1
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Michel MA, Scutts S, Komander D. Secondary interactions in ubiquitin-binding domains achieve linkage or substrate specificity. Cell Rep 2024; 43:114545. [PMID: 39052481 PMCID: PMC11372445 DOI: 10.1016/j.celrep.2024.114545] [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: 03/13/2024] [Revised: 06/24/2024] [Accepted: 07/10/2024] [Indexed: 07/27/2024] Open
Abstract
Small ubiquitin-binding domains (UBDs) recognize small surface patches on ubiquitin with weak affinity, and it remains a conundrum how specific cellular responses may be achieved. Npl4-type zinc-finger (NZF) domains are ∼30 amino acid, compact UBDs that can provide two ubiquitin-binding interfaces, imposing linkage specificity to explain signaling outcomes. We here comprehensively characterize the linkage preference of human NZF domains. TAB2 prefers Lys6 and Lys63 linkages phosphorylated on Ser65, explaining why TAB2 recognizes depolarized mitochondria. Surprisingly, most NZF domains do not display chain linkage preference, despite conserved, secondary interaction surfaces. This suggests that some NZF domains may specifically bind ubiquitinated substrates by simultaneously recognizing substrate and an attached ubiquitin. We show biochemically and structurally that the NZF1 domain of the E3 ligase HOIPbinds preferentially to site-specifically ubiquitinated forms of NEMO and optineurin. Thus, despite their small size, UBDs may impose signaling specificity via multivalent interactions with ubiquitinated substrates.
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Affiliation(s)
- Martin A Michel
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, CB2 0QH Cambridge, UK
| | - Simon Scutts
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department for Medical Biology, University of Melbourne, Melbourne, VIC 3000, Australia
| | - David Komander
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, CB2 0QH Cambridge, UK; The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department for Medical Biology, University of Melbourne, Melbourne, VIC 3000, Australia.
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2
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Hadian K, Stockwell BR. The therapeutic potential of targeting regulated non-apoptotic cell death. Nat Rev Drug Discov 2023; 22:723-742. [PMID: 37550363 DOI: 10.1038/s41573-023-00749-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/16/2023] [Indexed: 08/09/2023]
Abstract
Cell death is critical for the development and homeostasis of almost all multicellular organisms. Moreover, its dysregulation leads to diverse disease states. Historically, apoptosis was thought to be the major regulated cell death pathway, whereas necrosis was considered to be an unregulated form of cell death. However, research in recent decades has uncovered several forms of regulated necrosis that are implicated in degenerative diseases, inflammatory conditions and cancer. The growing insight into these regulated, non-apoptotic cell death pathways has opened new avenues for therapeutic targeting. Here, we describe the regulatory pathways of necroptosis, pyroptosis, parthanatos, ferroptosis, cuproptosis, lysozincrosis and disulfidptosis. We discuss small-molecule inhibitors of the pathways and prospects for future drug discovery. Together, the complex mechanisms governing these pathways offer strategies to develop therapeutics that control non-apoptotic cell death.
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Affiliation(s)
- Kamyar Hadian
- Research Unit Signaling and Translation, Helmholtz Zentrum München, Neuherberg, Germany.
| | - Brent R Stockwell
- Department of Biological Sciences and Department of Chemistry, Columbia University, New York, NY, USA.
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3
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Goel S, Oliva R, Jeganathan S, Bader V, Krause LJ, Kriegler S, Stender ID, Christine CW, Nakamura K, Hoffmann JE, Winter R, Tatzelt J, Winklhofer KF. Linear ubiquitination induces NEMO phase separation to activate NF-κB signaling. Life Sci Alliance 2023; 6:e202201607. [PMID: 36720498 PMCID: PMC9889916 DOI: 10.26508/lsa.202201607] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 01/09/2023] [Accepted: 01/09/2023] [Indexed: 02/02/2023] Open
Abstract
The NF-κB essential modulator NEMO is the core regulatory component of the inhibitor of κB kinase complex, which is a critical checkpoint in canonical NF-κB signaling downstream of innate and adaptive immune receptors. In response to various stimuli, such as TNF or IL-1β, NEMO binds to linear or M1-linked ubiquitin chains generated by LUBAC, promoting its oligomerization and subsequent activation of the associated kinases. Here we show that M1-ubiquitin chains induce phase separation of NEMO and the formation of NEMO assemblies in cells after exposure to IL-1β. Phase separation is promoted by both binding of NEMO to linear ubiquitin chains and covalent linkage of M1-ubiquitin to NEMO and is essential but not sufficient for its phase separation. Supporting the functional relevance of NEMO phase separation in signaling, a pathogenic NEMO mutant, which is impaired in both binding and linkage to linear ubiquitin chains, does not undergo phase separation and is defective in mediating IL-1β-induced NF-κB activation.
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Affiliation(s)
- Simran Goel
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Rosario Oliva
- Physical Chemistry I-Biophysical Chemistry, Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Sadasivam Jeganathan
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Verian Bader
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
- Department Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Laura J Krause
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
- RESOLV Cluster of Excellence, Ruhr University Bochum, Bochum, Germany
| | - Simon Kriegler
- Physical Chemistry I-Biophysical Chemistry, Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Isabelle D Stender
- Protein Chemistry Facility, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | | | - Ken Nakamura
- Department of Neurology, UCSF, San Francisco, CA, USA
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA, USA
| | - Jan-Erik Hoffmann
- Protein Chemistry Facility, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Roland Winter
- Physical Chemistry I-Biophysical Chemistry, Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
- RESOLV Cluster of Excellence, Ruhr University Bochum, Bochum, Germany
| | - Jörg Tatzelt
- RESOLV Cluster of Excellence, Ruhr University Bochum, Bochum, Germany
- Department Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Konstanze F Winklhofer
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
- RESOLV Cluster of Excellence, Ruhr University Bochum, Bochum, Germany
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4
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Henley MJ, Koehler AN. Advances in targeting 'undruggable' transcription factors with small molecules. Nat Rev Drug Discov 2021; 20:669-688. [PMID: 34006959 DOI: 10.1038/s41573-021-00199-0] [Citation(s) in RCA: 156] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2021] [Indexed: 02/07/2023]
Abstract
Transcription factors (TFs) represent key biological players in diseases including cancer, autoimmunity, diabetes and cardiovascular disease. However, outside nuclear receptors, TFs have traditionally been considered 'undruggable' by small-molecule ligands due to significant structural disorder and lack of defined small-molecule binding pockets. Renewed interest in the field has been ignited by significant progress in chemical biology approaches to ligand discovery and optimization, especially the advent of targeted protein degradation approaches, along with increasing appreciation of the critical role a limited number of collaborators play in the regulation of key TF effector genes. Here, we review current understanding of TF-mediated gene regulation, discuss successful targeting strategies and highlight ongoing challenges and emerging approaches to address them.
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Affiliation(s)
- Matthew J Henley
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA. .,The Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Angela N Koehler
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA. .,The Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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5
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Labrecque CL, Hilton CN, Airas J, Blake A, Rubenstein KJ, Parish CA, Pollock JA. Identification of Phenazine-Based MEMO1 Small-Molecule Inhibitors: Virtual Screening, Fluorescence Polarization Validation, and Inhibition of Breast Cancer Migration. ChemMedChem 2021; 16:1163-1171. [PMID: 33332774 DOI: 10.1002/cmdc.202000797] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 12/15/2020] [Indexed: 11/10/2022]
Abstract
Phosphorylation-dependent protein-protein interactions play a significant role in biological signaling pathways; therefore, small molecules that are capable of influencing these interactions can be valuable research tools and have potential as pharmaceutical agents. MEMO1 (mediator of ErbB2-cell driven motility) is a phosphotyrosine-binding protein that interacts with a variety of protein partners and has been found to be upregulated in breast cancer patients. Herein, we report the first small-molecule inhibitors of MEMO1 interactions identified through a virtual screening platform and validated in a competitive fluorescence polarization assay. Initial structure-activity relationships have been investigated for these phenazine-core inhibitors and the binding sites have been postulated using molecular dynamics simulations. The most potent biochemical inhibitor is capable of disrupting the large protein interface with a KI of 2.7 μm. In addition, the most promising phenazine core compounds slow the migration of breast cancer cell lines in a scratch assay.
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Affiliation(s)
- Courtney L Labrecque
- Department of Chemistry, University of Richmond, 138 UR Drive, Richmond, VA 23173, USA
| | - Cassidy N Hilton
- Department of Chemistry, University of Richmond, 138 UR Drive, Richmond, VA 23173, USA
| | - Justin Airas
- Department of Chemistry, University of Richmond, 138 UR Drive, Richmond, VA 23173, USA
| | - Alexis Blake
- Department of Chemistry, University of Richmond, 138 UR Drive, Richmond, VA 23173, USA
| | - Kristen J Rubenstein
- Department of Chemistry, University of Richmond, 138 UR Drive, Richmond, VA 23173, USA
| | - Carol A Parish
- Department of Chemistry, University of Richmond, 138 UR Drive, Richmond, VA 23173, USA
| | - Julie A Pollock
- Department of Chemistry, University of Richmond, 138 UR Drive, Richmond, VA 23173, USA
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6
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Jussupow A, Messias AC, Stehle R, Geerlof A, Solbak SMØ, Paissoni C, Bach A, Sattler M, Camilloni C. The dynamics of linear polyubiquitin. SCIENCE ADVANCES 2020; 6:6/42/eabc3786. [PMID: 33055165 PMCID: PMC7556843 DOI: 10.1126/sciadv.abc3786] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 08/25/2020] [Indexed: 05/17/2023]
Abstract
Polyubiquitin chains are flexible multidomain proteins, whose conformational dynamics enable them to regulate multiple biological pathways. Their dynamic is determined by the linkage between ubiquitins and by the number of ubiquitin units. Characterizing polyubiquitin behavior as a function of their length is hampered because of increasing system size and conformational variability. Here, we introduce a new approach to efficiently integrating small-angle x-ray scattering with simulations allowing us to accurately characterize the dynamics of linear di-, tri-, and tetraubiquitin in the free state as well as of diubiquitin in complex with NEMO, a central regulator in the NF-κB pathway. Our results show that the behavior of the diubiquitin subunits is independent of the presence of additional ubiquitin modules and that the dynamics of polyubiquitins with different lengths follow a simple model. Together with experimental data from multiple biophysical techniques, we then rationalize the 2:1 NEMO:polyubiquitin binding.
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Affiliation(s)
- Alexander Jussupow
- Department of Chemistry and Institute for Advanced Study, Technical University of Munich, Garching 85747, Germany
| | - Ana C Messias
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg 85764, Germany
- Center for Integrated Protein Science Munich at Department of Chemistry, Technical University of Munich, Garching 85747, Germany
| | - Ralf Stehle
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg 85764, Germany
- Center for Integrated Protein Science Munich at Department of Chemistry, Technical University of Munich, Garching 85747, Germany
| | - Arie Geerlof
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg 85764, Germany
- Center for Integrated Protein Science Munich at Department of Chemistry, Technical University of Munich, Garching 85747, Germany
| | - Sara M Ø Solbak
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Cristina Paissoni
- Dipartimento di Bioscienze, Università degli studi di Milano, 20133 Milano, Italy
| | - Anders Bach
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg 85764, Germany.
- Center for Integrated Protein Science Munich at Department of Chemistry, Technical University of Munich, Garching 85747, Germany
| | - Carlo Camilloni
- Department of Chemistry and Institute for Advanced Study, Technical University of Munich, Garching 85747, Germany.
- Dipartimento di Bioscienze, Università degli studi di Milano, 20133 Milano, Italy
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7
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Preventing the Interaction between Coronaviruses Spike Protein and Angiotensin I Converting Enzyme 2: An In Silico Mechanistic Case Study on Emodin as a Potential Model Compound. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10186358] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Emodin, a widespread natural anthraquinone, has many biological activities including health-protective and adverse effects. Amongst beneficial effects, potential antiviral activity against coronavirus responsible for the severe acute respiratory syndrome outbreak in 2002–2003 has been described associated with the inhibition of the host cells target receptors recognition by the viral Spike protein. However, the inhibition mechanisms have not been fully characterized, hindering the rational use of emodin as a model compound to develop more effective analogues. This work investigates emodin interaction with the Spike protein to provide a mechanistic explanation of such inhibition. A 3D molecular modeling approach consisting of docking simulations, pharmacophoric analysis and molecular dynamics was used. The plausible mechanism is described as an interaction of emodin at the protein–protein interface which destabilizes the viral protein-target receptor complex. This analysis has been extended to the Spike protein of the coronavirus responsible for the current pandemic hypothesizing emodin’s functional conservation. This solid knowledge-based foothold provides a possible mechanistic rationale of the antiviral activity of emodin as a future basis for the potential development of efficient antiviral cognate compounds. Data gaps and future work on emodin-related adverse effects in parallel to its antiviral pharmacology are explored.
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8
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Maculins T, Garcia-Pardo J, Skenderovic A, Gebel J, Putyrski M, Vorobyov A, Busse P, Varga G, Kuzikov M, Zaliani A, Rahighi S, Schaeffer V, Parnham MJ, Sidhu SS, Ernst A, Dötsch V, Akutsu M, Dikic I. Discovery of Protein-Protein Interaction Inhibitors by Integrating Protein Engineering and Chemical Screening Platforms. Cell Chem Biol 2020; 27:1441-1451.e7. [PMID: 32726587 DOI: 10.1016/j.chembiol.2020.07.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 06/24/2020] [Accepted: 07/09/2020] [Indexed: 02/06/2023]
Abstract
Protein-protein interactions (PPIs) govern intracellular life, and identification of PPI inhibitors is challenging. Roadblocks in assay development stemming from weak binding affinities of natural PPIs impede progress in this field. We postulated that enhancing binding affinity of natural PPIs via protein engineering will aid assay development and hit discovery. This proof-of-principle study targets PPI between linear ubiquitin chains and NEMO UBAN domain, which activates NF-κB signaling. Using phage display, we generated ubiquitin variants that bind to the functional UBAN epitope with high affinity, act as competitive inhibitors, and structurally maintain the existing PPI interface. When utilized in assay development, variants enable generation of robust cell-based assays for chemical screening. Top compounds identified using this approach directly bind to UBAN and dampen NF-κB signaling. This study illustrates advantages of integrating protein engineering and chemical screening in hit identification, a development that we anticipate will have wide application in drug discovery.
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Affiliation(s)
- Timurs Maculins
- Institute of Biochemistry II, Goethe University, Frankfurt am Main, Germany; Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine and Pharmacology, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany.
| | - Javier Garcia-Pardo
- Institute of Biochemistry II, Goethe University, Frankfurt am Main, Germany; Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine and Pharmacology, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
| | | | - Jakob Gebel
- Institute of Biophysical Chemistry & Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main, Germany
| | - Mateusz Putyrski
- Institute of Biochemistry II, Goethe University, Frankfurt am Main, Germany; Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine and Pharmacology, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Andrew Vorobyov
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine and Pharmacology, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Philipp Busse
- Institute of Biochemistry II, Goethe University, Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
| | - Gabor Varga
- Institute of Biochemistry II, Goethe University, Frankfurt am Main, Germany; Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine and Pharmacology, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Maria Kuzikov
- Fraunhofer Institute for Molecular Biology and Applied Ecology Screening Port, Hamburg, Germany
| | - Andrea Zaliani
- Fraunhofer Institute for Molecular Biology and Applied Ecology Screening Port, Hamburg, Germany
| | - Simin Rahighi
- Chapman University School of Pharmacy (CUSP), Harry and Diane Rinker Health Science Campus, Chapman University, Irvine, CA 92618, USA
| | | | - Michael J Parnham
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine and Pharmacology, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Sachdev S Sidhu
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Andreas Ernst
- Institute of Biochemistry II, Goethe University, Frankfurt am Main, Germany; Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine and Pharmacology, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Volker Dötsch
- Institute of Biophysical Chemistry & Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main, Germany
| | - Masato Akutsu
- Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
| | - Ivan Dikic
- Institute of Biochemistry II, Goethe University, Frankfurt am Main, Germany; Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine and Pharmacology, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany.
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9
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Paissoni C, Jussupow A, Camilloni C. Determination of Protein Structural Ensembles by Hybrid-Resolution SAXS Restrained Molecular Dynamics. J Chem Theory Comput 2020; 16:2825-2834. [PMID: 32119546 PMCID: PMC7997378 DOI: 10.1021/acs.jctc.9b01181] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
![]()
Small-angle
X-ray scattering (SAXS) experiments provide low-resolution
but valuable information about the dynamics of biomolecular systems,
which could be ideally integrated into molecular dynamics (MD) simulations
to accurately determine conformational ensembles of flexible proteins.
The applicability of this strategy is hampered by the high computational
cost required to calculate scattering intensities from three-dimensional
structures. We previously presented a hybrid resolution method that
makes atomistic SAXS-restrained MD simulation feasible by adopting
a coarse-grained approach to efficiently back-calculate scattering
intensities; here, we extend this technique, applying it in the framework
of metainference with the aim to investigate the dynamical behavior
of flexible biomolecules. The efficacy of the method is assessed on
the K63-diubiquitin, showing that the inclusion of SAXS restraints
is effective in generating a reliable conformational ensemble, improving
the agreement with independent experimental data.
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Affiliation(s)
- Cristina Paissoni
- Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, 20133 Milano, Italy
| | - Alexander Jussupow
- Department of Chemistry and Institute of Advanced Study, Technical University of Munich, Garching 85747, Germany
| | - Carlo Camilloni
- Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, 20133 Milano, Italy
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10
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Chen A, Koehler AN. Transcription Factor Inhibition: Lessons Learned and Emerging Targets. Trends Mol Med 2020; 26:508-518. [PMID: 32359481 DOI: 10.1016/j.molmed.2020.01.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 01/10/2020] [Accepted: 01/21/2020] [Indexed: 12/15/2022]
Abstract
Transcription factors have roles at focal points in signaling pathways, controlling many normal cellular processes, such as cell growth and proliferation, metabolism, apoptosis, immune responses, and differentiation. Their activity is frequently deregulated in disease and targeting this class of proteins is a major focus of interest. However, the structural disorder and lack of binding pockets have made design of small molecules for transcription factors challenging. Here, we review some of the most recent developments for small molecule inhibitors of transcription factors emphasized in James Darnell's vision 17 years ago. We also discuss the progress so far on transcription factors recently nominated by genome-scale loss-of-function screens from the cancer dependency map project.
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Affiliation(s)
- Andrew Chen
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, MA 02139, USA; MIT Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts, MA 02142, USA
| | - Angela N Koehler
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, MA 02139, USA; MIT Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts, MA 02142, USA; Broad Institute of MIT and Harvard, Cambridge, Massachusetts, MA 02142, USA.
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11
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Venkatesh J, Sekhar SC, Cheriyan VT, Muthu M, Meister P, Levi E, Dzinic S, Gauld JW, Polin LA, Rishi AK. Antagonizing binding of cell cycle and apoptosis regulatory protein 1 (CARP-1) to the NEMO/IKKγ protein enhances the anticancer effect of chemotherapy. J Biol Chem 2020; 295:3532-3552. [PMID: 32024692 DOI: 10.1074/jbc.ra119.009898] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 01/03/2020] [Indexed: 12/11/2022] Open
Abstract
NF-κB is a pro-inflammatory transcription factor that critically regulates immune responses and other distinct cellular pathways. However, many NF-κB-mediated pathways for cell survival and apoptosis signaling in cancer remain to be elucidated. Cell cycle and apoptosis regulatory protein 1 (CARP-1 or CCAR1) is a perinuclear phosphoprotein that regulates signaling induced by anticancer chemotherapy and growth factors. Although previous studies have reported that CARP-1 is a part of the NF-κB proteome, regulation of NF-κB signaling by CARP-1 and the molecular mechanism(s) involved are unclear. Here, we report that CARP-1 directly binds the NF-κB-activating kinase IκB kinase subunit γ (NEMO or NF-κB essential modulator) and regulates the chemotherapy-activated canonical NF-κB pathway. Importantly, blockade of NEMO-CARP-1 binding diminished NF-κB activation, indicated by reduced phosphorylation of its subunit p65/RelA by the chemotherapeutic agent adriamycin (ADR), but not NF-κB activation induced by tumor necrosis factor α (TNFα), interleukin (IL)-1β, or epidermal growth factor. High-throughput screening of a chemical library yielded a small molecule inhibitor of NEMO-CARP-1 binding, termed selective NF-κB inhibitor 1 (SNI)-1). We noted that SNI-1 enhances chemotherapy-dependent growth inhibition of a variety of cancer cells, including human triple-negative breast cancer (TNBC) and patient-derived TNBC cells in vitro, and attenuates chemotherapy-induced secretion of the pro-inflammatory cytokines TNFα, IL-1β, and IL-8. SNI-1 also enhanced ADR or cisplatin inhibition of murine TNBC tumors in vivo and reduced systemic levels of pro-inflammatory cytokines. We conclude that inhibition of NEMO-CARP-1 binding enhances responses of cancer cells to chemotherapy.
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Affiliation(s)
- Jaganathan Venkatesh
- John D. Dingell Veterans Affairs Medical Center, Wayne State University, Detroit, Michigan 48201; Karmanos Cancer Institute, Wayne State University, Detroit, Michigan 48201; Department of Oncology, Wayne State University, Detroit, Michigan 48201
| | - Sreeja C Sekhar
- John D. Dingell Veterans Affairs Medical Center, Wayne State University, Detroit, Michigan 48201; Karmanos Cancer Institute, Wayne State University, Detroit, Michigan 48201; Department of Oncology, Wayne State University, Detroit, Michigan 48201
| | - Vino T Cheriyan
- John D. Dingell Veterans Affairs Medical Center, Wayne State University, Detroit, Michigan 48201; Karmanos Cancer Institute, Wayne State University, Detroit, Michigan 48201; Department of Oncology, Wayne State University, Detroit, Michigan 48201
| | - Magesh Muthu
- John D. Dingell Veterans Affairs Medical Center, Wayne State University, Detroit, Michigan 48201; Karmanos Cancer Institute, Wayne State University, Detroit, Michigan 48201; Department of Oncology, Wayne State University, Detroit, Michigan 48201
| | - Paul Meister
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - Edi Levi
- John D. Dingell Veterans Affairs Medical Center, Wayne State University, Detroit, Michigan 48201; Department of Pathology, Wayne State University, Detroit, Michigan 48201
| | - Sijana Dzinic
- Karmanos Cancer Institute, Wayne State University, Detroit, Michigan 48201
| | - James W Gauld
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - Lisa A Polin
- Karmanos Cancer Institute, Wayne State University, Detroit, Michigan 48201
| | - Arun K Rishi
- John D. Dingell Veterans Affairs Medical Center, Wayne State University, Detroit, Michigan 48201; Karmanos Cancer Institute, Wayne State University, Detroit, Michigan 48201; Department of Oncology, Wayne State University, Detroit, Michigan 48201.
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12
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Mader J, Huber J, Bonn F, Dötsch V, Rogov VV, Bremm A. Oxygen-dependent asparagine hydroxylation of the ubiquitin-associated (UBA) domain in Cezanne regulates ubiquitin binding. J Biol Chem 2020; 295:2160-2174. [PMID: 31937588 DOI: 10.1074/jbc.ra119.010315] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 12/27/2019] [Indexed: 12/26/2022] Open
Abstract
Deubiquitinases (DUBs) are vital for the regulation of ubiquitin signals, and both catalytic activity of and target recruitment by DUBs need to be tightly controlled. Here, we identify asparagine hydroxylation as a novel posttranslational modification involved in the regulation of Cezanne (also known as OTU domain-containing protein 7B (OTUD7B)), a DUB that controls key cellular functions and signaling pathways. We demonstrate that Cezanne is a substrate for factor inhibiting HIF1 (FIH1)- and oxygen-dependent asparagine hydroxylation. We found that FIH1 modifies Asn35 within the uncharacterized N-terminal ubiquitin-associated (UBA)-like domain of Cezanne (UBACez), which lacks conserved UBA domain properties. We show that UBACez binds Lys11-, Lys48-, Lys63-, and Met1-linked ubiquitin chains in vitro, establishing UBACez as a functional ubiquitin-binding domain. Our findings also reveal that the interaction of UBACez with ubiquitin is mediated via a noncanonical surface and that hydroxylation of Asn35 inhibits ubiquitin binding. Recently, it has been suggested that Cezanne recruitment to specific target proteins depends on UBACez Our results indicate that UBACez can indeed fulfill this role as regulatory domain by binding various ubiquitin chain types. They also uncover that this interaction with ubiquitin, and thus with modified substrates, can be modulated by oxygen-dependent asparagine hydroxylation, suggesting that Cezanne is regulated by oxygen levels.
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Affiliation(s)
- Julia Mader
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Jessica Huber
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue Strasse 9, 60438 Frankfurt am Main, Germany
| | - Florian Bonn
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Volker Dötsch
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue Strasse 9, 60438 Frankfurt am Main, Germany
| | - Vladimir V Rogov
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue Strasse 9, 60438 Frankfurt am Main, Germany
| | - Anja Bremm
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany.
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13
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Fang P, Yu H, Li M, He R, Zhu Y, Liu S. Rubicon: a facilitator of viral immune evasion. Cell Mol Immunol 2019; 16:770-771. [PMID: 31164715 PMCID: PMC6804746 DOI: 10.1038/s41423-019-0248-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 05/20/2019] [Indexed: 11/09/2022] Open
Affiliation(s)
- Peining Fang
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, 430072, Wuhan, China
| | - Haisheng Yu
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, 430072, Wuhan, China
| | - Mengqi Li
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, 430072, Wuhan, China
| | - Rui He
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, 430072, Wuhan, China
| | - Ying Zhu
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, 430072, Wuhan, China
| | - Shi Liu
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, 430072, Wuhan, China.
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14
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Martínez-Sánchez SM, Pérez-Sánchez H, Antonio Gabaldón J, Abellán-Alemán J, Montoro-García S. Multifunctional Peptides from Spanish Dry-Cured Pork Ham: Endothelial Responses and Molecular Modeling Studies. Int J Mol Sci 2019; 20:ijms20174204. [PMID: 31466215 PMCID: PMC6747274 DOI: 10.3390/ijms20174204] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 08/25/2019] [Accepted: 08/26/2019] [Indexed: 12/28/2022] Open
Abstract
Food peptides contain a very wide range of diversified structures, which explains their diverse range of functional activities. Proatherogenic endothelium is related to vasoconstriction, inflammation, and oxidative stress. In this line, four synthetic bioactive peptides from dry-cured pork ham, previously identified according to their Angiotensin I Converting Enzyme (ACE) inhibitory capacity and high bioavailability, were tested. Among them, KPVAAP displayed an estimated IC50 of 59.22 µM for human ACE inhibition, and docking simulations demonstrated the consistency of the noncompetitive binding with the protein. The addition of synthetic peptides to human endothelial cells significantly prevents the expression of genes related to endothelial dysfunction and inflammation (eNOS, ICAM-1, VCAM-1, IL-6) and lowers NF-κB activation (all p < 0.05). In silico dockings showed that the four bioactive peptides interact with the regulatory subunit NEMO of the NF-κB transcription factor at the same site as other characterized inhibitors (CC2-LZ region). This is the first study linking experimental and computational approaches that shows NF-κB to be the target of biopeptides of food origin. These multifunctional peptides from dry-cured pork ham make them good candidates for further research into their therapeutic or preventive use to attenuate the inflammatory atherosclerotic process.
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Affiliation(s)
- Sara María Martínez-Sánchez
- Laboratorio de Cultivo Celular, Facultad de Ciencias de la Salud, UCAM Universidad Católica San Antonio de Murcia, Campus de los Jerónimos s/n, Guadalupe 30107, Murcia, Spain
- Departamento Tecnología de la Alimentación y Nutrición, UCAM Universidad Católica San Antonio de Murcia, Campus de los Jerónimos s/n, Guadalupe 30107, Murcia, Spain
| | - Horacio Pérez-Sánchez
- Bioinformatics and High Performance Computing Research Group (BIO-HPC), Computer Engineering Department, Universidad Católica de Murcia (UCAM), Guadalupe 30107, Murcia, Spain
| | - José Antonio Gabaldón
- Departamento Tecnología de la Alimentación y Nutrición, UCAM Universidad Católica San Antonio de Murcia, Campus de los Jerónimos s/n, Guadalupe 30107, Murcia, Spain
| | - José Abellán-Alemán
- Cátedra de Riesgo Cardiovascular, UCAM Universidad Católica San Antonio de Murcia, Campus de los Jerónimos s/n, Guadalupe 30107, Murcia, Spain
| | - Silvia Montoro-García
- Laboratorio de Cultivo Celular, Facultad de Ciencias de la Salud, UCAM Universidad Católica San Antonio de Murcia, Campus de los Jerónimos s/n, Guadalupe 30107, Murcia, Spain.
- Cátedra de Riesgo Cardiovascular, UCAM Universidad Católica San Antonio de Murcia, Campus de los Jerónimos s/n, Guadalupe 30107, Murcia, Spain.
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15
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Herhaus L, van den Bedem H, Tang S, Maslennikov I, Wakatsuki S, Dikic I, Rahighi S. Molecular Recognition of M1-Linked Ubiquitin Chains by Native and Phosphorylated UBAN Domains. J Mol Biol 2019; 431:3146-3156. [DOI: 10.1016/j.jmb.2019.06.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 06/06/2019] [Accepted: 06/07/2019] [Indexed: 11/16/2022]
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16
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Ceccarelli DF, Ivantsiv S, Mullin AA, Coyaud E, Manczyk N, Maisonneuve P, Kurinov I, Zhao L, Go C, Gingras AC, Raught B, Cordes S, Sicheri F. FAM105A/OTULINL Is a Pseudodeubiquitinase of the OTU-Class that Localizes to the ER Membrane. Structure 2019; 27:1000-1012.e6. [PMID: 31056421 DOI: 10.1016/j.str.2019.03.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 02/23/2019] [Accepted: 03/27/2019] [Indexed: 12/16/2022]
Abstract
Pseudoenzymes have been identified across a diverse range of enzyme classes and fulfill important cellular functions. Examples of pseudoenzymes exist within ubiquitin conjugating and deubiquitinase (DUB) protein families. Here we characterize FAM105A/OTULINL, the only putative pseudodeubiquitinase of the ovarian tumor protease (OTU domain) family in humans. The crystal structure of FAM105A revealed that the OTU domain possesses structural deficiencies in both active site and substrate-binding infrastructure predicted to impair normal DUB function. We confirmed the absence of catalytic function against all ubiquitin linkages and an inability of FAM105A to bind ubiquitin compared with catalytically active FAM105B/OTULIN. FAM105A co-localized with KDEL markers and Lamin B1 at the endoplasmic reticulum (ER) and nuclear envelope, respectively. Accordingly, the FAM105A interactome exhibited significant enrichment in proteins localized to the ER/outer nuclear, Golgi and vesicular membranes. In light of undetectable deubiquitinase activity, we posit that FAM105A/OTULINL functions through its ability to mediate protein-protein interactions.
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Affiliation(s)
- Derek F Ceccarelli
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Sofiia Ivantsiv
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Amber Anne Mullin
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Etienne Coyaud
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Noah Manczyk
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Pierre Maisonneuve
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Igor Kurinov
- Department of Chemistry and Chemical Biology, Cornell University, NE-CAT, Argonne, IL 60439, USA
| | - Liang Zhao
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Chris Go
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Anne-Claude Gingras
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada.
| | - Sabine Cordes
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
| | - Frank Sicheri
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada.
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17
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Prescott JA, Cook SJ. Targeting IKKβ in Cancer: Challenges and Opportunities for the Therapeutic Utilisation of IKKβ Inhibitors. Cells 2018; 7:cells7090115. [PMID: 30142927 PMCID: PMC6162708 DOI: 10.3390/cells7090115] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 08/15/2018] [Accepted: 08/19/2018] [Indexed: 02/08/2023] Open
Abstract
Deregulated NF-κB signalling is implicated in the pathogenesis of numerous human inflammatory disorders and malignancies. Consequently, the NF-κB pathway has attracted attention as an attractive therapeutic target for drug discovery. As the primary, druggable mediator of canonical NF-κB signalling the IKKβ protein kinase has been the historical focus of drug development pipelines. Thousands of compounds with activity against IKKβ have been characterised, with many demonstrating promising efficacy in pre-clinical models of cancer and inflammatory disease. However, severe on-target toxicities and other safety concerns associated with systemic IKKβ inhibition have thus far prevented the clinical approval of any IKKβ inhibitors. This review will discuss the potential reasons for the lack of clinical success of IKKβ inhibitors to date, the challenges associated with their therapeutic use, realistic opportunities for their future utilisation, and the alternative strategies to inhibit NF-κB signalling that may overcome some of the limitations associated with IKKβ inhibition.
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Affiliation(s)
- Jack A Prescott
- Signalling Laboratory, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK.
| | - Simon J Cook
- Signalling Laboratory, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK.
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18
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Structures of REV1 UBM2 Domain Complex with Ubiquitin and with a Small-Molecule that Inhibits the REV1 UBM2–Ubiquitin Interaction. J Mol Biol 2018; 430:2857-2872. [DOI: 10.1016/j.jmb.2018.05.042] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 05/24/2018] [Accepted: 05/30/2018] [Indexed: 01/25/2023]
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19
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Brenke JK, Popowicz GM, Schorpp K, Rothenaigner I, Roesner M, Meininger I, Kalinski C, Ringelstetter L, R'kyek O, Jürjens G, Vincendeau M, Plettenburg O, Sattler M, Krappmann D, Hadian K. Targeting TRAF6 E3 ligase activity with a small-molecule inhibitor combats autoimmunity. J Biol Chem 2018; 293:13191-13203. [PMID: 29950522 DOI: 10.1074/jbc.ra118.002649] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 06/15/2018] [Indexed: 12/29/2022] Open
Abstract
Constitutive NF-κB signaling represents a hallmark of chronic inflammation and autoimmune diseases. The E3 ligase TNF receptor-associated factor 6 (TRAF6) acts as a key regulator bridging innate immunity, pro-inflammatory cytokines, and antigen receptors to the canonical NF-κB pathway. Structural analysis and point mutations have unraveled the essential role of TRAF6 binding to the E2-conjugating enzyme ubiquitin-conjugating enzyme E2 N (Ubc13 or UBE2N) to generate Lys63-linked ubiquitin chains for inflammatory and immune signal propagation. Genetic mutations disrupting TRAF6-Ubc13 binding have been shown to reduce TRAF6 activity and, consequently, NF-κB activation. However, to date, no small-molecule modulator is available to inhibit the TRAF6-Ubc13 interaction and thereby counteract NF-κB signaling and associated diseases. Here, using a high-throughput small-molecule screening approach, we discovered an inhibitor of the TRAF6-Ubc13 interaction that reduces TRAF6-Ubc13 activity both in vitro and in cells. We found that this compound, C25-140, impedes NF-κB activation in various immune and inflammatory signaling pathways also in primary human and murine cells. Importantly, C25-140 ameliorated inflammation and improved disease outcomes of autoimmune psoriasis and rheumatoid arthritis in preclinical in vivo mouse models. Hence, the first-in-class TRAF6-Ubc13 inhibitor C25-140 expands the toolbox for studying the impact of the ubiquitin system on immune signaling and underscores the importance of TRAF6 E3 ligase activity in psoriasis and rheumatoid arthritis. We propose that inhibition of TRAF6 activity by small molecules represents a promising novel strategy for targeting autoimmune and chronic inflammatory diseases.
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Affiliation(s)
- Jara K Brenke
- From the Assay Development and Screening Platform, Institute of Molecular Toxicology and Pharmacology
| | - Grzegorz M Popowicz
- the Institute of Structural Biology.,the Center for Integrated Protein Science Munich at Department Chemie, Technical University of Munich, Garching 85747, Germany
| | - Kenji Schorpp
- From the Assay Development and Screening Platform, Institute of Molecular Toxicology and Pharmacology
| | - Ina Rothenaigner
- From the Assay Development and Screening Platform, Institute of Molecular Toxicology and Pharmacology
| | | | - Isabel Meininger
- the Research Unit Cellular Signal Integration, Institute of Molecular Toxicology and Pharmacology
| | | | - Larissa Ringelstetter
- From the Assay Development and Screening Platform, Institute of Molecular Toxicology and Pharmacology
| | - Omar R'kyek
- the Institute of Medicinal Chemistry, and.,the Institute of Organic Chemistry, Leibnitz Universität Hannover, 30167 Hannover, Germany
| | - Gerrit Jürjens
- the Institute of Medicinal Chemistry, and.,the Institute of Organic Chemistry, Leibnitz Universität Hannover, 30167 Hannover, Germany
| | - Michelle Vincendeau
- the Research Unit Cellular Signal Integration, Institute of Molecular Toxicology and Pharmacology.,the Institute of Virology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Oliver Plettenburg
- the Institute of Medicinal Chemistry, and.,the Institute of Organic Chemistry, Leibnitz Universität Hannover, 30167 Hannover, Germany
| | - Michael Sattler
- the Institute of Structural Biology.,the Center for Integrated Protein Science Munich at Department Chemie, Technical University of Munich, Garching 85747, Germany
| | - Daniel Krappmann
- the Research Unit Cellular Signal Integration, Institute of Molecular Toxicology and Pharmacology
| | - Kamyar Hadian
- From the Assay Development and Screening Platform, Institute of Molecular Toxicology and Pharmacology,
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20
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Ran X, Gestwicki JE. Inhibitors of protein-protein interactions (PPIs): an analysis of scaffold choices and buried surface area. Curr Opin Chem Biol 2018; 44:75-86. [PMID: 29908451 DOI: 10.1016/j.cbpa.2018.06.004] [Citation(s) in RCA: 167] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 06/04/2018] [Indexed: 12/17/2022]
Abstract
Protein-protein interactions (PPI) were once considered 'undruggable', but clinical successes, driven by advanced methods in drug discovery, have challenged that notion. Here, we review the last three years of literature on PPI inhibitors to understand what is working and why. From the 66 recently reported PPI inhibitors, we found that the average molecular weight was significantly greater than 500Da, but that this trend was driven, in large part, by the contribution of peptide-based compounds. Despite differences in average molecular weight, we found that compounds based on small molecules or peptides were almost equally likely to be potent inhibitors (KD<1μM). Finally, we found PPIs with buried surface area (BSA) less than 2000Å2 were more likely to be inhibited by small molecules, while PPIs with larger BSA values were typically inhibited by peptides. PPIs with BSA values over 4000Å2 seemed to create a particular challenge, especially for orthosteric small molecules. Thus, it seems important to choose the inhibitor scaffold based on the properties of the target interaction. Moreover, this survey suggests a (more nuanced) conclusion to the question of whether PPIs are good drug targets; namely, that some PPIs are readily 'druggable' given the right choice of scaffold, while others still seem to deserve the 'undruggable' moniker.
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Affiliation(s)
- Xu Ran
- Institute for Neurodegenerative Diseases and Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, United States
| | - Jason E Gestwicki
- Institute for Neurodegenerative Diseases and Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, United States.
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21
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Fennell LM, Rahighi S, Ikeda F. Linear ubiquitin chain-binding domains. FEBS J 2018; 285:2746-2761. [PMID: 29679476 DOI: 10.1111/febs.14478] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 03/08/2018] [Accepted: 04/13/2018] [Indexed: 12/25/2022]
Abstract
Ubiquitin modification (ubiquitination) of target proteins can vary with respect to chain lengths, linkage type, and chain forms, such as homologous, mixed, and branched ubiquitin chains. Thus, ubiquitination can generate multiple unique surfaces on a target protein substrate. Ubiquitin-binding domains (UBDs) recognize ubiquitinated substrates, by specifically binding to these unique surfaces, modulate the formation of cellular signaling complexes and regulate downstream signaling cascades. Among the eight different homotypic chain types, Met1-linked (also termed linear) chains are the only chains in which linkage occurs on a non-Lys residue of ubiquitin. Linear ubiquitin chains have been implicated in immune responses, cell death and autophagy, and several UBDs - specific for linear ubiquitin chains - have been identified. In this review, we describe the main principles of ubiquitin recognition by UBDs, focusing on linear ubiquitin chains and their roles in biology.
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Affiliation(s)
- Lilian M Fennell
- Institute of Molecular Biotechnology (IMBA), Vienna Biocenter (VBC), Austria
| | - Simin Rahighi
- Chapman University School of Pharmacy (CUSP), Harry and Diane Health Science Campus, Chapman University, Irvine, CA, USA
| | - Fumiyo Ikeda
- Institute of Molecular Biotechnology (IMBA), Vienna Biocenter (VBC), Austria
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22
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Maubach G, Schmädicke AC, Naumann M. NEMO Links Nuclear Factor-κB to Human Diseases. Trends Mol Med 2017; 23:1138-1155. [PMID: 29128367 DOI: 10.1016/j.molmed.2017.10.004] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 10/16/2017] [Accepted: 10/19/2017] [Indexed: 12/13/2022]
Abstract
The nuclear factor (NF)-κB essential modulator (NEMO) is a key regulator in NF-κB-mediated signaling. By transmitting extracellular or intracellular signals, NEMO can control NF-κB-regulated genes. NEMO dysfunction is associated with inherited diseases such as incontinentia pigmenti (IP), ectodermal dysplasia, anhidrotic, with immunodeficiency (EDA-ID), and some cancers. We focus on molecular studies, human case reports, and mouse models emphasizing the significance of NEMO molecular interactions and modifications in health and diseases. This knowledge opens new opportunities to engineer suitable drugs that may putatively target precise NEMO functions attributable to various diseases, while leaving other functions intact, and eliminating cytotoxicity. Indeed, with the advent of novel gene editing tools such as clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas)9, treating some inherited diseases may in the long run, become a reality.
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Affiliation(s)
- Gunter Maubach
- Institute of Experimental Internal Medicine, Otto von Guericke University, Magdeburg, Germany
| | - Ann-Christin Schmädicke
- Institute of Experimental Internal Medicine, Otto von Guericke University, Magdeburg, Germany
| | - Michael Naumann
- Institute of Experimental Internal Medicine, Otto von Guericke University, Magdeburg, Germany.
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23
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Begalli F, Bennett J, Capece D, Verzella D, D'Andrea D, Tornatore L, Franzoso G. Unlocking the NF-κB Conundrum: Embracing Complexity to Achieve Specificity. Biomedicines 2017; 5:E50. [PMID: 28829404 PMCID: PMC5618308 DOI: 10.3390/biomedicines5030050] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 08/04/2017] [Accepted: 08/10/2017] [Indexed: 12/12/2022] Open
Abstract
Transcription factors of the nuclear factor κB (NF-κB) family are central coordinating regulators of the host defence responses to stress, injury and infection. Aberrant NF-κB activation also contributes to the pathogenesis of some of the most common current threats to global human health, including chronic inflammatory diseases, autoimmune disorders, diabetes, vascular diseases and the majority of cancers. Accordingly, the NF-κB pathway is widely considered an attractive therapeutic target in a broad range of malignant and non-malignant diseases. Yet, despite the aggressive efforts by the pharmaceutical industry to develop a specific NF-κB inhibitor, none has been clinically approved, due to the dose-limiting toxicities associated with the global suppression of NF-κB. In this review, we summarise the main strategies historically adopted to therapeutically target the NF-κB pathway with an emphasis on oncology, and some of the emerging strategies and newer agents being developed to pharmacologically inhibit this pathway.
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Affiliation(s)
- Federica Begalli
- Centre for Cell Signalling and Inflammation, Department of Medicine, Imperial College London, London W12 0NN, UK.
| | - Jason Bennett
- Centre for Cell Signalling and Inflammation, Department of Medicine, Imperial College London, London W12 0NN, UK.
| | - Daria Capece
- Centre for Cell Signalling and Inflammation, Department of Medicine, Imperial College London, London W12 0NN, UK.
| | - Daniela Verzella
- Centre for Cell Signalling and Inflammation, Department of Medicine, Imperial College London, London W12 0NN, UK.
| | - Daniel D'Andrea
- Centre for Cell Signalling and Inflammation, Department of Medicine, Imperial College London, London W12 0NN, UK.
| | - Laura Tornatore
- Centre for Cell Signalling and Inflammation, Department of Medicine, Imperial College London, London W12 0NN, UK.
| | - Guido Franzoso
- Centre for Cell Signalling and Inflammation, Department of Medicine, Imperial College London, London W12 0NN, UK.
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24
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