leysen S, Burnley RJ, Rodriguez E, Milroy LG, Soini L, Adamski CJ, Nitschke L, Davis R, Obsil T, Brunsveld L, Crabbe T, Zoghbi HY, Ottmann C, Davis JM. A Structural Study of the Cytoplasmic Chaperone Effect of 14-3-3 Proteins on Ataxin-1. J Mol Biol 2021; 433:167174. [PMID: 34302818 PMCID: PMC8505757 DOI: 10.1016/j.jmb.2021.167174] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 12/20/2022]
Abstract
Expansion of the polyglutamine tract in the N terminus of Ataxin-1 is the main cause of the neurodegenerative disease, spinocerebellar ataxia type 1 (SCA1). However, the C-terminal part of the protein - including its AXH domain and a phosphorylation on residue serine 776 - also plays a crucial role in disease development. This phosphorylation event is known to be crucial for the interaction of Ataxin-1 with the 14-3-3 adaptor proteins and has been shown to indirectly contribute to Ataxin-1 stability. Here we show that 14-3-3 also has a direct anti-aggregation or "chaperone" effect on Ataxin-1. Furthermore, we provide structural and biophysical information revealing how phosphorylated S776 in the intrinsically disordered C terminus of Ataxin-1 mediates the cytoplasmic interaction with 14-3-3 proteins. Based on these findings, we propose that 14-3-3 exerts the observed chaperone effect by interfering with Ataxin-1 dimerization through its AXH domain, reducing further self-association. The chaperone effect is particularly important in the context of SCA1, as it was previously shown that a soluble form of mutant Ataxin-1 is the major driver of pathology.
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Affiliation(s)
- Seppe Leysen
- Global Chemistry, UCB Biopharma UK, Slough SL1 3WE, UK
| | | | | | - Lech-Gustav Milroy
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Eindhoven 5600 MB, the Netherlands
| | - Lorenzo Soini
- Global Chemistry, UCB Biopharma UK, Slough SL1 3WE, UK; Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Eindhoven 5600 MB, the Netherlands
| | - Carolyn J Adamski
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA
| | - Larissa Nitschke
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rachel Davis
- Global Chemistry, UCB Biopharma UK, Slough SL1 3WE, UK
| | - Tomas Obsil
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Prague 12843, Czech Republic
| | - Lucas Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Eindhoven 5600 MB, the Netherlands
| | - Tom Crabbe
- Immuno-Bone Discovery, UCB Biopharma UK, Slough SL1 3WE, UK
| | - Huda Yahya Zoghbi
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Eindhoven 5600 MB, the Netherlands
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Horvath M, Petrvalska O, Herman P, Obsilova V, Obsil T. 14-3-3 proteins inactivate DAPK2 by promoting its dimerization and protecting key regulatory phosphosites. Commun Biol 2021; 4:986. [PMID: 34413451 PMCID: PMC8376927 DOI: 10.1038/s42003-021-02518-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/03/2021] [Indexed: 01/05/2023] Open
Abstract
Death-associated protein kinase 2 (DAPK2) is a CaM-regulated Ser/Thr protein kinase, involved in apoptosis, autophagy, granulocyte differentiation and motility regulation, whose activity is controlled by autoinhibition, autophosphorylation, dimerization and interaction with scaffolding proteins 14-3-3. However, the structural basis of 14-3-3-mediated DAPK2 regulation remains unclear. Here, we structurally and biochemically characterize the full-length human DAPK2:14-3-3 complex by combining several biophysical techniques. The results from our X-ray crystallographic analysis revealed that Thr369 phosphorylation at the DAPK2 C terminus creates a high-affinity canonical mode III 14-3-3-binding motif, further enhanced by the diterpene glycoside Fusicoccin A. Moreover, concentration-dependent DAPK2 dimerization is disrupted by Ca2+/CaM binding and stabilized by 14-3-3 binding in solution, thereby protecting the DAPK2 inhibitory autophosphorylation site Ser318 against dephosphorylation and preventing Ca2+/CaM binding. Overall, our findings provide mechanistic insights into 14-3-3-mediated DAPK2 inhibition and highlight the potential of the DAPK2:14-3-3 complex as a target for anti‐inflammatory therapies. Horvath et al. structurally and biochemically characterize the full-length human DAPK2-14-3-3 complex to investigate the effects of binding to DAPK2 on its dimerization, activation by dephosphorylation of Ser318, and Ca2+/calmodulin binding. Their results provide mechanistic insights into 14- 3-3-mediated DAPK2 inhibition and highlight the potential of the DAPK2:14-3-3 complex as a target for anti-inflammatory therapies.
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Affiliation(s)
- Matej Horvath
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Prague, Czech Republic.,Department of Structural Biology of Signaling Proteins, Division BIOCEV, Institute of Physiology of the Czech Academy of Sciences, Vestec, Czech Republic
| | - Olivia Petrvalska
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Prague, Czech Republic.,Department of Structural Biology of Signaling Proteins, Division BIOCEV, Institute of Physiology of the Czech Academy of Sciences, Vestec, Czech Republic
| | - Petr Herman
- Institute of Physics, Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic
| | - Veronika Obsilova
- Department of Structural Biology of Signaling Proteins, Division BIOCEV, Institute of Physiology of the Czech Academy of Sciences, Vestec, Czech Republic.
| | - Tomas Obsil
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Prague, Czech Republic. .,Department of Structural Biology of Signaling Proteins, Division BIOCEV, Institute of Physiology of the Czech Academy of Sciences, Vestec, Czech Republic.
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Soini L, Leysen S, Crabbe T, Davis J, Ottmann C. The identification and structural analysis of potential 14-3-3 interaction sites on the bone regulator protein Schnurri-3. Acta Crystallogr F Struct Biol Commun 2021; 77:254-261. [PMID: 34341191 PMCID: PMC8329713 DOI: 10.1107/s2053230x21006658] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 06/25/2021] [Indexed: 11/10/2022] Open
Abstract
14-3-3 proteins regulate many intracellular processes and their ability to bind in subtly different fashions to their numerous partner proteins provides attractive drug-targeting points for a range of diseases. Schnurri-3 is a suppressor of mouse bone formation and a candidate target for novel osteoporosis therapeutics, and thus it is of interest to determine whether it interacts with 14-3-3. In this work, potential 14-3-3 interaction sites on mammalian Schnurri-3 were identified by an in silico analysis of its protein sequence. Using fluorescence polarization, isothermal titration calorimetry and X-ray crystallography, it is shown that synthetic peptides containing either phosphorylated Thr869 or Ser542 can indeed interact with 14-3-3, with the latter capable of forming an interprotein disulfide bond with 14-3-3σ: a hitherto unreported phenomenon.
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Affiliation(s)
- Lorenzo Soini
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
- Department of Chemistry, UCB Celltech, Slough, United Kingdom
| | - Seppe Leysen
- Department of Structural Biology and Biophysics, UCB Celltech, Slough, United Kingdom
| | - Tom Crabbe
- New Targets, UCB Celltech, Slough, United Kingdom
| | - Jeremy Davis
- Department of Chemistry, UCB Celltech, Slough, United Kingdom
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
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Sijbesma E, Hallenbeck KK, Andrei SA, Rust RR, Adriaans JMC, Brunsveld L, Arkin MR, Ottmann C. Exploration of a 14-3-3 PPI Pocket by Covalent Fragments as Stabilizers. ACS Med Chem Lett 2021; 12:976-982. [PMID: 34136078 PMCID: PMC8201753 DOI: 10.1021/acsmedchemlett.1c00088] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 05/04/2021] [Indexed: 12/20/2022] Open
Abstract
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The systematic discovery
of functional fragments binding to the
composite interface of protein complexes is a first critical step
for the development of orthosteric stabilizers of protein–protein
interactions (PPIs). We have previously shown that disulfide trapping
successfully yielded covalent stabilizers for the PPI of 14-3-3 with
the estrogen receptor ERα. Here we provide an assessment of
the composite PPI target pocket and the molecular characteristics
of various fragments binding to a specific subpocket. Evaluating structure–activity
relationships highlights the basic principles for PPI stabilization
by these covalent fragments that engage a relatively large and exposed
binding pocket at the protein/peptide interface with a “molecular
glue” mode of action.
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Affiliation(s)
- Eline Sijbesma
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Kenneth K. Hallenbeck
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center (SMDC), University of California, San Francisco 94134, United States
| | - Sebastian A. Andrei
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Reanne R. Rust
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Joris M. C. Adriaans
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Michelle R. Arkin
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center (SMDC), University of California, San Francisco 94134, United States
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
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Cossar PJ, Wolter M, van Dijck L, Valenti D, Levy LM, Ottmann C, Brunsveld L. Reversible Covalent Imine-Tethering for Selective Stabilization of 14-3-3 Hub Protein Interactions. J Am Chem Soc 2021; 143:8454-8464. [PMID: 34047554 PMCID: PMC8193639 DOI: 10.1021/jacs.1c03035] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
The stabilization
of protein complexes has emerged as a promising
modality, expanding the number of entry points for novel therapeutic
intervention. Targeting proteins that mediate protein–protein
interactions (PPIs), such as hub proteins, is equally challenging
and rewarding as they offer an intervention platform for a variety
of diseases, due to their large interactome. 14-3-3 hub proteins bind
phosphorylated motifs of their interaction partners in a conserved
binding channel. The 14-3-3 PPI interface is consequently only diversified
by its different interaction partners. Therefore, it is essential
to consider, additionally to the potency, also the selectivity of
stabilizer molecules. Targeting a lysine residue at the interface
of the composite 14-3-3 complex, which can be targeted explicitly
via aldimine-forming fragments, we studied the de novo design of PPI stabilizers under consideration of potential selectivity.
By applying cooperativity analysis of ternary complex formation, we
developed a reversible covalent molecular glue for the 14-3-3/Pin1
interaction. This small fragment led to a more than 250-fold stabilization
of the 14-3-3/Pin1 interaction by selective interfacing with a unique
tryptophan in Pin1. This study illustrates how cooperative complex
formation drives selective PPI stabilization. Further, it highlights
how specific interactions within a hub proteins interactome can be
stabilized over other interactions with a common binding motif.
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Affiliation(s)
- Peter J Cossar
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Madita Wolter
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Lars van Dijck
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Dario Valenti
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands.,Taros Chemicals GmbH & Co. KG, Emil-Figge-Straße 76a, 44227 Dortmund, Germany
| | - Laura M Levy
- Taros Chemicals GmbH & Co. KG, Emil-Figge-Straße 76a, 44227 Dortmund, Germany
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
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Target identification for small-molecule discovery in the FOXO3a tumor-suppressor pathway using a biodiverse peptide library. Cell Chem Biol 2021; 28:1602-1615.e9. [PMID: 34111400 PMCID: PMC8610377 DOI: 10.1016/j.chembiol.2021.05.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 03/03/2021] [Accepted: 05/14/2021] [Indexed: 12/12/2022]
Abstract
Genetic screening technologies to identify and validate macromolecular interactions (MMIs) essential for complex pathways remain an important unmet need for systems biology and therapeutics development. Here, we use a library of peptides from diverse prokaryal genomes to screen MMIs promoting the nuclear relocalization of Forkhead Box O3 (FOXO3a), a tumor suppressor more frequently inactivated by post-translational modification than mutation. A hit peptide engages the 14-3-3 family of signal regulators through a phosphorylation-dependent interaction, modulates FOXO3a-mediated transcription, and suppresses cancer cell growth. In a crystal structure, the hit peptide occupies the phosphopeptide-binding groove of 14-3-3ε in a conformation distinct from its natural peptide substrates. A biophysical screen identifies drug-like small molecules that displace the hit peptide from 14-3-3ε, providing starting points for structure-guided development. Our findings exemplify “protein interference,” an approach using evolutionarily diverse, natural peptides to rapidly identify, validate, and develop chemical probes against MMIs essential for complex cellular phenotypes. We describe protein interference, an approach to identify and validate new drug targets A genetic screen identifies a protein interference probe inducing FOXO3a reactivation The probe defines a druggable binding site in the 14-3-3 signal regulator family We illustrate a workflow to parse complex cellular pathways for new drug targets
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Tugaeva KV, Hawkins DEDP, Smith JLR, Bayfield OW, Ker DS, Sysoev AA, Klychnikov OI, Antson AA, Sluchanko NN. The Mechanism of SARS-CoV-2 Nucleocapsid Protein Recognition by the Human 14-3-3 Proteins. J Mol Biol 2021; 433:166875. [PMID: 33556408 PMCID: PMC7863765 DOI: 10.1016/j.jmb.2021.166875] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 01/27/2021] [Accepted: 01/29/2021] [Indexed: 12/24/2022]
Abstract
The coronavirus nucleocapsid protein (N) controls viral genome packaging and contains numerous phosphorylation sites located within unstructured regions. Binding of phosphorylated SARS-CoV N to the host 14-3-3 protein in the cytoplasm was reported to regulate nucleocytoplasmic N shuttling. All seven isoforms of the human 14-3-3 are abundantly present in tissues vulnerable to SARS-CoV-2, where N can constitute up to ~1% of expressed proteins during infection. Although the association between 14-3-3 and SARS-CoV-2 N proteins can represent one of the key host-pathogen interactions, its molecular mechanism and the specific critical phosphosites are unknown. Here, we show that phosphorylated SARS-CoV-2 N protein (pN) dimers, reconstituted via bacterial co-expression with protein kinase A, directly associate, in a phosphorylation-dependent manner, with the dimeric 14-3-3 protein, but not with its monomeric mutant. We demonstrate that pN is recognized by all seven human 14-3-3 isoforms with various efficiencies and deduce the apparent KD to selected isoforms, showing that these are in a low micromolar range. Serial truncations pinpointed a critical phosphorylation site to Ser197, which is conserved among related zoonotic coronaviruses and located within the functionally important, SR-rich region of N. The relatively tight 14-3-3/pN association could regulate nucleocytoplasmic shuttling and other functions of N via occlusion of the SR-rich region, and could also hijack cellular pathways by 14-3-3 sequestration. As such, the assembly may represent a valuable target for therapeutic intervention.
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Affiliation(s)
- Kristina V Tugaeva
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Dorothy E D P Hawkins
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Jake L R Smith
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Oliver W Bayfield
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - De-Sheng Ker
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Andrey A Sysoev
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Oleg I Klychnikov
- Department of Biochemistry, School of Biology, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Alfred A Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom.
| | - Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia.
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39
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Munier CC, De Maria L, Edman K, Gunnarsson A, Longo M, MacKintosh C, Patel S, Snijder A, Wissler L, Brunsveld L, Ottmann C, Perry MWD. Glucocorticoid receptor Thr524 phosphorylation by MINK1 induces interactions with 14-3-3 protein regulators. J Biol Chem 2021; 296:100551. [PMID: 33744286 PMCID: PMC8080530 DOI: 10.1016/j.jbc.2021.100551] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 03/08/2021] [Accepted: 03/16/2021] [Indexed: 01/10/2023] Open
Abstract
The glucocorticoid receptor (GR) is a ligand-dependent transcription factor that plays a central role in inflammation. The GR activity is also modulated via protein–protein interactions, including binding of 14-3-3 proteins induced by GR phosphorylation. However, the specific phosphorylation sites on the GR that trigger these interactions and their functional consequences are less clear. Hence, we sought to examine this system in more detail. We used phosphorylated GR peptides, biophysical studies, and X-ray crystallography to identify key residues within the ligand-binding domain of the GR, T524 and S617, whose phosphorylation results in binding of the representative 14-3-3 protein 14-3-3ζ. A kinase screen identified misshapen-like kinase 1 (MINK1) as responsible for phosphorylating T524 and Rho-associated protein kinase 1 for phosphorylating S617; cell-based approaches confirmed the importance of both GR phosphosites and MINK1 but not Rho-associated protein kinase 1 alone in inducing GR–14-3-3 binding. Together our results provide molecular-level insight into 14-3-3-mediated regulation of the GR and highlight both MINK1 and the GR–14-3-3 axis as potential targets for future therapeutic intervention.
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Affiliation(s)
- Claire C Munier
- Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden; Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Eindhoven, The Netherlands
| | - Leonardo De Maria
- Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Karl Edman
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Anders Gunnarsson
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Marianna Longo
- Division of Cell and Developmental Biology (C.M.), College of Life Sciences, University of Dundee, Dundee, Scotland, UK
| | - Carol MacKintosh
- Division of Cell and Developmental Biology (C.M.), College of Life Sciences, University of Dundee, Dundee, Scotland, UK
| | - Saleha Patel
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Arjan Snijder
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Lisa Wissler
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Eindhoven, The Netherlands
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Eindhoven, The Netherlands
| | - Matthew W D Perry
- Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.
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40
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Gogl G, Tugaeva KV, Eberling P, Kostmann C, Trave G, Sluchanko NN. Hierarchized phosphotarget binding by the seven human 14-3-3 isoforms. Nat Commun 2021; 12:1677. [PMID: 33723253 PMCID: PMC7961048 DOI: 10.1038/s41467-021-21908-8] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 02/17/2021] [Indexed: 02/07/2023] Open
Abstract
The seven 14-3-3 isoforms are highly abundant human proteins encoded by similar yet distinct genes. 14-3-3 proteins recognize phosphorylated motifs within numerous human and viral proteins. Here, we analyze by X-ray crystallography, fluorescence polarization, mutagenesis and fusicoccin-mediated modulation the structural basis and druggability of 14-3-3 binding to four E6 oncoproteins of tumorigenic human papillomaviruses. 14-3-3 isoforms bind variant and mutated phospho-motifs of E6 and unrelated protein RSK1 with different affinities, albeit following an ordered affinity ranking with conserved relative KD ratios. Remarkably, 14-3-3 isoforms obey the same hierarchy when binding to most of their established targets, as supported by literature and a recent human complexome map. This knowledge allows predicting proportions of 14-3-3 isoforms engaged with phosphoproteins in various tissues. Notwithstanding their individual functions, cellular concentrations of 14-3-3 may be collectively adjusted to buffer the strongest phosphorylation outbursts, explaining their expression variations in different tissues and tumors.
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Affiliation(s)
- Gergo Gogl
- Equipe Labellisee Ligue 2015, Department of Integrated Structural Biology, Institut de Genetique et de Biologie Moleculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Universite de Strasbourg, Illkirch, France.
| | - Kristina V Tugaeva
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Pascal Eberling
- Equipe Labellisee Ligue 2015, Department of Integrated Structural Biology, Institut de Genetique et de Biologie Moleculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Universite de Strasbourg, Illkirch, France
| | - Camille Kostmann
- Equipe Labellisee Ligue 2015, Department of Integrated Structural Biology, Institut de Genetique et de Biologie Moleculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Universite de Strasbourg, Illkirch, France
| | - Gilles Trave
- Equipe Labellisee Ligue 2015, Department of Integrated Structural Biology, Institut de Genetique et de Biologie Moleculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Universite de Strasbourg, Illkirch, France.
| | - Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia.
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Ruks T, Loza K, Heggen M, Ottmann C, Bayer P, Beuck C, Epple M. Targeting the Surface of the Protein 14-3-3 by Ultrasmall (1.5 nm) Gold Nanoparticles Carrying the Specific Peptide CRaf. Chembiochem 2021; 22:1456-1463. [PMID: 33275809 PMCID: PMC8248332 DOI: 10.1002/cbic.202000761] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 12/04/2020] [Indexed: 12/11/2022]
Abstract
The surface of ultrasmall gold nanoparticles with an average diameter of 1.55 nm was conjugated with a 14-3-3 protein-binding peptide derived from CRaf. Each particle carries 18 CRaf peptides, leading to an overall stoichiometry of Au(115)Craf(18). The binding to the protein 14-3-3 was probed by isothermal titration calorimetry (ITC) and fluorescence polarization spectroscopy (FP). The dissociation constant (KD ) was measured as 5.0 μM by ITC and 0.9 μM by FP, which was close to the affinity of dissolved CRaf to 14-3-3σ. In contrast to dissolved CRaf, which alone did not enter HeLa cells, CRAF-conjugated gold nanoparticles were well taken up by HeLa cells, opening the opportunity to target the protein inside a cell.
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Affiliation(s)
- Tatjana Ruks
- Inorganic Chemistry and Center for Nanointegration Duisburg-Essen (CeNIDE), University of Duisburg-Essen, Universitätsstrasse 5-7, 45117, Essen, Germany
| | - Kateryna Loza
- Inorganic Chemistry and Center for Nanointegration Duisburg-Essen (CeNIDE), University of Duisburg-Essen, Universitätsstrasse 5-7, 45117, Essen, Germany
| | - Marc Heggen
- Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Christian Ottmann
- Laboratory of Chemical Biology Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, P.O. Box 513, 5600MB, Eindhoven, The Netherlands
| | - Peter Bayer
- Department of Structural and Medicinal Biochemistry, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, 45117, Essen, Germany
| | - Christine Beuck
- Department of Structural and Medicinal Biochemistry, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, 45117, Essen, Germany
| | - Matthias Epple
- Inorganic Chemistry and Center for Nanointegration Duisburg-Essen (CeNIDE), University of Duisburg-Essen, Universitätsstrasse 5-7, 45117, Essen, Germany
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Hu J, Sun XM, Su JY, Zhao YF, Chen YX. Different phosphorylation and farnesylation patterns tune Rnd3-14-3-3 interaction in distinct mechanisms. Chem Sci 2021; 12:4432-4442. [PMID: 34163708 PMCID: PMC8179448 DOI: 10.1039/d0sc05838f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 01/21/2021] [Indexed: 11/29/2022] Open
Abstract
Protein posttranslational modifications (PTMs) are often involved in the mediation or inhibition of protein-protein interactions (PPIs) within many cellular signaling pathways. Uncovering the molecular mechanism of PTM-induced multivalent PPIs is vital to understand the regulatory factors to promote inhibitor development. Herein, Rnd3 peptides with different PTM patterns as the binding epitopes and 14-3-3ζ protein were used as models to elucidate the influences of phosphorylation and farnesylation on binding thermodynamics and kinetics and their molecular mechanism. The quantitative thermodynamic results indicate that phosphorylated residues S210 and S218 (pS210 and pS218) and farnesylated C241 (fC241) enhance Rnd3-14-3-3ζ interactions in the presence of the essential pS240. However, distinct PTM patterns greatly affect the binding process. Initial association of pS240 with the phosphate-binding pocket of one monomer of the 14-3-3ζ dimer triggers the binding of pS210 or pS218 to another monomer, whereas the binding of fC241 to the hydrophobic groove on one 14-3-3ζ monomer induces the subsequent binding of pS240 to the adjacent pocket on the same monomer. Based on the experimental and molecular simulation results, we estimate that pS210/pS218 and pS240 mediate the multivalent interaction through an additive mechanism, whereas fC241 and pS240 follow an induced fit mechanism, in which the cooperativity of these two adjacent PTMs is reflected by the index ε described in our established thermodynamic binding model. Besides, these proposed binding models have been further used for describing the interaction between 14-3-3ζ and other substrates containing adjacent phosphorylation and lipidation groups, indicating their potential in general applications. These mechanistic insights are significant for understanding the regulatory factors and the design of PPI modulators.
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Affiliation(s)
- Jun Hu
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University Beijing 100084 China
| | - Xue-Meng Sun
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University Beijing 100084 China
| | - Jing-Yun Su
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University Beijing 100084 China
| | - Yu-Fen Zhao
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University Beijing 100084 China
| | - Yong-Xiang Chen
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University Beijing 100084 China
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Kiehstaller S, Ottmann C, Hennig S. MMP activation-associated aminopeptidase N reveals a bivalent 14-3-3 binding motif. J Biol Chem 2020; 295:18266-18275. [PMID: 33109610 PMCID: PMC7939381 DOI: 10.1074/jbc.ra120.014708] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 10/21/2020] [Indexed: 12/27/2022] Open
Abstract
Aminopeptidase N (APN, CD13) is a transmembrane ectopeptidase involved in many crucial cellular functions. Besides its role as a peptidase, APN also mediates signal transduction and is involved in the activation of matrix metalloproteinases (MMPs). MMPs function in tissue remodeling within the extracellular space and are therefore involved in many human diseases, such as fibrosis, rheumatoid arthritis, tumor angiogenesis, and metastasis, as well as viral infections. However, the exact mechanism that leads to APN-driven MMP activation is unclear. It was previously shown that extracellular 14-3-3 adapter proteins bind to APN and thereby induce the transcription of MMPs. As a first step, we sought to identify potential 14-3-3-binding sites in the APN sequence. We constructed a set of phosphorylated peptides derived from APN to probe for interactions. We identified and characterized a canonical 14-3-3-binding site (site 1) within the flexible, structurally unresolved N-terminal APN region using direct binding fluorescence polarization assays and thermodynamic analysis. In addition, we identified a secondary, noncanonical binding site (site 2), which enhances the binding affinity in combination with site 1 by many orders of magnitude. Finally, we solved crystal structures of 14-3-3σ bound to mono- and bis-phosphorylated APN-derived peptides, which revealed atomic details of the binding mode of mono- and bivalent 14-3-3 interactions. Therefore, our findings shed some light on the first steps of APN-mediated MMP activation and open the field for further investigation of this important signaling pathway.
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Affiliation(s)
- Sebastian Kiehstaller
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, Netherlands; Amsterdam Institute of Molecular and Life Sciences (AIMMS), VU University Amsterdam, Amsterdam, Netherlands
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, Netherlands
| | - Sven Hennig
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, Netherlands; Amsterdam Institute of Molecular and Life Sciences (AIMMS), VU University Amsterdam, Amsterdam, Netherlands.
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44
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Haq IJ, Althaus M, Gardner AI, Yeoh HY, Joshi U, Saint-Criq V, Verdon B, Townshend J, O'Brien C, Ben-Hamida M, Thomas M, Bourke S, van der Sluijs P, Braakman I, Ward C, Gray MA, Brodlie M. Clinical and molecular characterization of the R751L-CFTR mutation. Am J Physiol Lung Cell Mol Physiol 2020; 320:L288-L300. [PMID: 33296276 PMCID: PMC8476205 DOI: 10.1152/ajplung.00137.2020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Cystic fibrosis (CF) arises from mutations in the CF transmembrane conductance regulator (CFTR) gene, resulting in progressive and life-limiting respiratory disease. R751L is a rare CFTR mutation that is poorly characterized. Our aims were to describe the clinical and molecular phenotypes associated with R751L. Relevant clinical data were collected from three heterozygote individuals harboring R751L (2 patients with G551D/R751L and 1 with F508del/R751L). Assessment of R751L-CFTR function was made in primary human bronchial epithelial cultures (HBEs) and Xenopus oocytes. Molecular properties of R751L-CFTR were investigated in the presence of known CFTR modulators. Although sweat chloride was elevated in all three patients, the clinical phenotype associated with R751L was mild. Chloride secretion in F508del/R751L HBEs was reduced compared with non-CF HBEs and associated with a reduction in sodium absorption by the epithelial sodium channel (ENaC). However, R751L-CFTR function in Xenopus oocytes, together with folding and cell surface transport of R751L-CFTR, was not different from wild-type CFTR. Overall, R751L-CFTR was associated with reduced sodium chloride absorption but had functional properties similar to wild-type CFTR. This is the first report of R751L-CFTR that combines clinical phenotype with characterization of functional and biological properties of the mutant channel. Our work will build upon existing knowledge of mutations within this region of CFTR and, importantly, inform approaches for clinical management. Elevated sweat chloride and reduced chloride secretion in HBEs may be due to alternative non-CFTR factors, which require further investigation.
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Affiliation(s)
- Iram J Haq
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom.,Paediatric Respiratory Medicine, Great North Children's Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Mike Althaus
- Institute for Functional Gene Analytics, Department of Natural Sciences, Bonn-Rhein-Sieg University of Applied Sciences, Rheinbach, Germany
| | - Aaron Ions Gardner
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Hui Ying Yeoh
- Cellular Protein Chemistry, Science4Life, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Urjita Joshi
- Cellular Protein Chemistry, Science4Life, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Vinciane Saint-Criq
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Bernard Verdon
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Jennifer Townshend
- Paediatric Respiratory Medicine, Great North Children's Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Christopher O'Brien
- Paediatric Respiratory Medicine, Great North Children's Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Mahfud Ben-Hamida
- Department of Paediatrics, West Cumberland Hospital, Whitehaven, United Kingdom
| | - Matthew Thomas
- Paediatric Respiratory Medicine, Great North Children's Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Stephen Bourke
- Respiratory Medicine, Royal Victoria Infirmary, Newcastle upon Tyne, United Kingdom
| | - Peter van der Sluijs
- Cellular Protein Chemistry, Science4Life, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Ineke Braakman
- Cellular Protein Chemistry, Science4Life, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Chris Ward
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Michael A Gray
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Malcolm Brodlie
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom.,Paediatric Respiratory Medicine, Great North Children's Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
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45
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Soini L, Leysen S, Davis J, Ottmann C. A biophysical and structural analysis of the interaction of BLNK with 14-3-3 proteins. J Struct Biol 2020; 212:107662. [PMID: 33176192 DOI: 10.1016/j.jsb.2020.107662] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 11/02/2020] [Accepted: 11/03/2020] [Indexed: 01/14/2023]
Abstract
B-cell linker protein (BLNK) is an adaptor protein that orchestrates signalling downstream of B-cell receptors. It has been reported to undergo proteasomal degradation upon binding to 14-3-3 proteins. Here, we report the first biophysical and structural study of this protein-protein interaction (PPI). Specifically, we investigated the binding of mono- and di- phosphorylated BLNK peptides to 14-3-3 using fluorescent polarization (FP) and isothermal titration calorimetry assays (ITC). Our results suggest that BLNK interacts with 14-3-3 according to the gatekeeper model, where HPK1 mediated phosphorylation of Thr152 (pT152) allows BLNK anchoring to 14-3-3, and an additional phosphorylation of Ser285 (pS285) by AKT, then further improves the affinity. Finally, we have also solved a crystal structure of the BLNKpT152 peptide bound to 14-3-3σ. These findings could serve as important tool for compound discovery programs aiming to modulate this interaction with 14-3-3.
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Affiliation(s)
- Lorenzo Soini
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, the Netherlands; Department of Chemistry, UCB Celltech, Slough, UK
| | - Seppe Leysen
- Department of Structural Biology and Biophysics, UCB Celltech, Slough, UK
| | - Jeremy Davis
- Department of Chemistry, UCB Celltech, Slough, UK
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, the Netherlands.
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46
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Soini L, Leysen S, Davis J, Westwood M, Ottmann C. The 14-3-3/SLP76 protein-protein interaction in T-cell receptor signalling: a structural and biophysical characterization. FEBS Lett 2020; 595:404-414. [PMID: 33159816 DOI: 10.1002/1873-3468.13993] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/13/2020] [Accepted: 11/01/2020] [Indexed: 12/18/2022]
Abstract
The SH2 domain-containing protein of 76 kDa, SLP76, is an important adaptor protein that coordinates a complex protein network downstream of T-cell receptors (TCR), ultimately regulating the immune response. Upon phosphorylation on Ser376, SLP76 interacts with 14-3-3 adaptor proteins, which leads to its proteolytic degradation. This provides a negative feedback mechanism by which TCR signalling can be controlled. To gain insight into the 14-3-3/SLP76 protein-protein interaction (PPI), we have determined a high-resolution crystal structure of a SLP76 synthetic peptide containing Ser376 with 14-3-3σ. We then characterized its binding to 14-3-3 proteins biophysically by means of fluorescence polarization and isothermal titration calorimetry. Furthermore, we generated two recombinant SLP76 protein constructs and characterized their binding to 14-3-3. Our work lays the foundation for drug design efforts aimed at targeting the 14-3-3/SLP76 interaction and, thereby, TCR signalling.
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Affiliation(s)
- Lorenzo Soini
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, the Netherlands.,Department of Chemistry, UCB Celltech, Slough, UK
| | - Seppe Leysen
- Department of Structural Biology and Biophysics, UCB Celltech, Slough, UK
| | - Jeremy Davis
- Department of Chemistry, UCB Celltech, Slough, UK
| | | | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, the Netherlands
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47
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Ballone A, Picarazzi F, Prosser C, Davis J, Ottmann C, Mori M. Experimental and Computational Druggability Exploration of the 14-3-3ζ/SOS1pS 1161 PPI Interface. J Chem Inf Model 2020; 60:6555-6565. [PMID: 33138374 DOI: 10.1021/acs.jcim.0c00722] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The exploration of the druggability of certain protein-protein interactions (PPIs) still remains a challenging task in drug discovery. Here, we present a case study using the 14-3-3-PPI, showing how small molecules can be located that are able to modulate this key oncogenic pathway. A workflow embracing biophysical techniques and MD simulations was developed to evaluate the potential of a 14-3-3ζ PPI system to bind new tool compounds. The significance of the use of computational approaches to compensate for the limitations of experimental techniques is demonstrated.
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Affiliation(s)
- Alice Ballone
- Department of Biochemical Engineering and Institute for Complex Molecular Systems, Laboratory of Chemical Biology, University of Technology Eindhoven, 5600 MB, Eindhoven, The Netherlands.,Department of Biotechnology, Chemistry and Pharmacy, Department of Excellence 2018-2022, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy.,Department of Chemistry, UCB Pharma SPRL, 216 Bath Rd., Slough SL1 3WE, United Kingdom
| | - Francesca Picarazzi
- Department of Biotechnology, Chemistry and Pharmacy, Department of Excellence 2018-2022, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Christine Prosser
- Department of Chemistry, UCB Pharma SPRL, 216 Bath Rd., Slough SL1 3WE, United Kingdom
| | - Jeremy Davis
- Department of Chemistry, UCB Pharma SPRL, 216 Bath Rd., Slough SL1 3WE, United Kingdom
| | - Christian Ottmann
- Department of Biochemical Engineering and Institute for Complex Molecular Systems, Laboratory of Chemical Biology, University of Technology Eindhoven, 5600 MB, Eindhoven, The Netherlands
| | - Mattia Mori
- Department of Biotechnology, Chemistry and Pharmacy, Department of Excellence 2018-2022, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
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48
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Reading the phosphorylation code: binding of the 14-3-3 protein to multivalent client phosphoproteins. Biochem J 2020; 477:1219-1225. [PMID: 32271882 DOI: 10.1042/bcj20200084] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 03/18/2020] [Accepted: 03/18/2020] [Indexed: 12/24/2022]
Abstract
Many major protein-protein interaction networks are maintained by 'hub' proteins with multiple binding partners, where interactions are often facilitated by intrinsically disordered protein regions that undergo post-translational modifications, such as phosphorylation. Phosphorylation can directly affect protein function and control recognition by proteins that 'read' the phosphorylation code, re-wiring the interactome. The eukaryotic 14-3-3 proteins recognizing multiple phosphoproteins nicely exemplify these concepts. Although recent studies established the biochemical and structural basis for the interaction of the 14-3-3 dimers with several phosphorylated clients, understanding their assembly with partners phosphorylated at multiple sites represents a challenge. Suboptimal sequence context around the phosphorylated residue may reduce binding affinity, resulting in quantitative differences for distinct phosphorylation sites, making hierarchy and priority in their binding rather uncertain. Recently, Stevers et al. [Biochemical Journal (2017) 474: 1273-1287] undertook a remarkable attempt to untangle the mechanism of 14-3-3 dimer binding to leucine-rich repeat kinase 2 (LRRK2) that contains multiple candidate 14-3-3-binding sites and is mutated in Parkinson's disease. By using the protein-peptide binding approach, the authors systematically analyzed affinities for a set of LRRK2 phosphopeptides, alone or in combination, to a 14-3-3 protein and determined crystal structures for 14-3-3 complexes with selected phosphopeptides. This study addresses a long-standing question in the 14-3-3 biology, unearthing a range of important details that are relevant for understanding binding mechanisms of other polyvalent proteins.
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49
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Munier CC, Ottmann C, Perry MWD. 14-3-3 modulation of the inflammatory response. Pharmacol Res 2020; 163:105236. [PMID: 33053447 DOI: 10.1016/j.phrs.2020.105236] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 10/02/2020] [Accepted: 10/04/2020] [Indexed: 01/11/2023]
Abstract
Regulation of inflammation is a central part of the maintenance of homeostasis by the immune system. One important class of regulatory protein that has been shown to have effects on the inflammatory process are the 14-3-3 proteins. Herein we describe the roles that have been identified for 14-3-3 in regulation of the inflammatory response. These roles encompass regulation of the response that affect inflammation at the genetic, molecular and cellular levels. At a genetic level 14-3-3 is involved in the regulation of multiple transcription factors and affects the transcription of key effectors of the immune response. At a molecular level many of the constituent parts of the inflammatory process, such as pattern recognition receptors, protease activated receptors and cytokines are regulated through phosphorylation and recognition by 14-3-3 whilst disruption of the recognition processes has been observed to result in clinical syndromes. 14-3-3 is also involved in the regulation of cell proliferation and differentiation, this has been shown to affect the immune system, particularly T- and B-cells. Finally, we discuss how abnormal levels of 14-3-3 contribute to undesirable immune responses and chronic inflammatory conditions.
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Affiliation(s)
- Claire C Munier
- Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden; Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Den Dolech 2, 5612 AZ Eindhoven, the Netherlands
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Den Dolech 2, 5612 AZ Eindhoven, the Netherlands
| | - Matthew W D Perry
- Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.
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50
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Sengupta A, Liriano J, Bienkiewicz EA, Miller BG, Frederich JH. Probing the 14-3-3 Isoform-Specificity Profile of Protein-Protein Interactions Stabilized by Fusicoccin A. ACS OMEGA 2020; 5:25029-25035. [PMID: 33043180 PMCID: PMC7542595 DOI: 10.1021/acsomega.0c01454] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 09/10/2020] [Indexed: 06/11/2023]
Abstract
Fusicoccin A (FC) is a fungal phytotoxin that stabilizes protein-protein interactions (PPIs) between 14-3-3 adapter proteins and their phosphoprotein interaction partners. Recently, FC has emerged as an important chemical probe of human 14-3-3 PPIs involved in cancer and neurobiology. These previous studies have established the structural requirements for FC-induced stabilization of 14-3-3·client phosphoprotein complexes; however, the effect of 14-3-3 isoforms on FC activity remains underexplored. This is a relevant question for the continued development of FC variants because there are seven isoforms of 14-3-3 in humans. Despite their sequence and structural similarities, a growing body of experimental evidence supports both tissue-specific expression of 14-3-3 isoforms and isoform-specific functions in vivo. Herein, we interrogate the isoform-specificity profile of FC in vitro using recombinant 14-3-3 isoforms and a library of fluorescein-labeled hexaphosphopeptides mimicking the C-terminal recognition domains of client proteins that are characterized targets of FC in vivo. Our results reveal modest isoform preferences for individual client phospholigands and demonstrate that FC differentially stabilizes PPIs involving 14-3-3σ. Together, these data support the feasibility of developing FC variants with enhanced isoform selectivity.
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Affiliation(s)
- Ananya Sengupta
- Department
of Chemistry and Biochemistry, Florida State
University, 95 Chieftan Way, Tallahassee, Florida 32306, United
States
| | - Josue Liriano
- Department
of Chemistry and Biochemistry, Florida State
University, 95 Chieftan Way, Tallahassee, Florida 32306, United
States
| | - Ewa A. Bienkiewicz
- Department
of Biomedical Sciences, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, Florida 32306, United
States
| | - Brian G. Miller
- Department
of Chemistry and Biochemistry, Florida State
University, 95 Chieftan Way, Tallahassee, Florida 32306, United
States
| | - James H. Frederich
- Department
of Chemistry and Biochemistry, Florida State
University, 95 Chieftan Way, Tallahassee, Florida 32306, United
States
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