1
|
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.
Collapse
|
2
|
Gauto DF, Macek P, Malinverni D, Fraga H, Paloni M, Sučec I, Hessel A, Bustamante JP, Barducci A, Schanda P. Functional control of a 0.5 MDa TET aminopeptidase by a flexible loop revealed by MAS NMR. Nat Commun 2022; 13:1927. [PMID: 35395851 PMCID: PMC8993905 DOI: 10.1038/s41467-022-29423-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 03/14/2022] [Indexed: 02/07/2023] Open
Abstract
Large oligomeric enzymes control a myriad of cellular processes, from protein synthesis and degradation to metabolism. The 0.5 MDa large TET2 aminopeptidase, a prototypical protease important for cellular homeostasis, degrades peptides within a ca. 60 Å wide tetrahedral chamber with four lateral openings. The mechanisms of substrate trafficking and processing remain debated. Here, we integrate magic-angle spinning (MAS) NMR, mutagenesis, co-evolution analysis and molecular dynamics simulations and reveal that a loop in the catalytic chamber is a key element for enzymatic function. The loop is able to stabilize ligands in the active site and may additionally have a direct role in activating the catalytic water molecule whereby a conserved histidine plays a key role. Our data provide a strong case for the functional importance of highly dynamic - and often overlooked - parts of an enzyme, and the potential of MAS NMR to investigate their dynamics at atomic resolution.
Collapse
Affiliation(s)
- Diego F Gauto
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, F-38044, Grenoble, France
- ICSN, CNRS UPR2301, Univ. Paris-Saclay, Gif-sur-Yvette, France
| | - Pavel Macek
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, F-38044, Grenoble, France
- Celonic AG, Eulerstrasse 55, 4051, Basel, Switzerland
| | - Duccio Malinverni
- Department of Structural Biology and Center for Data Driven Discovery, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Hugo Fraga
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, F-38044, Grenoble, France
- Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Porto, Portugal
- i3S, Instituto de Investigacao e Inovacao em Saude, Universidade do Porto, Porto, Portugal
| | - Matteo Paloni
- CBS (Centre de Biologie Structurale), Univ Montpellier, CNRS, INSERM, Montpellier, France
| | - Iva Sučec
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, F-38044, Grenoble, France
| | - Audrey Hessel
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, F-38044, Grenoble, France
| | - Juan Pablo Bustamante
- Instituto de Bioingenieria y Bioinformatica, IBB (CONICET-UNER), Oro Verde, Entre Rios, Argentina
| | - Alessandro Barducci
- CBS (Centre de Biologie Structurale), Univ Montpellier, CNRS, INSERM, Montpellier, France.
| | - Paul Schanda
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, F-38044, Grenoble, France.
- Institute of Science and Technology Austria, Am Campus 1, A-3400, Klosterneuburg, Austria.
| |
Collapse
|
3
|
Bang ML, Bogomolovas J, Chen J. Understanding the molecular basis of cardiomyopathy. Am J Physiol Heart Circ Physiol 2022; 322:H181-H233. [PMID: 34797172 PMCID: PMC8759964 DOI: 10.1152/ajpheart.00562.2021] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/16/2021] [Accepted: 11/16/2021] [Indexed: 02/03/2023]
Abstract
Inherited cardiomyopathies are a major cause of mortality and morbidity worldwide and can be caused by mutations in a wide range of proteins located in different cellular compartments. The present review is based on Dr. Ju Chen's 2021 Robert M. Berne Distinguished Lectureship of the American Physiological Society Cardiovascular Section, in which he provided an overview of the current knowledge on the cardiomyopathy-associated proteins that have been studied in his laboratory. The review provides a general summary of the proteins in different compartments of cardiomyocytes associated with cardiomyopathies, with specific focus on the proteins that have been studied in Dr. Chen's laboratory.
Collapse
Affiliation(s)
- Marie-Louise Bang
- Institute of Genetic and Biomedical Research (IRGB), National Research Council (CNR), Milan Unit, Milan, Italy
- IRCCS Humanitas Research Hospital, Rozzano (Milan), Italy
| | - Julius Bogomolovas
- Division of Cardiovascular Medicine, Department of Medicine Cardiology, University of California, San Diego, La Jolla, California
| | - Ju Chen
- Division of Cardiovascular Medicine, Department of Medicine Cardiology, University of California, San Diego, La Jolla, California
| |
Collapse
|
4
|
Andreeva L, David L, Rawson S, Shen C, Pasricha T, Pelegrin P, Wu H. NLRP3 cages revealed by full-length mouse NLRP3 structure control pathway activation. Cell 2021; 184:6299-6312.e22. [PMID: 34861190 PMCID: PMC8763037 DOI: 10.1016/j.cell.2021.11.011] [Citation(s) in RCA: 119] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/17/2021] [Accepted: 11/08/2021] [Indexed: 12/24/2022]
Abstract
The NACHT-, leucine-rich-repeat- (LRR), and pyrin domain-containing protein 3 (NLRP3) is emerging to be a critical intracellular inflammasome sensor of membrane integrity and a highly important clinical target against chronic inflammation. Here, we report that an endogenous, stimulus-responsive form of full-length mouse NLRP3 is a 12- to 16-mer double-ring cage held together by LRR-LRR interactions with the pyrin domains shielded within the assembly to avoid premature activation. Surprisingly, this NLRP3 form is predominantly membrane localized, which is consistent with previously noted localization of NLRP3 at various membrane organelles. Structure-guided mutagenesis reveals that trans-Golgi network dispersion into vesicles, an early event observed for many NLRP3-activating stimuli, requires the double-ring cages of NLRP3. Double-ring-defective NLRP3 mutants abolish inflammasome punctum formation, caspase-1 processing, and cell death. Thus, our data uncover a physiological NLRP3 oligomer on the membrane that is poised to sense diverse signals to induce inflammasome activation.
Collapse
Affiliation(s)
- Liudmila Andreeva
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Liron David
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Shaun Rawson
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Harvard Cryo-EM Center for Structural Biology, Boston, MA 02115, USA
| | - Chen Shen
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Teerithveen Pasricha
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Northeastern University, Boston, MA 02115, USA
| | - Pablo Pelegrin
- Instituto Murciano de Investigación Biosanitaria (IMIB-Arrixaca), Universidad de Murcia, Murcia, Spain
| | - Hao Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA.
| |
Collapse
|
5
|
Wang L, Yu F, Xu N, Lu L. Grass carp reovirus capsid protein interacts with cellular proteasome subunit beta-type 7: Evidence for the involvement of host proteasome during aquareovirus infection. FISH & SHELLFISH IMMUNOLOGY 2020; 98:77-86. [PMID: 31846778 DOI: 10.1016/j.fsi.2019.12.047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 12/09/2019] [Accepted: 12/13/2019] [Indexed: 06/10/2023]
Abstract
The eukaryotic proteasome is a large multi-subunit complex that plays an important role in a wide range of fundamental cellular functions by degrading un-needed or damaged proteins, which also can be inverted or manipulated by viruses to favor viral infection. In this study, we demonstrated that proteasome subunit beta-type 7 (PSMB7), a proteasome-constitutive protein that is important for proteasome assembly, interacts with grass carp reovirus (GCRV) capsid proteins. Yeast 2-hybrid assay indicates that capsid protein VP38 of genotype Ⅲ GCRV could bind PSMB7, and this mutual interaction was further confirmed by pull-down, co-immunoprecipitation and subcellular co-localization assays. Furthermore, VP38 homologous proteins, VP7 from genotype I and VP35 from genotype II GCRV, can also interact with host PSMB7 in similar protein-protein interaction assays. Finally, PSMB7 expression level remains stable during GCRV infection, while, psmb7 gene transcription was repressed upon GCRV challenge; interaction with PSMB7 doesn't result in protein degradation of either VP7 or VP38 during viral infection. Thus, the interaction between host PSMB7 and viral capsid protein might suggest that interfering with PSMB7-mediated proteasome assembly should be involved in efficient aquareovirus infection.
Collapse
Affiliation(s)
- Longlong Wang
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, PR China
| | - Fei Yu
- Key Laboratory of Agriculture Ministry for Freshwater Aquatic Genetic Resources, Shanghai Ocean University, Shanghai, PR China
| | - Ning Xu
- National Experimental Teaching Demonstration Center for Fishery Sciences, Shanghai Ocean University, Shanghai, PR China
| | - Liqun Lu
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, PR China.
| |
Collapse
|
6
|
Schütz S, Sprangers R. Methyl TROSY spectroscopy: A versatile NMR approach to study challenging biological systems. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2020; 116:56-84. [PMID: 32130959 DOI: 10.1016/j.pnmrs.2019.09.004] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 09/09/2019] [Accepted: 09/25/2019] [Indexed: 05/21/2023]
Abstract
A major goal in structural biology is to unravel how molecular machines function in detail. To that end, solution-state NMR spectroscopy is ideally suited as it is able to study biological assemblies in a near natural environment. Based on methyl TROSY methods, it is now possible to record high-quality data on complexes that are far over 100 kDa in molecular weight. In this review, we discuss the theoretical background of methyl TROSY spectroscopy, the information that can be extracted from methyl TROSY spectra and approaches that can be used to assign methyl resonances in large complexes. In addition, we touch upon insights that have been obtained for a number of challenging biological systems, including the 20S proteasome, the RNA exosome, molecular chaperones and G-protein-coupled receptors. We anticipate that methyl TROSY methods will be increasingly important in modern structural biology approaches, where information regarding static structures is complemented with insights into conformational changes and dynamic intermolecular interactions.
Collapse
Affiliation(s)
- Stefan Schütz
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Remco Sprangers
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany.
| |
Collapse
|
7
|
Vigneron N, Stroobant V, Ferrari V, Abi Habib J, Van den Eynde BJ. Production of spliced peptides by the proteasome. Mol Immunol 2019; 113:93-102. [DOI: 10.1016/j.molimm.2018.03.030] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 03/09/2018] [Accepted: 03/29/2018] [Indexed: 01/28/2023]
|
8
|
Xu Y, Yang X, Chen Y, Chen H, Sun H, Li W, Xie Q, Yu L, Shao L. Discovery of novel 20S proteasome inhibitors by rational topology-based scaffold hopping of bortezomib. Bioorg Med Chem Lett 2018; 28:2148-2152. [PMID: 29773504 DOI: 10.1016/j.bmcl.2018.05.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 04/25/2018] [Accepted: 05/08/2018] [Indexed: 01/05/2023]
Abstract
A series of structurally novel proteasome inhibitors 1-12 have been developed based rational topology-based scaffold hopping of bortezomib. Among these novel proteasome inhibitors, compound 10 represents an important advance due to the comparable proteasome-inhibitory activity (IC50 = 9.7 nM) to bortezomib (IC50 = 8.3 nM), the remarkably higher BEI and SEI values and the effectiveness in metabolic stability. Therefore, compound 10 provides an excellent lead suitable for further optimization.
Collapse
Affiliation(s)
- Yulong Xu
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Zhangjiang Hi-tech Park, Pudong, Shanghai 201203, China
| | - Xicheng Yang
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Zhangjiang Hi-tech Park, Pudong, Shanghai 201203, China
| | - Yiyi Chen
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Zhangjiang Hi-tech Park, Pudong, Shanghai 201203, China
| | - Hao Chen
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Zhangjiang Hi-tech Park, Pudong, Shanghai 201203, China
| | - Huijiao Sun
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Zhangjiang Hi-tech Park, Pudong, Shanghai 201203, China
| | - Wei Li
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Zhangjiang Hi-tech Park, Pudong, Shanghai 201203, China
| | - Qiong Xie
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Zhangjiang Hi-tech Park, Pudong, Shanghai 201203, China
| | - Linqian Yu
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Zhangjiang Hi-tech Park, Pudong, Shanghai 201203, China
| | - Liming Shao
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Zhangjiang Hi-tech Park, Pudong, Shanghai 201203, China; State Key Laboratory of Medical Neurobiology, Fudan University, 138 Yixueyuan Road, Shanghai 200032, China.
| |
Collapse
|
9
|
On the Trails of the Proteasome Fold: Structural and Functional Analysis of the Ancestral β-Subunit Protein Anbu. J Mol Biol 2018; 430:628-640. [DOI: 10.1016/j.jmb.2018.01.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 12/30/2017] [Accepted: 01/04/2018] [Indexed: 11/20/2022]
|
10
|
Milder degenerative effects of Carfilzomib vs. Bortezomib in the Drosophila model: a link to clinical adverse events. Sci Rep 2017; 7:17802. [PMID: 29259189 PMCID: PMC5736585 DOI: 10.1038/s41598-017-17596-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 11/27/2017] [Indexed: 12/15/2022] Open
Abstract
Proteasome inhibitors, e.g. Bortezomib (BTZ) and Carfilzomib (CFZ), have demonstrated clinical efficacy against haematological cancers. Interestingly, several adverse effects are less common, compared to BTZ, in patients treated with CFZ. As the molecular details of these observations remain not well understood we assayed the pathophysiological effects of CFZ vs. BTZ in the Drosophila experimental model. Mass Spectrometry analyses showed that neither CFZ nor BTZ are hydrolysed in flies’ tissues, while at doses inducing similar inhibition of the rate limiting for protein breakdown chymotrypsin-like (CT-L) proteasomal activity, CFZ treatment resulted in less intense increase of oxidative stress or activation of antioxidant and proteostatic modules. Also, despite comparable cardiotoxicity likely due to disrupted mitochondrial function, CFZ did not affect developmental processes, showed minimal neuromuscular defects and reduced to a lesser extent flies’ healthspan. Studies in flies, human cancer cell lines and blood cells isolated from Multiple Myeloma patients treated with CFZ or BTZ revealed, that the increased BTZ toxicity likely relates to partial co-inhibition of the caspase-like (C-L) proteasomal activity Supportively, co-treating flies with CFZ and a C-L selective proteasome inhibitor exacerbated CFZ-mediated toxicity. Our findings provide a reasonable explanation for the differential adverse effects of CFZ and BTZ in the clinic.
Collapse
|
11
|
Dato AD, Cunsolo A, Persico M, Santoro AM, D'Urso A, Milardi D, Purrello R, Stefanelli M, Paolesse R, Tundo GR, Sbardella D, Fattorusso C, Coletta M. Electrostatic Map Of Proteasome α-Rings Encodes The Design of Allosteric Porphyrin-Based Inhibitors Able To Affect 20S Conformation By Cooperative Binding. Sci Rep 2017; 7:17098. [PMID: 29213119 PMCID: PMC5719074 DOI: 10.1038/s41598-017-17008-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 11/20/2017] [Indexed: 12/13/2022] Open
Abstract
The importance of allosteric proteasome inhibition in the treatment of cancer is becoming increasingly evident. Motivated by this urgent therapeutic need, we have recently identified cationic porphyrins as a highly versatile class of molecules able to regulate proteasome activity by interfering with gating mechanisms. In the present study, the mapping of electrostatic contacts bridging the regulatory particles with the α-rings of the human 20S proteasome led us to the identification of (meso-tetrakis(4-N-methylphenyl pyridyl)-porphyrin (pTMPyPP4) as a novel non-competitive inhibitor of human 20S proteasome. pTMPyPP4 inhibition mechanism implies a positive cooperative binding to proteasome, which disappears when a permanently open proteasome mutant (α-3ΔN) is used, supporting the hypothesis that the events associated with allosteric proteasome inhibition by pTMPyPP4 interfere with 20S gating and affect its "open-closed" equilibrium. Therefore, we propose that the spatial distribution of the negatively charged residues responsible for the interaction with regulatory particles at the α-ring surface of human 20S may be exploited as a blueprint for the design of allosteric proteasome regulators.
Collapse
Affiliation(s)
- Antonio Di Dato
- Dipartimento di Farmacia Università di Napoli "Federico II", Via D. Montesano, 49 I, 80131, Napoli, Italy
| | - Alessandra Cunsolo
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale A. Doria 6, 95125, Catania, Italy
| | - Marco Persico
- Dipartimento di Farmacia Università di Napoli "Federico II", Via D. Montesano, 49 I, 80131, Napoli, Italy
| | - Anna Maria Santoro
- Istituto di Biostrutture e Bioimmagini-CNR sede secondaria di Catania, Via P. Gaifami, 9- 95126, Catania, Italy
| | - Alessandro D'Urso
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale A. Doria 6, 95125, Catania, Italy
| | - Danilo Milardi
- Istituto di Biostrutture e Bioimmagini-CNR sede secondaria di Catania, Via P. Gaifami, 9- 95126, Catania, Italy
| | - Roberto Purrello
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale A. Doria 6, 95125, Catania, Italy.
| | - Manuela Stefanelli
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata-Via della Ricerca Scientifica, 00133, Roma, Italy
| | - Roberto Paolesse
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata-Via della Ricerca Scientifica, 00133, Roma, Italy
| | - Grazia R Tundo
- Dipartimento di Scienze Cliniche e Medicina Traslazionale, Università di Roma Tor Vergata, Via Montpellier 1, 00133, Roma, Italy
| | - Diego Sbardella
- Dipartimento di Scienze Cliniche e Medicina Traslazionale, Università di Roma Tor Vergata, Via Montpellier 1, 00133, Roma, Italy
| | - Caterina Fattorusso
- Dipartimento di Farmacia Università di Napoli "Federico II", Via D. Montesano, 49 I, 80131, Napoli, Italy.
| | - Massimo Coletta
- Dipartimento di Scienze Cliniche e Medicina Traslazionale, Università di Roma Tor Vergata, Via Montpellier 1, 00133, Roma, Italy.
| |
Collapse
|
12
|
Agbowuro AA, Huston WM, Gamble AB, Tyndall JDA. Proteases and protease inhibitors in infectious diseases. Med Res Rev 2017; 38:1295-1331. [PMID: 29149530 DOI: 10.1002/med.21475] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 09/10/2017] [Accepted: 10/17/2017] [Indexed: 12/31/2022]
Abstract
There are numerous proteases of pathogenic organisms that are currently targeted for therapeutic intervention along with many that are seen as potential drug targets. This review discusses the chemical and biological makeup of some key druggable proteases expressed by the five major classes of disease causing agents, namely bacteria, viruses, fungi, eukaryotes, and prions. While a few of these enzymes including HIV protease and HCV NS3-4A protease have been targeted to a clinically useful level, a number are yet to yield any clinical outcomes in terms of antimicrobial therapy. A significant aspect of this review discusses the chemical and pharmacological characteristics of inhibitors of the various proteases discussed. A total of 25 inhibitors have been considered potent and safe enough to be trialed in humans and are at different levels of clinical application. We assess the mechanism of action and clinical performance of the protease inhibitors against infectious agents with their developmental strategies and look to the next frontiers in the use of protease inhibitors as anti-infective agents.
Collapse
Affiliation(s)
| | - Wilhelmina M Huston
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW, Australia
| | - Allan B Gamble
- School of Pharmacy, University of Otago, Dunedin, New Zealand
| | | |
Collapse
|
13
|
Agrawal A, Khan MJ, Graugnard DE, Vailati-Riboni M, Rodriguez-Zas SL, Osorio JS, Loor JJ. Prepartal Energy Intake Alters Blood Polymorphonuclear Leukocyte Transcriptome During the Peripartal Period in Holstein Cows. Bioinform Biol Insights 2017; 11:1177932217704667. [PMID: 28579762 PMCID: PMC5414586 DOI: 10.1177/1177932217704667] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 03/13/2017] [Indexed: 12/18/2022] Open
Abstract
In the dairy industry, cow health and farmer profits depend on the balance between diet (ie, nutrient composition, daily intake) and metabolism. This is especially true during the transition period, where dramatic physiological changes foster vulnerability to immunosuppression, negative energy balance, and clinical and subclinical disorders. Using an Agilent microarray platform, this study examined changes in the transcriptome of bovine polymorphonuclear leukocytes (PMNLs) due to prepartal dietary intake. Holstein cows were fed a high-straw, control-energy diet (CON; NEL = 1.34 Mcal/kg) or overfed a moderate-energy diet (OVE; NEL = 1.62 Mcal/kg) during the dry period. Blood for PMNL isolation and metabolite analysis was collected at −14 and +7 days relative to parturition. At an analysis of variance false discovery rate <0.05, energy intake (OVE vs CON) influenced 1806 genes. Dynamic Impact Approach bioinformatics analysis classified treatment effects on Kyoto Encyclopedia of Genes and Genomes pathways, including activated oxidative phosphorylation and biosynthesis of unsaturated fatty acids and inhibited RNA polymerase, proteasome, and toll-like receptor signaling pathway. This analysis indicates that processes critical for energy metabolism and cellular and immune function were affected with mixed results. However, overall interpretation of the transcriptome data agreed in part with literature documenting a potentially detrimental, chronic activation of PMNL in response to overfeeding. The widespread, transcriptome-level changes captured here confirm the importance of dietary energy adjustments around calving on the immune system.
Collapse
Affiliation(s)
- A Agrawal
- Division of Nutritional Sciences, Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - M J Khan
- Division of Nutritional Sciences, Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - D E Graugnard
- Division of Nutritional Sciences, Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - M Vailati-Riboni
- Division of Nutritional Sciences, Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - S L Rodriguez-Zas
- Division of Nutritional Sciences, Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - J S Osorio
- Department of Dairy Science, South Dakota State University, Brookings, SD, USA
| | - J J Loor
- Division of Nutritional Sciences, Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| |
Collapse
|
14
|
Siddiqui R, Saleem S, Khan NA. The effect of peptidic and non-peptidic proteasome inhibitors on the biological properties of Acanthamoeba castellanii belonging to the T4 genotype. Exp Parasitol 2016; 168:16-24. [PMID: 27327524 DOI: 10.1016/j.exppara.2016.06.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 06/01/2016] [Accepted: 06/17/2016] [Indexed: 10/21/2022]
Abstract
The treatment of Acanthamoeba infections remains problematic, suggesting that new targets and/or chemotherapeutic agents are needed. Bioassay-guided screening of drugs that are clinically-approved for non-communicable diseases against opportunistic eukaryotic pathogens is a viable strategy. With known targets and mode of action, such drugs can advance to clinical trials at a faster pace. Recently Bortezomib (proteasome inhibitor) has been approved by FDA in the treatment of multiple myeloma. As proteasomal pathways are well known regulators of a variety of eukaryotic cellular functions, the overall aim of the present study was to study the effects of peptidic and non-peptidic proteasome inhibitors on the biology and pathogenesis of Acanthamoeba castellanii of the T4 genotype, in vitro. Zymographic assays revealed that inhibition of proteasome had detrimental effects on the extracellular proteolytic activities of A. castellanii. Proteasome inhibition affected A. castellanii growth (using amoebistatic assays), but not viability of A. castellanii. Importantly, proteasome inhibitors affected encystation as determined by trophozoite transformation into the cyst form, as well as excystation, as determined by cyst transformation into the trophozoite form. The ability of proteasome inhibitor to block Acanthamoeba differentiation is significant, as it presents a major challenge in the successful treatment of Acanthamoeba infection. As these drugs are used clinically against non-communicable diseases, the findings reported here have the potential to be tested in a clinical setting against amoebic infections.
Collapse
Affiliation(s)
- Ruqaiyyah Siddiqui
- Department of Biological Sciences, Faculty of Science and Technology, Sunway University, Malaysia
| | - Sahreena Saleem
- Department of Biological and Biomedical Sciences, Aga Khan University, Pakistan
| | - Naveed Ahmed Khan
- Department of Biological Sciences, Faculty of Science and Technology, Sunway University, Malaysia.
| |
Collapse
|
15
|
Imkamp F, Ziemski M, Weber-Ban E. Pupylation-dependent and -independent proteasomal degradation in mycobacteria. Biomol Concepts 2016; 6:285-301. [PMID: 26352358 DOI: 10.1515/bmc-2015-0017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 07/08/2015] [Indexed: 02/02/2023] Open
Abstract
Bacteria make use of compartmentalizing protease complexes, similar in architecture but not homologous to the eukaryotic proteasome, for the selective and processive removal of proteins. Mycobacteria as members of the actinobacteria harbor proteasomes in addition to the canonical bacterial degradation complexes. Mycobacterial proteasomal degradation, although not essential during normal growth, becomes critical for survival under particular environmental conditions, like, for example, during persistence of the pathogenic Mycobacterium tuberculosis in host macrophages or of environmental mycobacteria under starvation. Recruitment of protein substrates for proteasomal degradation is usually mediated by pupylation, the post-translational modification of lysine side chains with the prokaryotic ubiquitin-like protein Pup. This substrate recruitment strategy is functionally reminiscent of ubiquitination in eukaryotes, but is the result of convergent evolution, relying on chemically and structurally distinct enzymes. Pupylated substrates are recognized by the ATP-dependent proteasomal regulator Mpa that associates with the 20S proteasome core. A pupylation-independent proteasome degradation pathway has recently been discovered that is mediated by the ATP-independent bacterial proteasome activator Bpa (also referred to as PafE), and that appears to play a role under stress conditions. In this review, mechanistic principles of bacterial proteasomal degradation are discussed and compared with functionally related elements of the eukaryotic ubiquitin-proteasome system. Special attention is given to an understanding on the molecular level based on structural and biochemical analysis. Wherever available, discussion of in vivo studies is included to highlight the biological significance of this unusual bacterial degradation pathway.
Collapse
|
16
|
Cross Talk of Proteostasis and Mitostasis in Cellular Homeodynamics, Ageing, and Disease. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2016; 2016:4587691. [PMID: 26977249 PMCID: PMC4763003 DOI: 10.1155/2016/4587691] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 12/24/2015] [Accepted: 12/31/2015] [Indexed: 12/26/2022]
Abstract
Mitochondria are highly dynamic organelles that provide essential metabolic functions and represent the major bioenergetic hub of eukaryotic cell. Therefore, maintenance of mitochondria activity is necessary for the proper cellular function and survival. To this end, several mechanisms that act at different levels and time points have been developed to ensure mitochondria quality control. An interconnected highly integrated system of mitochondrial and cytosolic chaperones and proteases along with the fission/fusion machinery represents the surveillance scaffold of mitostasis. Moreover, nonreversible mitochondrial damage targets the organelle to a specific autophagic removal, namely, mitophagy. Beyond the organelle dynamics, the constant interaction with the ubiquitin-proteasome-system (UPS) has become an emerging aspect of healthy mitochondria. Dysfunction of mitochondria and UPS increases with age and correlates with many age-related diseases including cancer and neurodegeneration. In this review, we discuss the functional cross talk of proteostasis and mitostasis in cellular homeodynamics and the impairment of mitochondrial quality control during ageing, cancer, and neurodegeneration.
Collapse
|
17
|
Voigt J, Woestemeyer J. Protease Inhibitors Cause Necrotic Cell Death in Chlamydomonas reinhardtii
by Inducing the Generation of Reactive Oxygen Species. J Eukaryot Microbiol 2015; 62:711-21. [DOI: 10.1111/jeu.12224] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 02/02/2015] [Accepted: 02/13/2015] [Indexed: 01/19/2023]
Affiliation(s)
- Juergen Voigt
- Institute for Biochemistry; Charité, Charité-Platz 1/Virchowweg 6; D-10117 Berlin Germany
- Institute of Microbiology; Friedrich-Schiller-University; Neugasse 24; D-07743 Jena Germany
| | - Johannes Woestemeyer
- Institute of Microbiology; Friedrich-Schiller-University; Neugasse 24; D-07743 Jena Germany
| |
Collapse
|
18
|
The amazing ubiquitin-proteasome system: structural components and implication in aging. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2014; 314:171-237. [PMID: 25619718 DOI: 10.1016/bs.ircmb.2014.09.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Proteome quality control (PQC) is critical for the maintenance of cellular functionality and it is assured by the curating activity of the proteostasis network (PN). PN is constituted of several complex protein machines that under conditions of proteome instability aim to, firstly identify, and then, either rescue or degrade nonnative polypeptides. Central to the PN functionality is the ubiquitin-proteasome system (UPS) which is composed from the ubiquitin-conjugating enzymes and the proteasome; the latter is a sophisticated multi-subunit molecular machine that functions in a bimodal way as it degrades both short-lived ubiquitinated normal proteins and nonfunctional polypeptides. UPS is also involved in PQC of the nucleus, the endoplasmic reticulum and the mitochondria and it also interacts with the other main cellular degradation axis, namely the autophagy-lysosome system. UPS functionality is optimum in the young organism but it is gradually compromised during aging resulting in increasing proteotoxic stress; these effects correlate not only with aging but also with most age-related diseases. Herein, we present a synopsis of the UPS components and of their functional alterations during cellular senescence or in vivo aging. We propose that mild UPS activation in the young organism will, likely, promote antiaging effects and/or suppress age-related diseases.
Collapse
|
19
|
Steers NJ, Peachman KK, Alving CR, Rao M. Isolation and purification of proteasomes from primary cells. CURRENT PROTOCOLS IN IMMUNOLOGY 2014; 107:16.4.1-16.4.20. [PMID: 25367127 DOI: 10.1002/0471142735.im1604s107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Proteasomes play an important role in cell homeostasis and in orchestrating the immune response by systematically degrading foreign proteins and misfolded or damaged host cell proteins. We describe a protocol to purify functionally active proteasomes from human CD4(+) T cells and dendritic cells derived from peripheral blood mononuclear cells. The purification is a three-step process involving ion-exchange chromatography, ammonium sulfate precipitation, and sucrose density gradient ultracentrifugation. This method can be easily adapted to purify proteasomes from cell lines or from organs. Methods to characterize and visualize the purified proteasomes are also described.
Collapse
Affiliation(s)
- Nicholas J Steers
- United States Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland
| | - Kristina K Peachman
- United States Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland
| | - Carl R Alving
- United States Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Mangala Rao
- United States Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
| |
Collapse
|
20
|
Dubiella C, Cui H, Gersch M, Brouwer AJ, Sieber SA, Krüger A, Liskamp RMJ, Groll M. Selective Inhibition of the Immunoproteasome by Ligand-Induced Crosslinking of the Active Site. Angew Chem Int Ed Engl 2014; 53:11969-73. [DOI: 10.1002/anie.201406964] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Indexed: 12/27/2022]
|
21
|
Dubiella C, Cui H, Gersch M, Brouwer AJ, Sieber SA, Krüger A, Liskamp RMJ, Groll M. Selektive Inhibition des Immunoproteasoms durch ligandeninduzierte Vernetzung des katalytischen Zentrums. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201406964] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
22
|
Sangith N, Srinivasaraghavan K, Sahu I, Desai A, Medipally S, Somavarappu AK, Verma C, Venkatraman P. Discovery of novel interacting partners of PSMD9, a proteasomal chaperone: Role of an Atypical and versatile PDZ-domain motif interaction and identification of putative functional modules. FEBS Open Bio 2014; 4:571-83. [PMID: 25009770 PMCID: PMC4087146 DOI: 10.1016/j.fob.2014.05.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 05/20/2014] [Accepted: 05/24/2014] [Indexed: 12/21/2022] Open
Abstract
The structure and functions of PSMD9, a proteasomal chaperone, are uncharacterized. PDZ-like domain of PSMD9 may recognize C-terminal residues in proteins. Using conserved C-terminal motifs in human proteome, we identify novel binding partners. hnRNPA1, GH, IL6-receptor, S14 and E12 interact with PSMD9 via a specific C-terminal motif. We predict and confirm residues in the PDZ domain that are involved in this interaction.
PSMD9 (Proteasome Macropain non-ATPase subunit 9), a proteasomal assembly chaperone, harbors an uncharacterized PDZ-like domain. Here we report the identification of five novel interacting partners of PSMD9 and provide the first glimpse at the structure of the PDZ-domain, including the molecular details of the interaction. We based our strategy on two propositions: (a) proteins with conserved C-termini may share common functions and (b) PDZ domains interact with C-terminal residues of proteins. Screening of C-terminal peptides followed by interactions using full-length recombinant proteins, we discovered hnRNPA1 (an RNA binding protein), S14 (a ribosomal protein), CSH1 (a growth hormone), E12 (a transcription factor) and IL6 receptor as novel PSMD9-interacting partners. Through multiple techniques and structural insights, we clearly demonstrate for the first time that human PDZ domain interacts with the predicted Short Linear Sequence Motif (SLIM) at the C-termini of the client proteins. These interactions are also recapitulated in mammalian cells. Together, these results are suggestive of the role of PSMD9 in transcriptional regulation, mRNA processing and editing, hormone and receptor activity and protein translation. Our proof-of-principle experiments endorse a novel and quick method for the identification of putative interacting partners of similar PDZ-domain proteins from the proteome and for discovering novel functions.
Collapse
Affiliation(s)
- Nikhil Sangith
- Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre (TMC), Kharghar, Navi Mumbai 410210, India
| | - Kannan Srinivasaraghavan
- Bioinformatics Institute ASTAR, 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore ; Experimental Therapeutics Centre (A*STAR), 31 Biopolis Street, #03-01 Helios, Singapore 138669, Singapore
| | - Indrajit Sahu
- Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre (TMC), Kharghar, Navi Mumbai 410210, India
| | - Ankita Desai
- Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre (TMC), Kharghar, Navi Mumbai 410210, India
| | - Spandana Medipally
- Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre (TMC), Kharghar, Navi Mumbai 410210, India
| | - Arun Kumar Somavarappu
- Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre (TMC), Kharghar, Navi Mumbai 410210, India
| | - Chandra Verma
- Bioinformatics Institute ASTAR, 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore ; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore ; Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
| | - Prasanna Venkatraman
- Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre (TMC), Kharghar, Navi Mumbai 410210, India
| |
Collapse
|
23
|
Shrestha RK, Ronau JA, Davies CW, Guenette RG, Strieter ER, Paul LN, Das C. Insights into the mechanism of deubiquitination by JAMM deubiquitinases from cocrystal structures of the enzyme with the substrate and product. Biochemistry 2014; 53:3199-217. [PMID: 24787148 PMCID: PMC4033627 DOI: 10.1021/bi5003162] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
AMSH, a conserved zinc metallo deubiquitinase,
controls downregulation
and degradation of cell-surface receptors mediated by the endosomal
sorting complexes required for transport (ESCRT) machinery. It displays
high specificity toward the Lys63-linked polyubiquitin chain, which
is used as a signal for ESCRT-mediated endosomal–lysosomal
sorting of receptors. Herein, we report the crystal structures of
the catalytic domain of AMSH orthologue Sst2 from fission yeast, its
ubiquitin (product)-bound form, and its Lys63-linked diubiquitin (substrate)-bound
form at 1.45, 1.7, and 2.3 Å, respectively. The structures reveal
that the P-side product fragment maintains nearly all the contacts
with the enzyme as seen with the P portion (distal ubiquitin) of the
Lys63-linked diubiquitin substrate, with additional coordination of
the Gly76 carboxylate group of the product with the active-site Zn2+. One of the product-bound structures described herein is
the result of an attempt to cocrystallize the diubiquitin substrate
bound to an active site mutant presumed to render the enzyme inactive,
instead yielding a cocrystal structure of the enzyme bound to the
P-side ubiquitin fragment of the substrate (distal ubiquitin). This
fragment was generated in situ from the residual
activity of the mutant enzyme. In this structure, the catalytic water
is seen placed between the active-site Zn2+ and the carboxylate
group of Gly76 of ubiquitin, providing what appears to be a snapshot
of the active site when the product is about to depart. Comparison
of this structure with that of the substrate-bound form suggests the
importance of dynamics of a flexible flap near the active site in
catalysis. The crystal structure of the Thr319Ile mutant of the catalytic
domain of Sst2 provides insight into structural basis of microcephaly
capillary malformation syndrome. Isothermal titration calorimetry
yields a dissociation constant (KD) of
10.2 ± 0.6 μM for the binding of ubiquitin to the enzyme,
a value comparable to the KM of the enzyme
catalyzing hydrolysis of the Lys63-linked diubiquitin substrate (∼20
μM). These results, together with the previously reported observation
that the intracellular concentration of free ubiquitin (∼20
μM) exceeds that of Lys63-linked polyubiquitin chains, imply
that the free, cytosolic form of the enzyme remains inhibited by being
tightly bound to free ubiquitin. We propose that when AMSH associates
with endosomes, inhibition would be relieved because of ubiquitin
binding domains present on its endosomal binding partners that would
shift the balance toward better recognition of polyubiquitin chains
via the avidity effect.
Collapse
Affiliation(s)
- Rashmi K Shrestha
- Department of Chemistry, Purdue University , 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | | | | | | | | | | | | |
Collapse
|
24
|
Kawamura S, Unno Y, Asai A, Arisawa M, Shuto S. Structurally Novel Highly Potent Proteasome Inhibitors Created by the Structure-Based Hybridization of Nonpeptidic Belactosin Derivatives and Peptide Boronates. J Med Chem 2014; 57:2726-35. [DOI: 10.1021/jm500045x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
| | - Yuka Unno
- Graduate
School of Pharmaceutical Sciences, University of Shizuoka, Yada, Shizuoka 422-8526, Japan
| | - Akira Asai
- Graduate
School of Pharmaceutical Sciences, University of Shizuoka, Yada, Shizuoka 422-8526, Japan
| | - Mitsuhiro Arisawa
- Graduate
School of Pharmaceutical Sciences, Osaka University, 1-6 Yamada-oka, Suita, Osaka 565-0871, Japan
| | | |
Collapse
|
25
|
Kawamura S, Unno Y, List A, Mizuno A, Tanaka M, Sasaki T, Arisawa M, Asai A, Groll M, Shuto S. Potent Proteasome Inhibitors Derived from the Unnatural cis-Cyclopropane Isomer of Belactosin A: Synthesis, Biological Activity, and Mode of Action. J Med Chem 2013; 56:3689-700. [DOI: 10.1021/jm4002296] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Shuhei Kawamura
- Faculty of
Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo
060-0812, Japan
| | - Yuka Unno
- Graduate
School of Pharmaceutical
Sciences, University of Shizuoka, Yada,
Shizuoka 422-8526, Japan
| | - Anja List
- Center for Integrated Protein
Science at the Department of Chemistry, Chair of Biochemistry, Technische Universität München, Lichtenbergstrasse
4, 85747 Garching, Germany
| | - Akirai Mizuno
- Faculty of
Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo
060-0812, Japan
| | - Motohiro Tanaka
- School of Pharmacy, Aichi Gakuin
University, 1-100 Kusumoto-cho, Chikusa-ku, Nagoya 464-8650, Japan
| | - Takuma Sasaki
- School of Pharmacy, Aichi Gakuin
University, 1-100 Kusumoto-cho, Chikusa-ku, Nagoya 464-8650, Japan
| | - Mitsuhiro Arisawa
- Faculty of
Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo
060-0812, Japan
| | - Akira Asai
- Graduate
School of Pharmaceutical
Sciences, University of Shizuoka, Yada,
Shizuoka 422-8526, Japan
| | - Michael Groll
- Center for Integrated Protein
Science at the Department of Chemistry, Chair of Biochemistry, Technische Universität München, Lichtenbergstrasse
4, 85747 Garching, Germany
| | - Satoshi Shuto
- Faculty of
Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo
060-0812, Japan
| |
Collapse
|
26
|
Lansdell TA, Hurchla MA, Xiang J, Hovde S, Weilbaecher KN, Henry RW, Tepe JJ. Noncompetitive modulation of the proteasome by imidazoline scaffolds overcomes bortezomib resistance and delays MM tumor growth in vivo. ACS Chem Biol 2013. [PMID: 23198928 DOI: 10.1021/cb300568r] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Multiple myeloma (MM) is a malignant disorder of differentiated B-cells for which standard care involves the inhibition of the proteasome. All clinically used proteasome inhibitors, including the chemotherapeutic drug bortezomib, target the catalytic active sites of the proteasome and inhibit protein proteolysis by competing with substrate binding. However, nearly all (~97%) patients become intolerant or resistant to treatments within a few years, after which the average survival time is less than 1 year. We describe herein the inhibition of the human proteasome via a noncompetitive mechanism by the imidazoline scaffold, TCH-13. Consistent with a mechanism distinct from that of competitive inhibitors, TCH-013 acts additively with and overcomes resistance to bortezomib. Importantly, TCH-013 induces apoptosis in a panel of myeloma and leukemia cell lines, but in contrast, normal lymphocytes, primary bone marrow stromal cells (hBMSC), and macrophages are resistant to its cytotoxic effects. TCH-013 was equally effective in blocking MM cell growth in co-cultures of MM cells with hBMSC isolated from CD138 negative bone marrow (BM) samples of MM patients. The cellular activity translated well in vivo where TCH-013 delayed tumor growth in an MM xenograft model to a similar extent as bortezomib.
Collapse
Affiliation(s)
| | - Michelle A. Hurchla
- Department of Medicine, Division
of Oncology, Washington University School of Medicine, St. Louis, Missouri, United States
| | - Jingyu Xiang
- Department of Medicine, Division
of Oncology, Washington University School of Medicine, St. Louis, Missouri, United States
| | | | - Katherine N. Weilbaecher
- Department of Medicine, Division
of Oncology, Washington University School of Medicine, St. Louis, Missouri, United States
| | | | | |
Collapse
|
27
|
Lansdell TA, Hewlett NM, Skoumbourdis AP, Fodor MD, Seiple IB, Su S, Baran PS, Feldman KS, Tepe JJ. Palau'amine and related oroidin alkaloids dibromophakellin and dibromophakellstatin inhibit the human 20S proteasome. JOURNAL OF NATURAL PRODUCTS 2012; 75:980-985. [PMID: 22591513 PMCID: PMC3367325 DOI: 10.1021/np300231f] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
We report herein that the oroidin-derived alkaloids palau'amine (1), dibromophakellin (2), and dibromophakellstatin (3) inhibit the proteolytic activity of the human 20S proteasome as well as the (i)20S immunoproteasome catalytic core. Palau'amine is found to prevent the degradation of ubiquitinylated proteins, including IκBα, in cell culture, which may be indicative of the potential mechanism by which these agents exhibit their exciting cytotoxic and immunosuppressive properties.
Collapse
Affiliation(s)
- Theresa A. Lansdell
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48823
| | - Nicole M. Hewlett
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48823
| | | | - Matthew D. Fodor
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802
| | - Ian B. Seiple
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | - Shun Su
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | - Phil. S. Baran
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | - Ken S. Feldman
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802
| | - Jetze J. Tepe
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48823
| |
Collapse
|
28
|
Natarajan S, Mathews R. Cloning, expression, crystallization and preliminary X-ray crystallographic analysis of aspartyl aminopeptidase from the apeB gene of Pseudomonas aeruginosa. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:207-10. [PMID: 22298001 PMCID: PMC3274405 DOI: 10.1107/s1744309111054388] [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: 10/28/2011] [Accepted: 12/17/2011] [Indexed: 05/31/2023]
Abstract
Aminopeptidases (APs) are a group of exopeptidases that catalyze the removal of amino acids from the N-termini of proteins and peptides. The APs are ubiquitous in nature and are of critical biological and medical importance because of their key role in protein degradation. Pseudomonas aeruginosa aspartyl aminopeptidase (PaAAP), which is encoded by the apeB gene, was expressed in Escherichia coli, purified and crystallized using the microbatch method. A preliminary structural study has been performed using the X-ray crystallographic method. The PaAAP crystal diffracted to 2.0 Å resolution and belonged to the rhombohedral space group H3, with unit-cell parameters a = b = 133.6, c = 321.2. The unit-cell volume of the crystal is compatible with the presence of four monomers in the asymmetric unit, with a corresponding Matthews coefficient V(M) of 2.95 Å(3) Da(-1) and a solvent content of 58.3%.
Collapse
Affiliation(s)
- Sampath Natarajan
- Department of Advanced Technology Fusion, Konkuk University, Seoul, Republic of Korea.
| | | |
Collapse
|
29
|
Chemical and biological evaluation of dipeptidyl boronic acid proteasome inhibitors for use in prodrugs and pro-soft drugs targeting solid tumors. J Med Chem 2011; 54:4365-77. [PMID: 21634429 DOI: 10.1021/jm200460q] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Bortezomib, a dipeptidyl boronic acid and potent inhibitor of the 26S proteasome, is remarkably effective against multiple myeloma (MM) but not against solid tumors. Dose-limiting adverse effects from "on target" inhibition of the proteasome in normal cells and tissues appear to be a key obstacle. Achieving efficacy against solid tumors therefore is likely to require making the inhibitor more selective for tumor tissue over normal tissues. The simplest strategy that might provide such tissue specificity would be to employ a tumor specific protease to release an inhibitor from a larger, noninhibitory structure. However, such release would necessarily generate an inhibitor with a free N-terminal amino group, raising a key question: Can short peptide boronic acids with N-terminal amino groups have the requisite properties to serve as warheads in prodrugs? Here we show that dipeptides of boroLeu, the smallest plausible candidates for the task, can indeed be sufficiently potent, cell-penetrating, cytotoxic, and stable to degradation by cellular peptidases to serve in this capacity.
Collapse
|
30
|
Suskiewicz MJ, Sussman JL, Silman I, Shaul Y. Context-dependent resistance to proteolysis of intrinsically disordered proteins. Protein Sci 2011; 20:1285-97. [PMID: 21574196 DOI: 10.1002/pro.657] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2011] [Accepted: 05/05/2011] [Indexed: 01/08/2023]
Abstract
Intrinsically disordered proteins (IDPs), also known as intrinsically unstructured proteins (IUPs), lack a well-defined 3D structure in vitro and, in some cases, also in vivo. Here, we discuss the question of proteolytic sensitivity of IDPs, with a view to better explaining their in vivo characteristics. After an initial assessment of the status of IDPs in vivo, we briefly survey the intracellular proteolytic systems. Subsequently, we discuss the evidence for IDPs being inherently sensitive to proteolysis. Such sensitivity would not, however, result in enhanced degradation if the protease-sensitive sites were sequestered. Accordingly, IDP access to and degradation by the proteasome, the major proteolytic complex within eukaryotic cells, are discussed in detail. The emerging picture appears to be that IDPs are inherently sensitive to proteasomal degradation along the lines of the "degradation by default" model. However, available data sets of intracellular protein half-lives suggest that intrinsic disorder does not imply a significantly shorter half-life. We assess the power of available systemic half-life measurements, but also discuss possible mechanisms that could protect IDPs from intracellular degradation. Finally, we discuss the relevance of the proteolytic sensitivity of IDPs to their function and evolution.
Collapse
Affiliation(s)
- Marcin J Suskiewicz
- The Israel Structural Proteomics Center, Weizmann Institute of Science, Rehovot, Israel
| | | | | | | |
Collapse
|
31
|
Gülcemal D, Alankuş-Çalışkan Ö, Karaalp C, Örs AU, Ballar P, Bedir E. Phenolic Glycosides with antiproteasomal activity from Centaurea urvillei DC. subsp. urvillei. Carbohydr Res 2010; 345:2529-33. [DOI: 10.1016/j.carres.2010.09.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2010] [Accepted: 09/01/2010] [Indexed: 11/30/2022]
|
32
|
Kumar B, Kim YC, DeMartino GN. The C terminus of Rpt3, an ATPase subunit of PA700 (19 S) regulatory complex, is essential for 26 S proteasome assembly but not for activation. J Biol Chem 2010; 285:39523-35. [PMID: 20937828 DOI: 10.1074/jbc.m110.153627] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
PA700, the 19 S regulatory subcomplex of the 26 S proteasome, contains a heterohexameric ring of AAA subunits (Rpt1 to -6) that forms the binding interface with a heteroheptameric ring of α subunits (α1 to -7) of the 20 S proteasome. Binding of these subcomplexes is mediated by interactions of C termini of certain Rpt subunits with cognate binding sites on the 20 S proteasome. Binding of two Rpt subunits (Rpt2 and Rpt5) depends on their last three residues, which share an HbYX motif (where Hb is a hydrophobic amino acid) and open substrate access gates in the center of the α ring. The relative roles of other Rpt subunits for proteasome binding and activation remain poorly understood. Here we demonstrate that the C-terminal HbYX motif of Rpt3 binds to the 20 S proteasome but does not promote proteasome gating. Binding requires the last three residues and occurs at a dedicated site on the proteasome. A C-terminal peptide of Rpt3 blocked ATP-dependent in vitro assembly of 26 S proteasome from PA700 and 20 S proteasome. In HEK293 cells, wild-type Rpt3, but not Rpt3 lacking the HbYX motif was incorporated into 26 S proteasome. These results indicate that the C terminus of Rpt3 was required for cellular assembly of this subunit into 26 S proteasome. Mutant Rpt3 was assembled into intact PA700. This result indicates that intact PA700 can be assembled independently of association with 20 S proteasome and thus may be a direct precursor for 26 S proteasome assembly under normal conditions. These results provide new insights to the non-equivalent roles of Rpt subunits in 26 S proteasome function and identify specific roles for Rpt3.
Collapse
Affiliation(s)
- Brajesh Kumar
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9040, USA
| | | | | |
Collapse
|
33
|
Gan N, Wu YC, Brunet M, Garrido C, Chung FL, Dai C, Mi L. Sulforaphane activates heat shock response and enhances proteasome activity through up-regulation of Hsp27. J Biol Chem 2010; 285:35528-36. [PMID: 20833711 DOI: 10.1074/jbc.m110.152686] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
It is conceivable that stimulating proteasome activity for rapid removal of misfolded and oxidized proteins is a promising strategy to prevent and alleviate aging-related diseases. Sulforaphane (SFN), an effective cancer preventive agent derived from cruciferous vegetables, has been shown to enhance proteasome activities in mammalian cells and to reduce the level of oxidized proteins and amyloid β-induced cytotoxicity. Here, we report that SFN activates heat shock transcription factor 1-mediated heat shock response. Specifically, SFN-induced expression of heat shock protein 27 (Hsp27) underlies SFN-stimulated proteasome activity. SFN-induced proteasome activity was significantly enhanced in Hsp27-overexpressing cells but absent in Hsp27-silenced cells. The role of Hsp27 in regulating proteasome activity was further confirmed in isogenic REG cells, in which SFN-induced proteasome activation was only observed in cells stably overexpressing Hsp27, but not in the Hsp27-free parental cells. Finally, we demonstrated that phosphorylation of Hsp27 is irrelevant to SFN-induced proteasome activation. This study provides a novel mechanism underlying SFN-induced proteasome activity. This is the first report to show that heat shock response by SFN, in addition to the antioxidant response mediated by the Keap1-Nrf2 pathway, may contribute to cytoprotection.
Collapse
Affiliation(s)
- Nanqin Gan
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA
| | | | | | | | | | | | | |
Collapse
|
34
|
Groll M, Gallastegui N, Maréchal X, Le Ravalec V, Basse N, Richy N, Genin E, Huber R, Moroder L, Vidal J, Reboud-Ravaux M. 20S Proteasome Inhibition: Designing Noncovalent Linear Peptide Mimics of the Natural Product TMC-95A. ChemMedChem 2010; 5:1701-5. [DOI: 10.1002/cmdc.201000293] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|
35
|
Waring JF, Ciurlionis R, Marsh K, Klein LL, Degoey DA, Randolph JT, Spear B, Kempf DJ. Identification of proteasome gene regulation in a rat model for HIV protease inhibitor-induced hyperlipidemia. Arch Toxicol 2010; 84:263-70. [PMID: 20213465 DOI: 10.1007/s00204-010-0527-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2010] [Accepted: 02/16/2010] [Indexed: 11/25/2022]
Abstract
Patients treated with highly active antiretroviral therapy may develop metabolic side effects such as hyperlipidemia, insulin resistance, lipoatrophy and lactic acidosis. The pathophysiology of these metabolic abnormalities is unknown, although some, e.g., lactic acidosis and lipoatrophy, are more associated with nucleoside use while protease inhibitors (PIs) have been shown to contribute to hyperlipidemia and insulin resistance. Identifying new PIs that are not associated with dyslipidemia has been hindered by the lack of mechanistic information and the unavailability of relevant animal models. In order to understand the molecular mechanism behind the hyperlipidemia associated with other protease inhibitors, and to develop a more effective, faster screen for compounds with this liability, we have analyzed expression profiles from PI-treated animals. Previously, we have shown that treatment of rats with ritonavir results in increases in the expression of proteasomal subunit genes in the liver. We show this increase is similar in rats treated with bortezomib, a proteasome inhibitor. In addition, we have treated rats with additional protease inhibitors, including atazanavir, which is associated with lower rates of lipid elevations in the clinic when administered in the absence of ritonavir. Our results indicate a strong correlation between proteasomal induction and lipid elevations, and have allowed us to develop a rapid screen for identifying novel PIs that do not induce the proteasome.
Collapse
Affiliation(s)
- Jeffrey F Waring
- Abbott Laboratories Global Pharmaceuticals Research and Development, 100 Abbott Park Rd, Abbott Park, IL 60064-6123, USA.
| | | | | | | | | | | | | | | |
Collapse
|
36
|
Lee MM, Isaza CE, White JD, Chen RPY, Liang GFC, He HTF, Chan SI, Chan MK. Insight into the substrate length restriction of M32 carboxypeptidases: characterization of two distinct subfamilies. Proteins 2010; 77:647-57. [PMID: 19544567 DOI: 10.1002/prot.22478] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
M32 carboxypeptidases are a distinct family of HEXXH metalloproteases whose structures exhibit a narrow substrate groove that is blocked at one end. Structural alignments with other HEXXH metalloprotease-peptide complexes suggested an orientation in which the substrate is directed towards the back of the groove. This led us to hypothesize, and subsequently confirm that the maximum substrate length for M32 carboxypeptidases is restricted. Structural and sequence analyses implicate a highly conserved Arg at the back of the groove as being critical for this length restriction. However, the Thermus thermophilus and Bacillus subtilis M32 members lack this conserved Arg. Herein, we present the biochemical and structural characterization of these two proteins. Our findings support the important role of the conserved Arg in maintaining the length restriction, and reveal a proline-rich loop as an alternate blocking strategy. Based on our results, we propose that M32 carboxypeptidases from Bacilli belong to a separate subfamily.
Collapse
Affiliation(s)
- Marianne M Lee
- The Ohio State Biophysics Program, The Ohio State University, 484 West 12th Avenue, Columbus, Ohio 43210, USA
| | | | | | | | | | | | | | | |
Collapse
|
37
|
Malik S, Shukla A, Sen P, Bhaumik SR. The 19 s proteasome subcomplex establishes a specific protein interaction network at the promoter for stimulated transcriptional initiation in vivo. J Biol Chem 2010; 284:35714-24. [PMID: 19843524 DOI: 10.1074/jbc.m109.035709] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The 26 S proteasome complex that comprises the 20 S core and 19 S regulatory (with six ATPases) particles is engaged in an ATP-dependent degradation of a variety of key regulatory proteins and, thus, controls important cellular processes. Interestingly, several recent studies have implicated the 19 S regulatory particle in controlling eukaryotic transcriptional initiation or activation independently of the 20 S core particle. However, the mechanism of action of the 19 S proteasome subcomplex in regulation of eukaryotic transcriptional activation is not clearly understood in vivo. Here, using a chromatin immunoprecipitation assay in conjunction with mutational and transcriptional analyses in Saccharomyces cerevisiae, we show that the 19 S proteasomal subcomplex establishes a specific protein interaction network at the upstream activating sequence of the promoter. Such an interaction network is essential for formation of the preinitiation complex at the core promoter to initiate transcription. Furthermore, we demonstrate that the formation of the transcription complex assembly at the promoter is dependent on 19 S ATPase activity. Intriguingly, 19 S ATPases appear to cross-talk for stimulation of the assembly of transcription factors at the promoter. Together, these results provide significant insights as to how the 19 S proteasome subcomplex regulates the formation of the active transcription complex assembly (and, hence, transcriptional initiation) at the promoter in vivo.
Collapse
Affiliation(s)
- Shivani Malik
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, Illinois 62901, USA
| | | | | | | |
Collapse
|
38
|
Sollner S, Macheroux P. New roles of flavoproteins in molecular cell biology: An unexpected role for quinone reductases as regulators of proteasomal degradation. FEBS J 2009; 276:4313-24. [DOI: 10.1111/j.1742-4658.2009.07143.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
39
|
Multivalency-assisted control of intracellular signaling pathways: application for ubiquitin- dependent N-end rule pathway. ACTA ACUST UNITED AC 2009; 16:121-31. [PMID: 19246002 DOI: 10.1016/j.chembiol.2009.01.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2008] [Revised: 01/04/2009] [Accepted: 01/21/2009] [Indexed: 11/23/2022]
Abstract
Intracellular signaling is often mediated by a family of functionally overlapping signal mediators that contain multiple sites interacting with other proteins or ligands with weak affinity (K(d) > microM). Conjugation of multiple low-affinity ligands into a high-affinity multivalent molecule provides a means to control the entire protein family within a single intracellular pathway. The N-end rule pathway is a ubiquitin (Ub)-dependent proteolytic system where at least four Ub ligases, called N-recognins, have a common domain critical for binding to type 1 (basic) and type 2 (bulky hydrophobic) destabilizing N-terminal residues of substrates as degrons. The recent development of a heterodivalent inhibitor targeting type 1 and type 2 substrate binding sites of the N-recognin family provides new opportunities to manipulate this proteolytic pathway in biochemical and pathophysiological conditions. We overview the N-end rule pathway as an intracellular target for heterodivalent molecules and discuss the basis of thermodynamics and kinetics related to heterodivalent interactions.
Collapse
|
40
|
Chandra J. Oxidative stress by targeted agents promotes cytotoxicity in hematologic malignancies. Antioxid Redox Signal 2009; 11:1123-37. [PMID: 19018667 PMCID: PMC2842131 DOI: 10.1089/ars.2008.2302] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The past decade has seen an exponential increase in the number of cancer therapies with defined molecular targets. Interestingly, many of these new agents are also documented to raise levels of intracellular reactive oxygen species (ROS) in addition to inhibiting a biochemical target. In most cases, the exact link between the primary target of the drug and effects on cellular redox status is unknown. However, it is important to understand the role of oxidative stress in promoting cytotoxicity by these agents, because the design of multiregimen strategies could conceivably build on these redox alterations. Also, drug resistance mediated by antioxidant defenses could potentially be anticipated and circumvented with improved knowledge of the redox-related effects of these targeted agents. Given the large number of targeted chemotherapies, in this review, we focus on selected agents that have shown promise in hematologic malignancies: proteasome inhibitors, histone deacetylase inhibitors, Bcl-2-targeted agents, and a kinase inhibitor called adaphostin. Despite structural differences within classes of these compounds, a commonality of causing increased oxidative stress exists, which contributes to induction of cell death.
Collapse
Affiliation(s)
- Joya Chandra
- Department of Pediatrics Research, Unit 853, The University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, USA.
| |
Collapse
|
41
|
Groll M, Huber R, Moroder L. The persisting challenge of selective and specific proteasome inhibition. J Pept Sci 2009; 15:58-66. [PMID: 19109822 DOI: 10.1002/psc.1107] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Since the discovery of the proteasome and its structure elucidation intensive research programs in academic institutions and pharmaceutical industries led to identification of a wide spectrum of synthetic and natural small proteasomal inhibitors. Activity studies with these small molecules helped to deeply understand the complex biochemical organization and functioning of the proteasome. The new structural and biochemical insights placed the proteasome as an important anti-cancer drug target, as revealed by the dipeptide boronate proteasome inhibitor, bortezomib, which is currently used for treatment of multiple myeloma. Serious side effects and partial cell resistance against bortezomib demand creation and discovery of new improved generations of more specific and potent proteasomal inhibitors.
Collapse
Affiliation(s)
- Michael Groll
- Chemie Department, Technische Universität München, D-85747-Garching, Germany
| | | | | |
Collapse
|
42
|
Zhang P, Martin PD, Purcarea C, Vaishnav A, Brunzelle JS, Fernando R, Guy-Evans HI, Evans DR, Edwards BFP. Dihydroorotase from the hyperthermophile Aquifex aeolicus is activated by stoichiometric association with aspartate transcarbamoylase and forms a one-pot reactor for pyrimidine biosynthesis. Biochemistry 2009; 48:766-78. [PMID: 19128030 DOI: 10.1021/bi801831r] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In prokaryotes, the first three enzymes in pyrimidine biosynthesis, carbamoyl phosphate synthetase (CPS), aspartate transcarbamoylase (ATC), and dihydroorotase (DHO), are commonly expressed separately and either function independently (Escherichia coli) or associate into multifunctional complexes (Aquifex aeolicus). In mammals the enzymes are expressed as a single polypeptide chain (CAD) in the order CPS-DHO-ATC and associate into a hexamer. This study presents the three-dimensional structure of the noncovalent hexamer of DHO and ATC from the hyperthermophile A. aeolicus at 2.3 A resolution. It is the first structure of any multienzyme complex in pyrimidine biosynthesis and is a possible model for the core of mammalian CAD. The structure has citrate, a near isosteric analogue of carbamoyl aspartate, bound to the active sites of both enzymes. Three active site loops that are intrinsically disordered in the free, inactive DHO are ordered in the complex. The reorganization also changes the peptide bond between Asp153, a ligand of the single zinc atom in DHO, and Gly154, to the rare cis conformation. In the crystal structure, six DHO and six ATC chains form a hollow dodecamer, in which the 12 active sites face an internal reaction chamber that is approximately 60 A in diameter and connected to the cytosol by narrow tunnels. The entrances and the interior of the chamber are both electropositive, which suggests that the architecture of this nanoreactor modifies the kinetics of the bisynthase, not only by steric channeling but also by preferential escape of the product, dihydroorotase, which is less negatively charged than its precursors, carbamoyl phosphate, aspartate, or carbamoyl aspartate.
Collapse
Affiliation(s)
- Pengfei Zhang
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, 540 East Canfield Street, Detroit, Michigan 48201, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
43
|
Bhaumik SR, Malik S. Diverse regulatory mechanisms of eukaryotic transcriptional activation by the proteasome complex. Crit Rev Biochem Mol Biol 2009; 43:419-33. [PMID: 19058045 DOI: 10.1080/10409230802605914] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The life of any protein within a cell begins with transcriptional activation, and ends with proteolytic degradation. Intriguingly, the 26S proteasome complex, a non-lysosomal protein degradation machine comprising the 20S proteolytic core and 19S regulatory particles, has been implicated in intimate regulation of eukaryotic transcriptional activation through diverse mechanisms in a proteolysis-dependent as well as independent manner. Here, we discuss the intricate mechanisms of such proteasomal regulation of eukaryotic gene activation via multiple pathways.
Collapse
Affiliation(s)
- Sukesh R Bhaumik
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA.
| | | |
Collapse
|
44
|
Abstract
A functional ubiquitin proteasome system is essential for all eukaryotic cells and therefore any alteration to its components has potential pathological consequences. Though the exact underlying mechanism is unclear, an age-related decrease in proteasome activity weakens cellular capacity to remove oxidatively modified proteins and favours the development of neurodegenerative and cardiac diseases. Up-regulation of proteasome activity is characteristic of muscle wasting conditions including sepsis, cachexia and uraemia, but may not be rate limiting. Meanwhile, enhanced presence of immunoproteasomes in aging brain and muscle tissue could reflect a persistent inflammatory defence and anti-stress mechanism, whereas in cancer cells, their down-regulation reflects a means by which to escape immune surveillance. Hence, induction of apoptosis by synthetic proteasome inhibitors is a potential treatment strategy for cancer, whereas for other diseases such as neurodegeneration, the use of proteasome-activating or -modulating compounds could be more effective. Publication history: Republished from Current BioData's Targeted Proteins database (TPdb; http://www.targetedproteinsdb.com).
Collapse
Affiliation(s)
- Burkhardt Dahlmann
- Institut für Biochemie, Charité-Universitätsmedizin-Berlin, Monbijoustr, 2, 10117 Berlin, Germany.
| |
Collapse
|
45
|
Azim MK, Noor S. Characterization of protomer interfaces in HslV protease; the bacterial homologue of 20S proteasome. Protein J 2007; 26:213-9. [PMID: 17522969 DOI: 10.1007/s10930-006-9048-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
HslVU, a two-component proteasome-related prokaryotic system is composed of HslV protease and HslU ATPase. HslV protomers assemble in a dodecamer of two-stacked hexameric rings that form a complex with HslU hexamers. The intra- and inter-ring protomer interfaces in the HslV dodecamer underpin the integrity and functionality of HslVU. Structural characterization of HslV from different bacteria illustrated considerable differences in interacting residues, accessible surface and gap volumes at the intra-ring interface that is primarily stabilized by polar interactions. Amino acid residues Lys28, Arg83 and Asp111 have envisaged as hot spots at this HslU-interacting interface. The inter-ring interfaces that are made up of side chain packing of hydrophobic residues are structurally conserved. Hyperthermostable bacterium T. maritima HslV has extensively networked polar/nonpolar interactions and highly packed environment at all interfaces. Present data demonstrates that HslV protomer interfaces perform distinct functions; whereas intra-ring interface participates in HslV:HslU interaction resulting in allosteric activation of HslV protease by HslU, the inter-ring interfaces uphold the oligomeric form of HslV.
Collapse
Affiliation(s)
- M Kamran Azim
- H.E.J. Research Institute of Chemistry, International Center for Chemical Sciences, University of Karachi, Karachi, Pakistan.
| | | |
Collapse
|
46
|
Tambyrajah WS, Bowler LD, Medina-Palazon C, Sinclair AJ. Cell cycle-dependent caspase-like activity that cleaves p27KIP1 is the β1 subunit of the 20S proteasome. Arch Biochem Biophys 2007; 466:186-93. [PMID: 17854759 DOI: 10.1016/j.abb.2007.07.019] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2007] [Revised: 07/13/2007] [Accepted: 07/17/2007] [Indexed: 11/18/2022]
Abstract
We previously described a caspase-like activity, which we termed KIPase that is implicated in the turnover of the mammalian cell cycle regulator p27(KIP1). KIPase cleaves a tetra-peptide substrate, Ac-DPSD-AMC, which mimics the target site in p27(KIP1), and inhibitors based on this tetra-peptide are ineffective against other known caspases. Here we describe the purification and characterization of KIPase, and trace its activity to the beta(1) subunit of the 20S proteasome. Further analyses revealed that the activity of the beta(1) subunit is up-regulated as cells enter the cell cycle without concomitant change in the levels of the proteasome beta(1), beta(2) or beta(5) subunits. To our knowledge, this is the first description of cell cycle regulation of the caspase-like activity of the 20S proteasome.
Collapse
|
47
|
Fortun J, Verrier JD, Go JC, Madorsky I, Dunn WA, Notterpek L. The formation of peripheral myelin protein 22 aggregates is hindered by the enhancement of autophagy and expression of cytoplasmic chaperones. Neurobiol Dis 2006; 25:252-65. [PMID: 17174099 PMCID: PMC1857308 DOI: 10.1016/j.nbd.2006.09.018] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2006] [Revised: 08/29/2006] [Accepted: 09/07/2006] [Indexed: 11/29/2022] Open
Abstract
The accumulation of misfolded proteins is associated with various neurodegenerative conditions. Peripheral myelin protein 22 (PMP22) is a hereditary neuropathy-linked, short-lived molecule that forms aggresomes when the proteasome is inhibited or the protein is mutated. We previously showed that the removal of pre-existing PMP22 aggregates is assisted by autophagy. Here we examined whether the accumulation of such aggregates could be suppressed by experimental induction of autophagy and/or chaperones. Enhancement of autophagy during proteasome inhibition hinders protein aggregate formation and correlates with a reduction in accumulated proteasome substrates. Conversely, simultaneous inhibition of autophagy and the proteasome augments the formation of aggregates. An increase of heat shock protein levels by geldanamycin treatment or heat shock preconditioning similarly hampers aggresome formation. The beneficial effects of autophagy and chaperones in preventing the accumulation of misfolded PMP22 are additive and provide a potential avenue for therapeutic approaches in hereditary neuropathies linked to PMP22 mutations.
Collapse
MESH Headings
- Animals
- Animals, Newborn
- Autophagy/physiology
- Cells, Cultured
- Cytoplasm/metabolism
- Cytoplasm/pathology
- Heat-Shock Proteins/metabolism
- Heredodegenerative Disorders, Nervous System/genetics
- Heredodegenerative Disorders, Nervous System/metabolism
- Heredodegenerative Disorders, Nervous System/physiopathology
- Inclusion Bodies/metabolism
- Inclusion Bodies/ultrastructure
- Mice
- Mice, Neurologic Mutants
- Microscopy, Electron, Transmission
- Molecular Chaperones/metabolism
- Myelin Proteins/metabolism
- Nerve Fibers, Myelinated/metabolism
- Nerve Fibers, Myelinated/pathology
- Peripheral Nerves/metabolism
- Peripheral Nerves/pathology
- Peripheral Nerves/physiopathology
- Peripheral Nervous System Diseases/genetics
- Peripheral Nervous System Diseases/metabolism
- Peripheral Nervous System Diseases/physiopathology
- Phagosomes/metabolism
- Phagosomes/ultrastructure
- Proteasome Endopeptidase Complex/metabolism
- Protein Folding
- Rats
Collapse
Affiliation(s)
- Jenny Fortun
- Department of Neuroscience, College of Medicine, McKnight Brain Institute, University of Florida, 100 Newell Drive, Box 100244, Gainesville, FL 32610-0244, USA
| | | | | | | | | | | |
Collapse
|
48
|
Richards TA, Dacks JB, Campbell SA, Blanchard JL, Foster PG, McLeod R, Roberts CW. Evolutionary origins of the eukaryotic shikimate pathway: gene fusions, horizontal gene transfer, and endosymbiotic replacements. EUKARYOTIC CELL 2006; 5:1517-31. [PMID: 16963634 PMCID: PMC1563581 DOI: 10.1128/ec.00106-06] [Citation(s) in RCA: 153] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Currently the shikimate pathway is reported as a metabolic feature of prokaryotes, ascomycete fungi, apicomplexans, and plants. The plant shikimate pathway enzymes have similarities to prokaryote homologues and are largely active in chloroplasts, suggesting ancestry from the plastid progenitor genome. Toxoplasma gondii, which also possesses an alga-derived plastid organelle, encodes a shikimate pathway with similarities to ascomycete genes, including a five-enzyme pentafunctional arom. These data suggests that the shikimate pathway and the pentafunctional arom either had an ancient origin in the eukaryotes or was conveyed by eukaryote-to-eukaryote horizontal gene transfer (HGT). We expand sampling and analyses of the shikimate pathway genes to include the oomycetes, ciliates, diatoms, basidiomycetes, zygomycetes, and the green and red algae. Sequencing of cDNA from Tetrahymena thermophila confirmed the presence of a pentafused arom, as in fungi and T. gondii. Phylogenies and taxon distribution suggest that the arom gene fusion event may be an ancient eukaryotic innovation. Conversely, the Plantae lineage (represented here by both Viridaeplantae and the red algae) acquired different prokaryotic genes for all seven steps of the shikimate pathway. Two of the phylogenies suggest a derivation of the Plantae genes from the cyanobacterial plastid progenitor genome, but if the full Plantae pathway was originally of cyanobacterial origin, then the five other shikimate pathway genes were obtained from a minimum of two other eubacterial genomes. Thus, the phylogenies demonstrate both separate HGTs and shared derived HGTs within the Plantae clade either by primary HGT transfer or secondarily via the plastid progenitor genome. The shared derived characters support the holophyly of the Plantae lineage and a single ancestral primary plastid endosymbiosis. Our analyses also pinpoints a minimum of 50 gene/domain loss events, demonstrating that loss and replacement events have been an important process in eukaryote genome evolution.
Collapse
Affiliation(s)
- Thomas A Richards
- Deparment of Zoology, The Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom
| | | | | | | | | | | | | |
Collapse
|
49
|
Madding LS, Michel JK, Shockley KR, Conners SB, Epting KL, Johnson MR, Kelly RM. Role of the beta1 subunit in the function and stability of the 20S proteasome in the hyperthermophilic archaeon Pyrococcus furiosus. J Bacteriol 2006; 189:583-90. [PMID: 17114253 PMCID: PMC1797377 DOI: 10.1128/jb.01382-06] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The hyperthermophilic archaeon Pyrococcus furiosus genome encodes three proteasome component proteins: one alpha protein (PF1571) and two beta proteins (beta1-PF1404 and beta2-PF0159), as well as an ATPase (PF0115), referred to as proteasome-activating nucleotidase. Transcriptional analysis of the P. furiosus dynamic heat shock response (shift from 90 to 105 degrees C) showed that the beta1 gene was up-regulated over twofold within 5 minutes, suggesting a specific role during thermal stress. Consistent with transcriptional data, two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed that incorporation of the beta1 protein relative to beta2 into the 20S proteasome (core particle [CP]) increased with increasing temperature for both native and recombinant versions. For the recombinant enzyme, the beta2/beta1 ratio varied linearly with temperature from 3.8, when assembled at 80 degrees C, to 0.9 at 105 degrees C. The recombinant alpha+beta1+beta2 CP assembled at 105 degrees C was more thermostable than either the alpha+beta1+beta2 version assembled at 90 degrees C or the alpha+beta2 version assembled at either 90 degrees C or 105 degrees C, based on melting temperature and the biocatalytic inactivation rate at 115 degrees C. The recombinant CP assembled at 105 degrees C was also found to have different catalytic rates and specificity for peptide hydrolysis, compared to the 90 degrees C assembly (measured at 95 degrees C). Combination of the alpha and beta1 proteins neither yielded a large proteasome complex nor demonstrated any significant activity. These results indicate that the beta1 subunit in the P. furiosus 20S proteasome plays a thermostabilizing role and influences biocatalytic properties, suggesting that beta subunit composition is a factor in archaeal proteasome function during thermal stress, when polypeptide turnover is essential to cell survival.
Collapse
Affiliation(s)
- Lara S Madding
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, USA
| | | | | | | | | | | | | |
Collapse
|
50
|
Abstract
Protein misfolding is a common event in living cells. In young and healthy cells, the misfolded protein load is disposed of by protein quality control (PQC) systems. In aging cells and in cells from certain individuals with genetic diseases, the load may overwhelm the PQC capacity, resulting in accumulation of misfolded proteins. Dependent on the properties of the protein and the efficiency of the PQC systems, the accumulated protein may be degraded or assembled into toxic oligomers and aggregates. To illustrate this concept, we discuss a number of very different protein misfolding diseases including phenylketonuria, Parkinson's disease, alpha-1-antitrypsin deficiency, familial neurohypophyseal diabetes insipidus, and short-chain acyl-CoA dehydrogenase deficiency. Despite the differences, an emerging paradigm suggests that the cellular effects of protein misfolding provide a common framework that may contribute to the elucidation of the cell pathology and guide intervention and treatment strategies of many genetic and age-dependent diseases.
Collapse
Affiliation(s)
- Niels Gregersen
- Research Unit for Molecular Medicine, Institute of Clinical Medicine, Aarhus University Hospital and Faculty of Health Sciences, University of Aarhus, Skejby Sygehus, 8200 Aarhus N, Denmark.
| | | | | | | |
Collapse
|