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Andres M, Hennuyer N, Zibar K, Bicharel-Leconte M, Duplan I, Enée E, Vallez E, Herledan A, Loyens A, Staels B, Deprez B, van Endert P, Deprez-Poulain R, Lancel S. Insulin-degrading enzyme inhibition increases the unfolded protein response and favours lipid accumulation in the liver. Br J Pharmacol 2024; 181:3610-3626. [PMID: 38812293 DOI: 10.1111/bph.16436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 04/03/2024] [Accepted: 04/25/2024] [Indexed: 05/31/2024] Open
Abstract
BACKGROUND AND PURPOSE Nonalcoholic fatty liver disease refers to liver pathologies, ranging from steatosis to steatohepatitis, with fibrosis ultimately leading to cirrhosis and hepatocellular carcinoma. Although several mechanisms have been suggested, including insulin resistance, oxidative stress, and inflammation, its pathophysiology remains imperfectly understood. Over the last decade, a dysfunctional unfolded protein response (UPR) triggered by endoplasmic reticulum (ER) stress emerged as one of the multiple driving factors. In parallel, growing evidence suggests that insulin-degrading enzyme (IDE), a highly conserved and ubiquitously expressed metallo-endopeptidase originally discovered for its role in insulin decay, may regulate ER stress and UPR. EXPERIMENTAL APPROACH We investigated, by genetic and pharmacological approaches, in vitro and in vivo, whether IDE modulates ER stress-induced UPR and lipid accumulation in the liver. KEY RESULTS We found that IDE-deficient mice display higher hepatic triglyceride content along with higher inositol-requiring enzyme 1 (IRE1) pathway activation. Upon induction of ER stress by tunicamycin or palmitate in vitro or in vivo, pharmacological inhibition of IDE, using its inhibitor BDM44768, mainly exacerbated ER stress-induced IRE1 activation and promoted lipid accumulation in hepatocytes, effects that were abolished by the IRE1 inhibitors 4μ8c and KIRA6. Finally, we identified that IDE knockout promotes lipolysis in adipose tissue and increases hepatic CD36 expression, which may contribute to steatosis. CONCLUSION AND IMPLICATIONS These results unravel a novel role for IDE in the regulation of ER stress and development of hepatic steatosis. These findings pave the way to innovative strategies modulating IDE to treat metabolic diseases.
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Affiliation(s)
- Marine Andres
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - EGID Drugs and Molecules for Living Systems, Lille, France
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, Lille, France
| | - Nathalie Hennuyer
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, Lille, France
| | - Khamis Zibar
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, Lille, France
| | | | - Isabelle Duplan
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, Lille, France
| | - Emmanuelle Enée
- Université Paris Cité, INSERM, CNRS, Institut Necker Enfants Malades, Paris, France
| | - Emmanuelle Vallez
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, Lille, France
| | - Adrien Herledan
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - EGID Drugs and Molecules for Living Systems, Lille, France
| | - Anne Loyens
- Univ. Lille, UMR-S 1172-JPArc Centre de Recherche Jean-Pierre Aubert Neurosciences et Cancer, Lille, France
| | - Bart Staels
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, Lille, France
| | - Benoit Deprez
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - EGID Drugs and Molecules for Living Systems, Lille, France
| | - Peter van Endert
- Université Paris Cité, INSERM, CNRS, Institut Necker Enfants Malades, Paris, France
- Service immunologie biologique, AP-HP, Hôpital Universitaire Necker-Enfants Malades, Paris, France
| | - Rebecca Deprez-Poulain
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - EGID Drugs and Molecules for Living Systems, Lille, France
- Institut Universitaire de France (IUF), Paris, France
| | - Steve Lancel
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, Lille, France
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, Lille, France
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2
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Geijtenbeek KW, Aranda AS, Sanz AS, Janzen J, Bury AE, Kors S, Al Amery N, Schmitz NCM, Reits EAJ, Schipper-Krom S. Insulin-Degrading Enzyme Efficiently Degrades polyQ Peptides but not Expanded polyQ Huntingtin Fragments. J Huntingtons Dis 2024; 13:201-214. [PMID: 38640164 DOI: 10.3233/jhd-230583] [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] [Indexed: 04/21/2024]
Abstract
Background Huntington's disease is an inheritable autosomal dominant disorder caused by an expanded CAG trinucleotide repeat within the Huntingtin gene, leading to a polyglutamine (polyQ) expansion in the mutant protein. Objective A potential therapeutic approach for delaying or preventing the onset of the disease involves enhancing the degradation of the aggregation-prone polyQ-expanded N-terminal mutant huntingtin (mHTT) exon1 fragment. A few proteases and peptidases have been identified that are able to cleave polyQ fragments with low efficiency. This study aims to identify a potent polyQ-degrading endopeptidase. Methods Here we used quenched polyQ peptides to identify a polyQ-degrading endopeptidase. Next we investigated its role on HTT turnover, using purified polyQ-expanded HTT fragments and striatal cells expressing mHTT exon1 peptides. Results We identified insulin-degrading enzyme (IDE) as a novel endopeptidase for degrading polyQ peptides. IDE was, however, ineffective in reducing purified polyQ-expanded HTT fragments. Similarly, in striatal cells expressing mHTT exon1 peptides, IDE did not enhance mHTT turnover. Conclusions This study shows that despite IDE's efficiency in degrading polyQ peptides, it does not contribute to the direct degradation of polyQ-expanded mHTT fragments.
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Affiliation(s)
- Karlijne W Geijtenbeek
- Amsterdam UMC, University of Amsterdam, Medical Biology, Meibergdreef, Amsterdam, Netherlands
| | - Angela Santiago Aranda
- Amsterdam UMC, University of Amsterdam, Medical Biology, Meibergdreef, Amsterdam, Netherlands
| | - Alicia Sanz Sanz
- Amsterdam UMC, University of Amsterdam, Medical Biology, Meibergdreef, Amsterdam, Netherlands
| | - Jolien Janzen
- Amsterdam UMC, University of Amsterdam, Medical Biology, Meibergdreef, Amsterdam, Netherlands
| | - Aleksandra E Bury
- Amsterdam UMC, University of Amsterdam, Medical Biology, Meibergdreef, Amsterdam, Netherlands
| | - Suzan Kors
- Amsterdam UMC, University of Amsterdam, Medical Biology, Meibergdreef, Amsterdam, Netherlands
| | | | - Nina C M Schmitz
- Amsterdam UMC, University of Amsterdam, Medical Biology, Meibergdreef, Amsterdam, Netherlands
| | - Eric A J Reits
- Amsterdam UMC, University of Amsterdam, Medical Biology, Meibergdreef, Amsterdam, Netherlands
| | - Sabine Schipper-Krom
- Amsterdam UMC, University of Amsterdam, Medical Biology, Meibergdreef, Amsterdam, Netherlands
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3
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Tundo GR, Grasso G, Persico M, Tkachuk O, Bellia F, Bocedi A, Marini S, Parravano M, Graziani G, Fattorusso C, Sbardella D. The Insulin-Degrading Enzyme from Structure to Allosteric Modulation: New Perspectives for Drug Design. Biomolecules 2023; 13:1492. [PMID: 37892174 PMCID: PMC10604886 DOI: 10.3390/biom13101492] [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: 07/31/2023] [Revised: 09/11/2023] [Accepted: 09/17/2023] [Indexed: 10/29/2023] Open
Abstract
The insulin-degrading enzyme (IDE) is a Zn2+ peptidase originally discovered as the main enzyme involved in the degradation of insulin and other amyloidogenic peptides, such as the β-amyloid (Aβ) peptide. Therefore, a role for the IDE in the cure of diabetes and Alzheimer's disease (AD) has been long envisaged. Anyway, its role in degrading amyloidogenic proteins remains not clearly defined and, more recently, novel non-proteolytic functions of the IDE have been proposed. From a structural point of view, the IDE presents an atypical clamshell structure, underscoring unique enigmatic enzymological properties. A better understanding of the structure-function relationship may contribute to solving some existing paradoxes of IDE biology and, in light of its multifunctional activity, might lead to novel therapeutic approaches.
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Affiliation(s)
- Grazia Raffaella Tundo
- Department of Clinical Science and Traslational Medicine, University of Rome Tor Vergata, Via Della Ricerca Scientifica 1, 00133 Rome, Italy; (G.R.T.)
| | - Giuseppe Grasso
- Department of Chemical Sciences, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy;
| | - Marco Persico
- Department of Pharmacy, University of Naples “Federico II”, Via D. Montesano 49, 80131 Napoli, Italy; (M.P.); (O.T.)
| | - Oleh Tkachuk
- Department of Pharmacy, University of Naples “Federico II”, Via D. Montesano 49, 80131 Napoli, Italy; (M.P.); (O.T.)
| | - Francesco Bellia
- Institute of Crystallography, CNR, Via Paolo Gaifami 18, 95126 Catania, Italy
| | - Alessio Bocedi
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy
| | - Stefano Marini
- Department of Clinical Science and Traslational Medicine, University of Rome Tor Vergata, Via Della Ricerca Scientifica 1, 00133 Rome, Italy; (G.R.T.)
| | | | - Grazia Graziani
- Department of Systems Medicine, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy;
| | - Caterina Fattorusso
- Department of Pharmacy, University of Naples “Federico II”, Via D. Montesano 49, 80131 Napoli, Italy; (M.P.); (O.T.)
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4
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He Z, Li X, Wang Z, Cao Y, Han S, Li N, Cai J, Cheng S, Liu Q. Protective effects of luteolin against amyloid beta-induced oxidative stress and mitochondrial impairments through peroxisome proliferator-activated receptor γ-dependent mechanism in Alzheimer's disease. Redox Biol 2023; 66:102848. [PMID: 37597424 PMCID: PMC10462892 DOI: 10.1016/j.redox.2023.102848] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/10/2023] [Accepted: 08/11/2023] [Indexed: 08/21/2023] Open
Abstract
Alzheimer's disease (AD) is a devastating neurodegenerative disorder characterized by the deposition of β-amyloid (Aβ) peptides and dysfunction of mitochondrion, which result in neuronal apoptosis and ultimately cognitive impairment. Inhibiting Aβ generation and repairing mitochondrial damage are prominent strategies in AD therapeutic treatment. Luteolin, a flavonoid compound, exhibits anti-inflammatory neuroprotective properties in AD mice. However, it is still unclear whether luteolin has any effect on Aβ pathology and mitochondrial dysfunction. In this study, the beneficial effect and underlying mechanism of luteolin were investigated in triple transgenic AD (3 × Tg-AD) mice and primary neurons. Our study showed that luteolin supplement significantly ameliorated memory and cognitive impairment of AD mice and exerted neuroprotection by inhibiting Aβ generation, repairing mitochondrial damage and reducing neuronal apoptosis. Further research revealed that luteolin could directly bind with peroxisome proliferator-activated receptor gama (PPARγ) to promote its expression and function. In the culture of hippocampus-derived primary neurons, addition of PPARγ antagonist GW9662 or knockdown of PPARγ with its siRNA could eliminate the effect of luteolin on AD pathologies. In summary, this work revealed for the first time that luteolin effectively improved cognitive deficits of 3 × Tg-AD mice and inhibited Aβ-induced oxidative stress, mitochondrial dysfunction and neuronal apoptosis via PPARγ-dependent mechanism. Hence, luteolin has the potential to serve as a therapeutic agent against AD.
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Affiliation(s)
- Zhijun He
- National R&D Center for Se-rich Agricultural Products Processing, Hubei Engineering Research Center for Deep Processing of Green Se-rich Agricultural Products, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan, 430023, China; Shenzhen Key Laboratory of Marine Biotechnology and Ecology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, 518055, China
| | - Xiaoqian Li
- Shenzhen Key Laboratory of Marine Biotechnology and Ecology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, 518055, China
| | - Zi Wang
- Shenzhen Key Laboratory of Marine Biotechnology and Ecology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, 518055, China
| | - Yingqi Cao
- Shenzhen Key Laboratory of Marine Biotechnology and Ecology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, 518055, China
| | - Shuangxue Han
- Shenzhen Key Laboratory of Marine Biotechnology and Ecology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, 518055, China
| | - Nan Li
- Shenzhen Key Laboratory of Marine Biotechnology and Ecology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, 518055, China; Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, 518055, China
| | - Jie Cai
- National R&D Center for Se-rich Agricultural Products Processing, Hubei Engineering Research Center for Deep Processing of Green Se-rich Agricultural Products, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan, 430023, China.
| | - Shuiyuan Cheng
- National R&D Center for Se-rich Agricultural Products Processing, Hubei Engineering Research Center for Deep Processing of Green Se-rich Agricultural Products, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan, 430023, China
| | - Qiong Liu
- Shenzhen Key Laboratory of Marine Biotechnology and Ecology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, 518055, China; Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, 518055, China.
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5
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Kemeh MM, Lazo ND. Modulation of the Activity of the Insulin-Degrading Enzyme by Aβ Peptides. ACS Chem Neurosci 2023; 14:2935-2943. [PMID: 37498802 DOI: 10.1021/acschemneuro.3c00384] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023] Open
Abstract
The insulin-degrading enzyme (IDE) is an evolutionarily conserved protease implicated in the degradation of insulin and amyloidogenic peptides. Most of the biochemical and biophysical characterization of IDE's catalytic activity has been conducted using solutions containing a single substrate, i.e., insulin or Aβ(1-40). IDE's activity toward a particular substrate, however, is likely to be influenced by the presence of other substrates. Here, we show by a kinetic assay based on insulin's helical circular dichroic signal and MALDI TOF mass spectrometry that Aβ peptides modulate IDE's activity toward insulin in opposing ways. Aβ(1-40) enhances IDE-dependent degradation of insulin, whereas Aβ(pyroE3-42), the most pathogenic pyroglutamate-modified Aβ peptide in AD, inhibits IDE's activity. Intriguingly, Aβ(pyroE3-42) also inhibits IDE's ability to degrade Aβ(1-40). Together, our results implicate Aβ peptides in the abnormal catabolism of IDE's key substrates.
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Affiliation(s)
- Merc M Kemeh
- Gustaf H. Carlson School of Chemistry and Biochemistry, Clark University, Worcester, Massachusetts 01610, United States
| | - Noel D Lazo
- Gustaf H. Carlson School of Chemistry and Biochemistry, Clark University, Worcester, Massachusetts 01610, United States
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6
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Yilmaz A, Guerrera C, Waeckel-Énée E, Lipecka J, Bertocci B, van Endert P. Insulin-Degrading Enzyme Interacts with Mitochondrial Ribosomes and Respiratory Chain Proteins. Biomolecules 2023; 13:890. [PMID: 37371470 DOI: 10.3390/biom13060890] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/18/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023] Open
Abstract
Insulin-degrading enzyme (IDE) is a highly conserved metalloprotease that is mainly localized in the cytosol. Although IDE can degrade insulin and some other low molecular weight substrates efficiently, its ubiquitous expression suggests additional functions supported by experimental findings, such as a role in stress responses and cellular protein homeostasis. The translation of a long full-length IDE transcript has been reported to result in targeting to mitochondria, but the role of IDE in this compartment is unknown. To obtain initial leads on the function of IDE in mitochondria, we used a proximity biotinylation approach to identify proteins interacting with wild-type and protease-dead IDE targeted to the mitochondrial matrix. We find that IDE interacts with multiple mitochondrial ribosomal proteins as well as with proteins involved in the synthesis and assembly of mitochondrial complex I and IV. The mitochondrial interactomes of wild type and mutant IDE are highly similar and do not reveal any likely proteolytic IDE substrates. We speculate that IDE could adopt similar additional non-proteolytic functions in mitochondria as in the cytosol, acting as a chaperone and contributing to protein homeostasis and stress responses.
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Affiliation(s)
- Ayse Yilmaz
- Institut Necker Enfants Malades, Université Paris Cité, INSERM, CNRS, F-75015 Paris, France
| | - Chiara Guerrera
- Structure Fédérative de Recherche Necker, Proteomics Platform, Université Paris Cité, INSERM, CNRS, F-75015 Paris, France
| | | | - Joanna Lipecka
- Structure Fédérative de Recherche Necker, Proteomics Platform, Université Paris Cité, INSERM, CNRS, F-75015 Paris, France
| | - Barbara Bertocci
- Institut Necker Enfants Malades, Université Paris Cité, INSERM, CNRS, F-75015 Paris, France
| | - Peter van Endert
- Institut Necker Enfants Malades, Université Paris Cité, INSERM, CNRS, F-75015 Paris, France
- Service Immunologie Biologique, AP-HP, Hôpital Universitaire Necker-Enfants Malades, F-75015 Paris, France
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7
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Wilson Alphonse CR, Rajesh Kannan R, Nagarajan N. PITRM1 interaction studies with amyloidogenic nonapeptide mutants of familial Alzheimer's disease. J Biomol Struct Dyn 2022:1-12. [PMID: 35751131 DOI: 10.1080/07391102.2022.2092554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Amyloid β-protein (ABP) is found to be the major cause for the development of neurodegeneration which leads to Alzheimer's. The Aβ nonapeptide segment, QKLVFFAED (amino acids 15-23) is the highly amyloidogenic central region of Aβ. Familial mutation in Aβ increases the aggregation property of the peptide compared to the Native (Wild) amyloid-beta (Aβ) and these mutations fall on the Aβ nonapeptide segment. The catalytic activity of pitrilysin metallopeptidase 1(PITRM1) with familial mutant Aβ (Flemish, Arctic, Dutch, Italian and Iowa) during interaction is examined using molecular dynamic simulation. The molecular dynamics simulation of PITRM1 and the Aβ nonapeptide segment showed similar RMSD with respect to stability. The active site amino acid (AA) H108, hydrophobic pocket AA residues L111, F123, F124, and L127 and the basic pocket AA residues R888 and H896 showed similar interactions with both wild and familial Aβ. The molecular level interaction between amyloid beta and PITRM1 were similar in the wild and familial mutants except for the Arctic mutant. The hydrophobic interaction was commonly observed between the S1 hydrophobic pocket and the LVFF region, the Arctic mutant showed less hydrogen bond formation consistently when compared to other complexes. This molecular information on catalytic activity suggests that modulating inactive PITRM1 or an increase in expression of PITRM1 can help in eliminating different kinds of familial mutant Aβ in neurodegenerative cells.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Carlton Ranjith Wilson Alphonse
- Neuroscience Lab, Centre for Molecular and Nanomedical Sciences, Centre for Nanoscience and Nanotechnology, School of Bio and Chemical Engineering, Sathyabama Institute of Science and Technology, Chennai, Tamil Nadu, India
| | - Rajaretinam Rajesh Kannan
- Neuroscience Lab, Centre for Molecular and Nanomedical Sciences, Centre for Nanoscience and Nanotechnology, School of Bio and Chemical Engineering, Sathyabama Institute of Science and Technology, Chennai, Tamil Nadu, India
| | - Nagasundaram Nagarajan
- Neuroscience Lab, Centre for Molecular and Nanomedical Sciences, Centre for Nanoscience and Nanotechnology, School of Bio and Chemical Engineering, Sathyabama Institute of Science and Technology, Chennai, Tamil Nadu, India.,School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
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8
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An SPR-based method for Hill coefficient measurements: the case of insulin-degrading enzyme. Anal Bioanal Chem 2022; 414:4793-4802. [PMID: 35577931 DOI: 10.1007/s00216-022-04122-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/02/2022] [Accepted: 05/05/2022] [Indexed: 11/01/2022]
Abstract
Insulin-degrading enzyme (IDE) is a highly conserved zinc metallopeptidase and is capable to catalytically cleave several substrates besides insulin, playing a pivotal role in several different biochemical pathways. Although its mechanism of action has been widely investigated, many conundrums still remain, hindering the possibility to rationally design specific modulators which could have important therapeutical applications in several diseases such as diabetes and Alzheimer's disease. In this scenario, we have developed a novel surface plasmon resonance (SPR) method which allows for directly measuring the enzyme cooperativity for the binding of insulin in the presence of different IDE activity modulators: carnosine, ATP, and EDTA. Results indicate that both positive and negative modulations of the IDE activity can be correlated to an increase and a decrease of the measured Hill coefficient, respectively, giving a new insight into the IDE activity mechanism. The use of the IDE R767A mutant for which oligomerization is hindered confirmed that the positive allosteric modulation of IDE by carnosine is due to a change in the enzyme oligomeric state occurring also for the enzyme immobilized on the gold SPR chip.
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9
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Lesire L, Leroux F, Deprez-Poulain R, Deprez B. Insulin-Degrading Enzyme, an Under-Estimated Potential Target to Treat Cancer? Cells 2022; 11:1228. [PMID: 35406791 PMCID: PMC8998118 DOI: 10.3390/cells11071228] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/31/2022] [Accepted: 04/01/2022] [Indexed: 02/04/2023] Open
Abstract
Insulin-degrading enzyme (IDE) is a multifunctional protease due to the variety of its substrates, its various cellular locations, its conservation between species and its many non-proteolytic functions. Numerous studies have successfully demonstrated its implication in two main therapeutic areas: metabolic and neuronal diseases. In recent years, several reports have underlined the overexpression of this enzyme in different cancers. Still, the exact role of IDE in the physiopathology of cancer remains to be elucidated. Known as the main enzyme responsible for the degradation of insulin, an essential growth factor for healthy cells and cancer cells, IDE has also been shown to behave like a chaperone and interact with the proteasome. The pharmacological modulation of IDE (siRNA, chemical compounds, etc.) has demonstrated interesting results in cancer models. All these results point towards IDE as a potential target in cancer. In this review, we will discuss evidence of links between IDE and cancer development or resistance, IDE's functions, catalytic or non-catalytic, in the context of cell proliferation, cancer development and the impact of the pharmacomodulation of IDE via cancer therapeutics.
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Affiliation(s)
| | | | - Rebecca Deprez-Poulain
- INSERM U1177 Drugs and Molecules for Living Systems, Institut Pasteur de Lille, European Genomic Institute for Diabetes, University of Lille, F-59000 Lille, France; (L.L.); (F.L.); (B.D.)
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10
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Structural basis for the mechanisms of human presequence protease conformational switch and substrate recognition. Nat Commun 2022; 13:1833. [PMID: 35383169 PMCID: PMC8983764 DOI: 10.1038/s41467-022-29322-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 03/04/2022] [Indexed: 11/08/2022] Open
Abstract
Presequence protease (PreP), a 117 kDa mitochondrial M16C metalloprotease vital for mitochondrial proteostasis, degrades presequence peptides cleaved off from nuclear-encoded proteins and other aggregation-prone peptides, such as amyloid β (Aβ). PreP structures have only been determined in a closed conformation; thus, the mechanisms of substrate binding and selectivity remain elusive. Here, we leverage advanced vitrification techniques to overcome the preferential denaturation of one of two ~55 kDa homologous domains of PreP caused by air-water interface adsorption. Thereby, we elucidate cryoEM structures of three apo-PreP open states along with Aβ- and citrate synthase presequence-bound PreP at 3.3–4.6 Å resolution. Together with integrative biophysical and pharmacological approaches, these structures reveal the key stages of the PreP catalytic cycle and how the binding of substrates or PreP inhibitor drives a rigid body motion of the protein for substrate binding and catalysis. Together, our studies provide key mechanistic insights into M16C metalloproteases for future therapeutic innovations. Presequence protease (PreP) is essential to mitochondrial proteostasis. This study leverages advanced vitrification techniques to solve cryoEM structures of apo- and substrate-bound PreP and integrates these data with other analysis to reveal key stages and mechanistic insights of the PreP catalytic cycle.
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11
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Xu M, Xu Q, Wang M, Qiu S, Xu D, Zhang W, Wang W, He J, Wang Q, Ran T, Sun B. Crystal structures of TTHA1265 and TTHA1264/TTHA1265 complex reveal an intrinsic heterodimeric assembly. Int J Biol Macromol 2022; 207:424-433. [PMID: 35276293 DOI: 10.1016/j.ijbiomac.2022.03.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 03/01/2022] [Accepted: 03/04/2022] [Indexed: 11/05/2022]
Abstract
Zinc peptidase M16 family members are widely distributed in most prokaryotic and eukaryotic organisms. M16 family has been divided into three subfamilies, M16A, M16B and M16C, based on sequence alignments and subunit connectivity. TTHA1264, an M16B protein found in Thermus thermophiles HB8, possesses an HXXEH motif essential for Zn2+ binding and catalytic activity. TTHA1265 is another member of M16B, which lacks the metal-binding motif but with a conserved active-site R/Y pair commonly found in the C-terminal half of M16 enzymes. Sequence analysis showed that two genes coding for TTHA1264 and TTHA1265 assemble into a single operon in the bacterial genome. Here, we report the crystal structure of TTHA1265 and TTHA1264/TTHA1265 complex from T. thermophilus HB8. Interestingly, when TTHA1264 and TTHA1265 are present alone, TTHA1264 forms a monomer, TTHA1265 forms a homodimer, respectively. However, TTHA264 and TTHA1265 assembled into a heterodimeric complex, indicating that they prefer to form heterodimer. Biochemical data further confirmed the heterodimeric assembly indicating intrinsic heterodimeric assembly of TTHA1264 and TTHA1265. This property of TTHA1264 and TTHA1265 is consistent with the characteristics of the M16B family.
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Affiliation(s)
- Mengxue Xu
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China.; Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, China
| | - Qin Xu
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China.; Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China
| | - Meitian Wang
- Swiss Light Source, Paul Scherrer Institute, CH-5232 Villigen PSI, Switzerland
| | - Shenshen Qiu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, China
| | - Dongqing Xu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, China
| | - Weizhe Zhang
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China
| | - Weiwu Wang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, China
| | - Jianhua He
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Qisheng Wang
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China.; Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China.
| | - Tingting Ran
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, China.
| | - Bo Sun
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China.; Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China.
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12
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Insulin-Degrading Enzyme Is a Non Proteasomal Target of Carfilzomib and Affects the 20S Proteasome Inhibition by the Drug. Biomolecules 2022; 12:biom12020315. [PMID: 35204815 PMCID: PMC8869475 DOI: 10.3390/biom12020315] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 01/12/2022] [Accepted: 01/27/2022] [Indexed: 02/07/2023] Open
Abstract
Carfilzomib is a last generation proteasome inhibitor (PI) with proven clinical efficacy in the treatment of relapsed/refractory multiple myeloma. This drug is considered to be extremely specific in inhibiting the chymotrypsin-like activity of the 20S proteasome, encoded by the β5 subunit, overcoming some bortezomib limitations, the first PI approved for multiple myeloma therapy which is however burdened by a significant toxicity profile, due also to its off-target effects. Here, molecular approaches coupled with molecular docking studies have been used to unveil that the Insulin-Degrading Enzyme, a ubiquitous and highly conserved Zn2+ peptidase, often found to associate with proteasome in cell-based models, is targeted by carfilzomib in vitro. The drug behaves as a modulator of IDE activity, displaying an inhibitory effect over 10-fold lower than for the 20S. Notably, the interaction of IDE with the 20S enhances in vitro the inhibitory power of carfilzomib on proteasome, so that the IDE-20S complex is an even better target of carfilzomib than the 20S alone. Furthermore, IDE gene silencing after delivery of antisense oligonucleotides (siRNA) significantly reduced carfilzomib cytotoxicity in rMC1 cells, a validated model of Muller glia, suggesting that, in cells, the inhibitory activity of this drug on cell proliferation is somewhat linked to IDE and, possibly, also to its interaction with proteasome.
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13
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Ghoula M, Janel N, Camproux AC, Moroy G. Exploring the Structural Rearrangements of the Human Insulin-Degrading Enzyme through Molecular Dynamics Simulations. Int J Mol Sci 2022; 23:ijms23031746. [PMID: 35163673 PMCID: PMC8836115 DOI: 10.3390/ijms23031746] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/24/2022] [Accepted: 01/29/2022] [Indexed: 11/16/2022] Open
Abstract
Insulin-degrading enzyme (IDE) is a ubiquitously expressed metallopeptidase that degrades insulin and a large panel of amyloidogenic peptides. IDE is thought to be a potential therapeutic target for type-2 diabetes and neurodegenerative diseases, such as Alzheimer’s disease. IDE catalytic chamber, known as a crypt, is formed, so that peptides can be enclosed and degraded. However, the molecular mechanism of the IDE function and peptide recognition, as well as its conformation changes, remains elusive. Our study elucidates IDE structural changes and explains how IDE conformational dynamics is important to modulate the catalytic cycle of IDE. In this aim, a free-substrate IDE crystallographic structure (PDB ID: 2JG4) was used to model a complete structure of IDE. IDE stability and flexibility were studied through molecular dynamics (MD) simulations to witness IDE conformational dynamics switching from a closed to an open state. The description of IDE structural changes was achieved by analysis of the cavity and its expansion over time. Moreover, the quasi-harmonic analysis of the hinge connecting IDE domains and the angles formed over the simulations gave more insights into IDE shifts. Overall, our results could guide toward the use of different approaches to study IDE with different substrates and inhibitors, while taking into account the conformational states resolved in our study.
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Affiliation(s)
- Mariem Ghoula
- Unité de Biologie Fonctionnelle et Adaptative, CNRS, INSERM, Université de Paris, F-75013 Paris, France;
| | - Nathalie Janel
- Unité de Biologie Fonctionnelle et Adaptative, CNRS, Université de Paris, F-75013 Paris, France;
| | - Anne-Claude Camproux
- Unité de Biologie Fonctionnelle et Adaptative, CNRS, INSERM, Université de Paris, F-75013 Paris, France;
- Correspondence: (A.-C.C.); (G.M.); Tel.: +33-1-57-27-83-77 (A.-C.C.); +33-1-57-27-83-85 (G.M.)
| | - Gautier Moroy
- Unité de Biologie Fonctionnelle et Adaptative, CNRS, INSERM, Université de Paris, F-75013 Paris, France;
- Correspondence: (A.-C.C.); (G.M.); Tel.: +33-1-57-27-83-77 (A.-C.C.); +33-1-57-27-83-85 (G.M.)
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14
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Kraupner N, Dinh CP, Wen X, Landry V, Herledan A, Leroux F, Bosc D, Charton J, Maillard C, Warenghem S, Duplan I, Piveteau C, Hennuyer N, Staels B, Deprez B, Deprez-Poulain R. Identification of indole-based activators of insulin degrading enzyme. Eur J Med Chem 2022; 228:113982. [PMID: 34815130 DOI: 10.1016/j.ejmech.2021.113982] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 11/05/2021] [Accepted: 11/06/2021] [Indexed: 11/29/2022]
Abstract
Insulin degrading enzyme (IDE) is a zinc metalloprotease that cleaves numerous substrates among which amyloid-β and insulin. It has been linked through genetic studies to the risk of type-2 diabetes (T2D) or Alzheimer's disease (AD). Pharmacological activation of IDE is an attractive therapeutic strategy in AD. While IDE inhibition gave paradoxal activity in glucose homeostasis, recent studies, in particular in the liver suggest that IDE activators could be also of interest in diabetes. Here we describe the discovery of an original series of IDE activators by screening and structure-activity relationships. Early cellular studies show that hit 1 decreases glucose-stimulating insulin secretion. Docking studies revealed it has an unprecedented extended binding to the polyanion-binding site of IDE. These indole-based pharmacological tools are activators of both Aβ and insulin hydrolysis by IDE and could be helpful to explore the multiple roles of IDE.
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Affiliation(s)
- Nicolas Kraupner
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Chau Phi Dinh
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Xiaoan Wen
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Valérie Landry
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Adrien Herledan
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Florence Leroux
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France; European Genomic Institute for Diabetes, EGID, University of Lille, F-59000, France
| | - Damien Bosc
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Julie Charton
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France; European Genomic Institute for Diabetes, EGID, University of Lille, F-59000, France
| | - Clara Maillard
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Sandrine Warenghem
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Isabelle Duplan
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, F-59000, Lille, France; European Genomic Institute for Diabetes, EGID, University of Lille, F-59000, France
| | - Catherine Piveteau
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Nathalie Hennuyer
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, F-59000, Lille, France; European Genomic Institute for Diabetes, EGID, University of Lille, F-59000, France
| | - Bart Staels
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, F-59000, Lille, France; European Genomic Institute for Diabetes, EGID, University of Lille, F-59000, France
| | - Benoit Deprez
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France; European Genomic Institute for Diabetes, EGID, University of Lille, F-59000, France
| | - Rebecca Deprez-Poulain
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France; European Genomic Institute for Diabetes, EGID, University of Lille, F-59000, France.
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15
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Zheng Q, Kebede MT, Lee B, Krasinski CA, Islam S, Wurfl LA, Kemeh MM, Ivancic VA, Jakobsche CE, Spratt DE, Lazo ND. Differential Effects of Polyphenols on Insulin Proteolysis by the Insulin-Degrading Enzyme. Antioxidants (Basel) 2021; 10:1342. [PMID: 34572974 PMCID: PMC8467823 DOI: 10.3390/antiox10091342] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/19/2021] [Accepted: 08/23/2021] [Indexed: 12/20/2022] Open
Abstract
The insulin-degrading enzyme (IDE) possesses a strong ability to degrade insulin and Aβ42 that has been linked to the neurodegeneration in Alzheimer's disease (AD). Given this, an attractive IDE-centric strategy for the development of therapeutics for AD is to boost IDE's activity for the clearance of Aβ42 without offsetting insulin proteostasis. Recently, we showed that resveratrol enhances IDE's activity toward Aβ42. In this work, we used a combination of chromatographic and spectroscopic techniques to investigate the effects of resveratrol on IDE's activity toward insulin. For comparison, we also studied epigallocatechin-3-gallate (EGCG). Our results show that the two polyphenols affect the IDE-dependent degradation of insulin in different ways: EGCG inhibits IDE while resveratrol has no effect. These findings suggest that polyphenols provide a path for developing therapeutic strategies that can selectively target IDE substrate specificity.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Noel D. Lazo
- Gustaf H. Carlson School of Chemistry and Biochemistry, Clark University, Worcester, MA 01610, USA; (Q.Z.); (M.T.K.); (B.L.); (C.A.K.); (S.I.); (L.A.W.); (M.M.K.); (V.A.I.); (C.E.J.); (D.E.S.)
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16
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Ramaraju B, Nelson SL, Zheng W, Ghirlando R, Deshmukh L. Quantitative NMR Study of Insulin-Degrading Enzyme Using Amyloid-β and HIV-1 p6 Elucidates Its Chaperone Activity. Biochemistry 2021; 60:2519-2523. [PMID: 34342986 PMCID: PMC8895387 DOI: 10.1021/acs.biochem.1c00342] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Insulin-degrading enzyme (IDE) hydrolyzes monomeric polypeptides, including amyloid-β (Aβ) and HIV-1 p6. It also acts as a nonproteolytic chaperone to prevent Aβ polymerization. Here we compare interactions of Aβ and non-amyloidogenic p6 with IDE. Although both exhibited similar proteolysis rates, the binding kinetics to an inactive IDE characterized using relaxation-based NMR were remarkably different. IDE and Aβ formed a sparsely populated complex with a lifetime of milliseconds in which a short hydrophobic cleavage segment of Aβ was anchored to IDE. Strikingly, a second and more stable complex was significantly populated with a subsecond lifetime owing to multiple intermolecular contacts between Aβ and IDE. By selectively sequestering Aβ in this nonproductive complex, IDE likely increases the critical concentration required for fibrillization. In contrast, IDE and p6 formed a transient, submillisecond complex involving a single anchoring p6 motif. Modulation of intermolecular interactions, thus, allows IDE to differentiate between non-amyloidogenic and amyloidogenic substrates.
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Affiliation(s)
- Bhargavi Ramaraju
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Spencer L Nelson
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Wenwei Zheng
- College of Integrative Sciences and Arts, Arizona State University, Mesa, Arizona 85212, United States
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Lalit Deshmukh
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
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17
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Adamek RN, Suire CN, Stokes RW, Brizuela MK, Cohen SM, Leissring MA. Hydroxypyridinethione Inhibitors of Human Insulin-Degrading Enzyme. ChemMedChem 2021; 16:1775-1787. [PMID: 33686743 DOI: 10.1002/cmdc.202100111] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 02/28/2021] [Indexed: 01/29/2023]
Abstract
Insulin-degrading enzyme (IDE) is a human mononuclear Zn2+ -dependent metalloenzyme that is widely regarded as the primary peptidase responsible for insulin degradation. Despite its name, IDE is also critically involved in the hydrolysis of several other disparate peptide hormones, including glucagon, amylin, and the amyloid β-protein. As such, the study of IDE inhibition is highly relevant to deciphering the role of IDE in conditions such as type-2 diabetes mellitus and Alzheimer disease. There have been few reported IDE inhibitors, and of these, inhibitors that directly target the active-site Zn2+ ion have yet to be fully explored. In an effort to discover new, zinc-targeting inhibitors of IDE, a library of ∼350 metal-binding pharmacophores was screened against IDE, resulting in the identification of 1-hydroxypyridine-2-thione (1,2-HOPTO) as an effective Zn2+ -binding scaffold. Screening a focused library of HOPTO compounds identified 3-sulfonamide derivatives of 1,2-HOPTO as inhibitors of IDE (Ki values of ∼50 μM). Further structure-activity relationship studies yielded several thiophene-sulfonamide HOPTO derivatives with good, broad-spectrum activity against IDE that have the potential to be useful pharmacological tools for future studies of IDE.
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Affiliation(s)
- Rebecca N Adamek
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Caitlin N Suire
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, Irvine, CA 92697, USA
| | - Ryjul W Stokes
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Monica K Brizuela
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, Irvine, CA 92697, USA
| | - Seth M Cohen
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Malcolm A Leissring
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, Irvine, CA 92697, USA
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18
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Modulation of Insulin Sensitivity by Insulin-Degrading Enzyme. Biomedicines 2021; 9:biomedicines9010086. [PMID: 33477364 PMCID: PMC7830943 DOI: 10.3390/biomedicines9010086] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 12/15/2022] Open
Abstract
Insulin-degrading enzyme (IDE) is a highly conserved and ubiquitously expressed metalloprotease that degrades insulin and several other intermediate-size peptides. For many decades, IDE had been assumed to be involved primarily in hepatic insulin clearance, a key process that regulates availability of circulating insulin levels for peripheral tissues. Emerging evidence, however, suggests that IDE has several other important physiological functions relevant to glucose and insulin homeostasis, including the regulation of insulin secretion from pancreatic β-cells. Investigation of mice with tissue-specific genetic deletion of Ide in the liver and pancreatic β-cells (L-IDE-KO and B-IDE-KO mice, respectively) has revealed additional roles for IDE in the regulation of hepatic insulin action and sensitivity. In this review, we discuss current knowledge about IDE’s function as a regulator of insulin secretion and hepatic insulin sensitivity, both evaluating the classical view of IDE as an insulin protease and also exploring evidence for several non-proteolytic functions. Insulin proteostasis and insulin sensitivity have both been highlighted as targets controlling blood sugar levels in type 2 diabetes, so a clearer understanding the physiological functions of IDE in pancreas and liver could led to the development of novel therapeutics for the treatment of this disease.
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19
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Abramov-Harpaz K, Miller Y. A zinc-dependent switching mechanism from an open to a new closed-state conformation of insulin-degrading enzyme. Inorg Chem Front 2021. [DOI: 10.1039/d1qi00284h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The switching mechanism between an open-state conformation and a newly closed-state conformation of IDE is stabilized by electrostatic interactions between domain D1 and domain D3.
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Affiliation(s)
- Karina Abramov-Harpaz
- Department of Chemistry
- Ben-Gurion University of the Negev
- Be'er Sheva 84105
- Israel
- Ilse Katz Institute for Nanoscale Science and Technology
| | - Yifat Miller
- Department of Chemistry
- Ben-Gurion University of the Negev
- Be'er Sheva 84105
- Israel
- Ilse Katz Institute for Nanoscale Science and Technology
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20
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Liang WG, Mancl JM, Zhao M, Tang WJ. Structural analysis of Mycobacterium tuberculosis M13 metalloprotease Zmp1 open states. Structure 2020; 29:709-720.e3. [PMID: 33378640 DOI: 10.1016/j.str.2020.12.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 10/12/2020] [Accepted: 12/04/2020] [Indexed: 12/16/2022]
Abstract
Zinc metalloprotease 1 (Zmp1), a Mycobacterium tuberculosis 75 kDa secreted enzyme, mediates key stages of tuberculosis disease progression. The biological activity of Zmp1 presumably stems from its ability to degrade bacterium- and/or host-derived peptides. The crystal structures of Zmp1 and related M13 metalloproteases, such as neprilysin and endothelin-converting enzyme-1 were determined only in the closed conformation, which cannot capture substrates or release proteolytic products. Thus, the mechanisms of substrate binding and selectivity remain elusive. Here we report two open-state cryo-EM structures of Zmp1, revealed by our SAXS analysis to be the dominant states in solution. Our structural analyses reveal how ligand binding induces a conformational switch in four linker regions to drive the rigid body motion of the D1 and D2 domains, which form the sizable catalytic chamber. Furthermore, they offer insights into the catalytic cycle and mechanism of substrate recognition of M13 metalloproteases for future therapeutic innovations.
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Affiliation(s)
- Wenguang G Liang
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Jordan M Mancl
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Minglei Zhao
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA.
| | - Wei-Jen Tang
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA.
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21
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Xie Z, Wu H, Zhao J. Multifunctional roles of zinc in Alzheimer’s disease. Neurotoxicology 2020; 80:112-123. [DOI: 10.1016/j.neuro.2020.07.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/13/2020] [Accepted: 07/16/2020] [Indexed: 02/06/2023]
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22
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Bellia F, Lanza V, Ahmed IMM, Garcia-Vinuales S, Veiss E, Arizzi M, Calcagno D, Milardi D, Grasso G. Site directed mutagenesis of insulin-degrading enzyme allows singling out the molecular basis of peptidase versus E1-like activity: the role of metal ions. Metallomics 2020; 11:278-281. [PMID: 30627720 DOI: 10.1039/c8mt00288f] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Four specifically designed IDE mutants have been used to unveil the molecular basis of peptidase versus E1-like activity of the enzyme. We have found that physiological concentrations of copper(ii) ions inhibit the proteolytic activity of the enzyme towards small and large substrates but have no effect on the E1-like activity of the enzyme.
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Affiliation(s)
- Francesco Bellia
- Institute of Biostructures and Bioimaging, National Research Council, Catania, Italy.
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23
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Leroux F, Bosc D, Beghyn T, Hermant P, Warenghem S, Landry V, Pottiez V, Guillaume V, Charton J, Herledan A, Urata S, Liang W, Sheng L, Tang WJ, Deprez B, Deprez-Poulain R. Identification of ebselen as a potent inhibitor of insulin degrading enzyme by a drug repurposing screening. Eur J Med Chem 2019; 179:557-566. [PMID: 31276900 DOI: 10.1016/j.ejmech.2019.06.057] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 06/18/2019] [Accepted: 06/19/2019] [Indexed: 12/15/2022]
Abstract
Insulin-degrading enzyme, IDE, is a metalloprotease implicated in the metabolism of key peptides such as insulin, glucagon, β-amyloid peptide. Recent studies have pointed out its broader role in the cell physiology. In order to identify new drug-like inhibitors of IDE with optimal pharmacokinetic properties to probe its multiple roles, we ran a high-throughput drug repurposing screening. Ebselen, cefmetazole and rabeprazole were identified as reversible inhibitors of IDE. Ebselen is the most potent inhibitor (IC50(insulin) = 14 nM). The molecular mode of action of ebselen was investigated by biophysical methods. We show that ebselen induces the disorder of the IDE catalytic cleft, which significantly differs from the previously reported IDE inhibitors. IDE inhibition by ebselen can explain some of its reported activities in metabolism as well as in neuroprotection.
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Affiliation(s)
- Florence Leroux
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177, Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Damien Bosc
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177, Drugs and Molecules for Living Systems, F-59000, Lille, France
| | | | - Paul Hermant
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177, Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Sandrine Warenghem
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177, Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Valérie Landry
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177, Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Virginie Pottiez
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177, Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Valentin Guillaume
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177, Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Julie Charton
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177, Drugs and Molecules for Living Systems, F-59000, Lille, France; European Genomic Institute for Diabetes, EGID, University of Lille, F-59000, France
| | - Adrien Herledan
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177, Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Sarah Urata
- Department of Medicine, University of California at San Diego, CA 92093, La Jolla, United States
| | - Wenguang Liang
- Ben-May Institute for Cancer Research, The University of Chicago, IL 60637, Chicago, United States
| | - Li Sheng
- Department of Medicine, University of California at San Diego, CA 92093, La Jolla, United States
| | - Wei-Jen Tang
- Ben-May Institute for Cancer Research, The University of Chicago, IL 60637, Chicago, United States
| | - Benoit Deprez
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177, Drugs and Molecules for Living Systems, F-59000, Lille, France; APTEEUS, F-59000, Lille, France; European Genomic Institute for Diabetes, EGID, University of Lille, F-59000, France
| | - Rebecca Deprez-Poulain
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177, Drugs and Molecules for Living Systems, F-59000, Lille, France; European Genomic Institute for Diabetes, EGID, University of Lille, F-59000, France; Institut Universitaire de France, F- 75231, Paris, France.
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24
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Substrate-selective inhibitors that reprogram the activity of insulin-degrading enzyme. Nat Chem Biol 2019; 15:565-574. [PMID: 31086331 PMCID: PMC6551522 DOI: 10.1038/s41589-019-0271-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 03/14/2019] [Indexed: 11/08/2022]
Abstract
Enzymes that act on multiple substrates are common in biology but pose unique challenges as therapeutic targets. The metalloprotease insulin-degrading enzyme (IDE) modulates blood glucose levels by cleaving insulin, a hormone that promotes glucose clearance. However, IDE also degrades glucagon, a hormone that elevates glucose levels and opposes the effect of insulin. IDE inhibitors to treat diabetes therefore should prevent IDE-mediated insulin degradation, but not glucagon degradation, in contrast with traditional modes of enzyme inhibition. Using a high-throughput screen for non-active-site ligands, we discovered potent and highly specific small-molecule inhibitors that alter IDE’s substrate selectivity. X-ray co-crystal structures, including an IDE-ligand-glucagon ternary complex, revealed substrate-dependent interactions that enable these inhibitors to potently block insulin binding while allowing glucagon cleavage, even at saturating inhibitor concentrations. These findings suggest a path for developing IDE-targeting therapeutics, and offer a blueprint for modulating other enzymes in a substrate-selective manner to unlock their therapeutic potential.
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25
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Bellia F, Lanza V, García-Viñuales S, Ahmed IMM, Pietropaolo A, Iacobucci C, Malgieri G, D'Abrosca G, Fattorusso R, Nicoletti VG, Sbardella D, Tundo GR, Coletta M, Pirone L, Pedone E, Calcagno D, Grasso G, Milardi D. Ubiquitin binds the amyloid β peptide and interferes with its clearance pathways. Chem Sci 2019; 10:2732-2742. [PMID: 30996991 PMCID: PMC6419943 DOI: 10.1039/c8sc03394c] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 01/09/2019] [Indexed: 12/22/2022] Open
Abstract
Several lines of evidence point to a compromised proteostasis associated with a reduction of the Ubiquitin Proteasome System (UPS) activity in patients affected by Alzheimer's Disease (AD) and suggest that the amyloid β peptide (Aβ) is an important player in the game. Inspired also by many reports, underlining the presence of ubiquitin (Ub) in the amyloid plaques of AD brains, here we set out to test whether Ub may bind the Aβ peptide and have any effect on its clearance pathways. By using an integrated array of MALDI-TOF/UPLC-HRMS, fluorescence, NMR, SPR, Microscale Thermophoresis (MST) and molecular dynamics studies, we consistently demonstrated that Aβ40 binds Ub with a 1 : 1 stoichiometry and K d in the high micromolar range. In particular, we show that the N-terminal domain of the Aβ peptide (through residues D1, E3 and R5) interacts with the C-terminal tail of Ub (involving residues K63 and E64), inducing the central region of Aβ (14HQKLVFFAEDVGSNK28) to adopt a mixed α-helix/β-turn structure. ELISA assays, carried out in neuroblastoma cell lysates, suggest that Aβ competitively binds Ub also in the presence of the entire pool of cytosolic Ub binding proteins. Ub-bound Aβ has a lower tendency to aggregate into amyloid-like fibrils and is more slowly degraded by the Insulin Degrading Enzyme (IDE). Finally, we observe that the water soluble fragment Aβ1-16 significantly inhibits Ub chain growth reactions. These results evidence how the non-covalent interaction between Aβ peptides and Ub may have relevant effects on the regulation of the upstream events of the UPS and pave the way to future in vivo studies addressing the role played by Aβ peptide in the malfunction of proteome maintenance occurring in AD.
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Affiliation(s)
- F Bellia
- Consiglio Nazionale delle Ricerche , Istituto di Biostrutture e Bioimmagini , Via P. Gaifami 18 , 95126 Catania , Italy .
| | - V Lanza
- Consiglio Nazionale delle Ricerche , Istituto di Biostrutture e Bioimmagini , Via P. Gaifami 18 , 95126 Catania , Italy .
| | - S García-Viñuales
- Consiglio Nazionale delle Ricerche , Istituto di Biostrutture e Bioimmagini , Via P. Gaifami 18 , 95126 Catania , Italy .
| | - I M M Ahmed
- Consiglio Nazionale delle Ricerche , Istituto di Biostrutture e Bioimmagini , Via P. Gaifami 18 , 95126 Catania , Italy .
| | - A Pietropaolo
- Dipartimento di Scienze della Salute , Università degli Studi Magna Graecia di Catanzaro , Viale Europa , 88100 , Catanzaro , Italy
| | - C Iacobucci
- Department of Pharmaceutical Chemistry & Bioanalytics , Institute of Pharmacy , Martin Luther University Halle-Wittenberg , 06120 Halle/Saale , Germany
| | - G Malgieri
- Department of Environmental , Biological and Pharmaceutical Sciences and Technologies , University of Campania "Luigi Vanvitelli" , Via Vivaldi 43 , 81100 Caserta , Italy
| | - G D'Abrosca
- Department of Environmental , Biological and Pharmaceutical Sciences and Technologies , University of Campania "Luigi Vanvitelli" , Via Vivaldi 43 , 81100 Caserta , Italy
| | - R Fattorusso
- Department of Environmental , Biological and Pharmaceutical Sciences and Technologies , University of Campania "Luigi Vanvitelli" , Via Vivaldi 43 , 81100 Caserta , Italy
| | - V G Nicoletti
- Dipartimento di Scienze Biomediche e Biotecnologiche (BIOMETEC) , sez. Biochimica medica , Università di Catania , Via Santa Sofia 97 , 95124 Catania , Italy
| | - D Sbardella
- Dipartimento di Scienze Cliniche e Medicina Traslazionale , Università di Roma Tor Vergata , Via Montpellier 1 , 00133 , Roma , Italy
| | - G R Tundo
- Dipartimento di Scienze Cliniche e Medicina Traslazionale , Università di Roma Tor Vergata , Via Montpellier 1 , 00133 , Roma , Italy
| | - M Coletta
- Dipartimento di Scienze Cliniche e Medicina Traslazionale , Università di Roma Tor Vergata , Via Montpellier 1 , 00133 , Roma , Italy
| | - L Pirone
- Consiglio Nazionale delle Ricerche , Istituto di Biostrutture e Bioimmagini , Via Mezzocannone, 16 , Naples I-80134 , Italy
| | - E Pedone
- Consiglio Nazionale delle Ricerche , Istituto di Biostrutture e Bioimmagini , Via Mezzocannone, 16 , Naples I-80134 , Italy
| | - D Calcagno
- Dipartimento di Scienze Chimiche , Università di Catania , V.le Andrea Doria 6 , 95125 Catania , Italy .
| | - G Grasso
- Dipartimento di Scienze Chimiche , Università di Catania , V.le Andrea Doria 6 , 95125 Catania , Italy .
| | - D Milardi
- Consiglio Nazionale delle Ricerche , Istituto di Biostrutture e Bioimmagini , Via P. Gaifami 18 , 95126 Catania , Italy .
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26
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Enzyme kinetics from circular dichroism of insulin reveals mechanistic insights into the regulation of insulin-degrading enzyme. Biosci Rep 2018; 38:BSR20181416. [PMID: 30305381 PMCID: PMC6239264 DOI: 10.1042/bsr20181416] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 10/03/2018] [Accepted: 10/05/2018] [Indexed: 12/17/2022] Open
Abstract
Insulin-degrading enzyme (IDE) is a zinc metalloprotease that selectively degrades biologically important substrates associated with type 2 diabetes and Alzheimer’s disease (AD). As such, IDE is an attractive target for therapeutic innovations. A major requirement is an understanding of how other molecules present in cells regulate the activity of the enzyme toward insulin, IDE’s most important physiologically relevant substrate. Previous kinetic studies of the IDE-dependent degradation of insulin in the presence of potential regulators have used iodinated insulin, a chemical modification that has been shown to alter the biological and biochemical properties of insulin. Here, we present a novel kinetic assay that takes advantage of the loss of helical circular dichroic signals of insulin with IDE-dependent degradation. As proof of concept, the resulting Michaelis–Menten kinetic constants accurately predict the known regulation of IDE by adenosine triphosphate (ATP). Intriguingly, we found that when Mg2+ is present with ATP, the regulation is abolished. The implication of this result for the development of preventative and therapeutic strategies for AD is discussed. We anticipate that the new assay presented here will lead to the identification of other small molecules that regulate the activity of IDE toward insulin.
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27
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Lai R, Tang WJ, Li H. Catalytic Mechanism of Amyloid-β Peptide Degradation by Insulin Degrading Enzyme: Insights from Quantum Mechanics and Molecular Mechanics Style Møller-Plesset Second Order Perturbation Theory Calculation. J Chem Inf Model 2018; 58:1926-1934. [PMID: 30133282 PMCID: PMC6670292 DOI: 10.1021/acs.jcim.8b00406] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Insulin degrading enzyme (IDE), a metalloprotease that degrades amyloid-β (Aβ) peptides and insulin, is associated with Alzheimer's disease and diabetes. The mechanism of IDE catalyzed degrading of Aβ peptides, which is of fundamental importance in the design of therapeutic methods for Alzheimer's disease, has not been fully understood. In this work, combined quantum mechanics and molecular mechanics (QM/MM) style Møller-Plesset second order perturbation theory (MP2) geometry optimization calculations are performed to investigate the catalytic mechanism of the Aβ40 Phe19-Phe20 peptide bond cleavage by human IDE. The analyses using QM/MM MP2 optimization suggest that a neutral water molecule is at the active site of the enzyme-substrate (ES) complex. The water molecule is in hydrogen bonding with the nearby anionic Glu111 of IDE but not directly bound to the catalytic Zn ion. This is confirmed by QM/MM DFTB3 molecular dynamics simulation. Our studies also reveal that the hydrolysis of the Aβ40 Phe19-Phe20 peptide bond by IDE consists of four key steps. The neutral water is first activated by moving toward and binding to the Zn ion. A gem-diol intermediate is then formed by the activated neutral water molecule attacking the C atom of the Phe19-Phe20 peptide bond. The next is the protonation of the N atom of Phe19-Phe20 peptide bond to form an intermediate with an elongated C-N bond. The final step is the breaking of the Phe19-Phe20 C-N bond. The final step is the rate-determining step with a calculated Gibbs free energy of activation of 17.34 kcal/mol, in good agreement with the experimental value 16.7 kcal/mol. This mechanism provides the basis for the design of biochemical methods to modulate the activity of IDE in humans.
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Affiliation(s)
- Rui Lai
- Department of Chemistry, Nebraska Center for Materials and Nanoscience, and Center for Integrated Biomolecular Communication , University of Nebraska-Lincoln , Lincoln , Nebraska 68588-0304 , United States
| | - Wei-Jen Tang
- Ben May Department for Cancer Research , The University of Chicago , Chicago , Illinois 60637 , United States
| | - Hui Li
- Department of Chemistry, Nebraska Center for Materials and Nanoscience, and Center for Integrated Biomolecular Communication , University of Nebraska-Lincoln , Lincoln , Nebraska 68588-0304 , United States
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28
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Lanza V, Bellia F, Rizzarelli E. An inorganic overview of natural Aβ fragments: Copper(II) and zinc(II)-mediated pathways. Coord Chem Rev 2018. [DOI: 10.1016/j.ccr.2018.04.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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29
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High resolution crystal structure of substrate-free human neprilysin. J Struct Biol 2018; 204:19-25. [PMID: 29906506 DOI: 10.1016/j.jsb.2018.06.004] [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: 05/11/2018] [Revised: 06/09/2018] [Accepted: 06/11/2018] [Indexed: 11/23/2022]
Abstract
Neprilysin is a transmembrane M13 zinc metalloprotease responsible for the degradation of several biologically active peptides including insulin, enkephalin, substance P, bradykinin, endothelin-1, neurotensin and amyloid-β. The protein has received attention for its role in modulating blood pressure responses with its inhibition producing an antihypertensive response. To date, several inhibitor bound crystal structures of the human neprilysin extracellular domain have been determined, but, a structure free of bound inhibitor or substrate has yet to be reported. Here, we report the first crystal structure free of substrate or inhibitor for the extracellular catalytic domain of human neprilysin at 1.9 Å resolution. This structure will provide a reference point for comparisons to future inhibitor or substrate bound structures. The neprilysin structure also reveals that a closed protein conformation can be adopted in protein crystals absent of bound substrate or inhibitor.
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30
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Zhang Z, Liang WG, Bailey LJ, Tan YZ, Wei H, Wang A, Farcasanu M, Woods VA, McCord LA, Lee D, Shang W, Deprez-Poulain R, Deprez B, Liu DR, Koide A, Koide S, Kossiakoff AA, Li S, Carragher B, Potter CS, Tang WJ. Ensemble cryoEM elucidates the mechanism of insulin capture and degradation by human insulin degrading enzyme. eLife 2018; 7:33572. [PMID: 29596046 PMCID: PMC5910022 DOI: 10.7554/elife.33572] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 03/28/2018] [Indexed: 11/29/2022] Open
Abstract
Insulin degrading enzyme (IDE) plays key roles in degrading peptides vital in type two diabetes, Alzheimer's, inflammation, and other human diseases. However, the process through which IDE recognizes peptides that tend to form amyloid fibrils remained unsolved. We used cryoEM to understand both the apo- and insulin-bound dimeric IDE states, revealing that IDE displays a large opening between the homologous ~55 kDa N- and C-terminal halves to allow selective substrate capture based on size and charge complementarity. We also used cryoEM, X-ray crystallography, SAXS, and HDX-MS to elucidate the molecular basis of how amyloidogenic peptides stabilize the disordered IDE catalytic cleft, thereby inducing selective degradation by substrate-assisted catalysis. Furthermore, our insulin-bound IDE structures explain how IDE processively degrades insulin by stochastically cutting either chain without breaking disulfide bonds. Together, our studies provide a mechanism for how IDE selectively degrades amyloidogenic peptides and offers structural insights for developing IDE-based therapies.
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Affiliation(s)
- Zhening Zhang
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, United States
| | - Wenguang G Liang
- Ben-May Institute for Cancer Research, The University of Chicago, Chicago, United States
| | - Lucas J Bailey
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, United States
| | - Yong Zi Tan
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, United States.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, United States
| | - Hui Wei
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, United States
| | - Andrew Wang
- Ben-May Institute for Cancer Research, The University of Chicago, Chicago, United States
| | - Mara Farcasanu
- Ben-May Institute for Cancer Research, The University of Chicago, Chicago, United States
| | - Virgil A Woods
- Department of Medicine, University of California, San Diego, La Jolla, United States
| | - Lauren A McCord
- Ben-May Institute for Cancer Research, The University of Chicago, Chicago, United States
| | - David Lee
- Department of Medicine, University of California, San Diego, La Jolla, United States
| | - Weifeng Shang
- BioCAT, Argonne National Laboratory, Illinois, United States
| | | | - Benoit Deprez
- Univ. Lille, INSERM, Institut Pasteur de Lille, Lille, France
| | - David R Liu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States
| | - Akiko Koide
- Perlmutter Cancer Center, New York University School of Medicine, New York, United States.,New York University Langone Medical Center, New York University School of Medicine, New York, United States.,Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, United States
| | - Shohei Koide
- Perlmutter Cancer Center, New York University School of Medicine, New York, United States.,New York University Langone Medical Center, New York University School of Medicine, New York, United States.,Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, United States
| | - Anthony A Kossiakoff
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, United States
| | - Sheng Li
- Department of Medicine, University of California, San Diego, La Jolla, United States
| | - Bridget Carragher
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, United States.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, United States
| | - Clinton S Potter
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, United States.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, United States
| | - Wei-Jen Tang
- Ben-May Institute for Cancer Research, The University of Chicago, Chicago, United States
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31
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Kurochkin IV, Guarnera E, Berezovsky IN. Insulin-Degrading Enzyme in the Fight against Alzheimer's Disease. Trends Pharmacol Sci 2017; 39:49-58. [PMID: 29132916 DOI: 10.1016/j.tips.2017.10.008] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 10/18/2017] [Accepted: 10/23/2017] [Indexed: 11/19/2022]
Abstract
After decades of research and clinical trials there is still no cure for Alzheimer's disease (AD). While impaired clearance of amyloid beta (Aβ) peptides is considered as one of the major causes of AD, it was recently complemented by a potential role of other toxic amyloidogenic species. Insulin-degrading enzyme (IDE) is the proteolytic culprit of various β-forming peptides, both extracellular and intracellular. On the basis of demonstrated allosteric activation of IDE against Aβ, it is possible to propose a new strategy for the targeted IDE-based cleansing of different toxic aggregation-prone peptides. Consequently, specific allosteric activation of IDE coupled with state-of-the-art compound delivery and CRISP-Cas9 technique of transgene insertion can be instrumental in the fight against AD and related neurodegenerative maladies.
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Affiliation(s)
- Igor V Kurochkin
- Sysmex Corporation, 4-4-4 Takatsukadai, Nishi-ku, Kobe 651-2271, Japan
| | - Enrico Guarnera
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, 07-01, Matrix, Singapore 138671
| | - Igor N Berezovsky
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, 07-01, Matrix, Singapore 138671; Department of Biological Sciences (DBS), National University of Singapore (NUS), 8 Medical Drive, Singapore 117579.
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32
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Tundo GR, Sbardella D, Ciaccio C, Grasso G, Gioia M, Coletta A, Polticelli F, Di Pierro D, Milardi D, Van Endert P, Marini S, Coletta M. Multiple functions of insulin-degrading enzyme: a metabolic crosslight? Crit Rev Biochem Mol Biol 2017. [PMID: 28635330 DOI: 10.1080/10409238.2017.1337707] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Insulin-degrading enzyme (IDE) is a ubiquitous zinc peptidase of the inverzincin family, which has been initially discovered as the enzyme responsible for insulin catabolism; therefore, its involvement in the onset of diabetes has been largely investigated. However, further studies on IDE unraveled its ability to degrade several other polypeptides, such as β-amyloid, amylin, and glucagon, envisaging the possible implication of IDE dys-regulation in the "aggregopathies" and, in particular, in neurodegenerative diseases. Over the last decade, a novel scenario on IDE biology has emerged, pointing out a multi-functional role of this enzyme in several basic cellular processes. In particular, latest advances indicate that IDE behaves as a heat shock protein and modulates the ubiquitin-proteasome system, suggesting a major implication in proteins turnover and cell homeostasis. In addition, recent observations have highlighted that the regulation of glucose metabolism by IDE is not merely based on its largely proposed role in the degradation of insulin in vivo. There is increasing evidence that improper IDE function, regulation, or trafficking might contribute to the etiology of metabolic diseases. In addition, the enzymatic activity of IDE is affected by metals levels, thus suggesting a role also in the metal homeostasis (metallostasis), which is thought to be tightly linked to the malfunction of the "quality control" machinery of the cell. Focusing on the physiological role of IDE, we will address a comprehensive vision of the very complex scenario in which IDE takes part, outlining its crucial role in interconnecting several relevant cellular processes.
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Affiliation(s)
- Grazia R Tundo
- a Department of Clinical Sciences and Translation Medicine , University of Roma Tor Vergata , Roma , Italy.,b CIRCMSB , Bari , Italy
| | - Diego Sbardella
- a Department of Clinical Sciences and Translation Medicine , University of Roma Tor Vergata , Roma , Italy.,b CIRCMSB , Bari , Italy.,c Center for TeleInfrastructures, University of Roma Tor Vergata , Roma , Italy
| | - Chiara Ciaccio
- a Department of Clinical Sciences and Translation Medicine , University of Roma Tor Vergata , Roma , Italy.,b CIRCMSB , Bari , Italy
| | - Giuseppe Grasso
- d Department of Chemistry , University of Catania , Catania , Italy.,e CNR IBB , Catania , Italy
| | - Magda Gioia
- a Department of Clinical Sciences and Translation Medicine , University of Roma Tor Vergata , Roma , Italy.,b CIRCMSB , Bari , Italy
| | - Andrea Coletta
- f Department of Chemistry , University of Aarhus , Aarhus , Denmark
| | | | - Donato Di Pierro
- a Department of Clinical Sciences and Translation Medicine , University of Roma Tor Vergata , Roma , Italy.,b CIRCMSB , Bari , Italy
| | | | - Peter Van Endert
- h Université Paris Descartes, INSERM, U1151, CNRS , Paris , France
| | - Stefano Marini
- a Department of Clinical Sciences and Translation Medicine , University of Roma Tor Vergata , Roma , Italy.,b CIRCMSB , Bari , Italy.,c Center for TeleInfrastructures, University of Roma Tor Vergata , Roma , Italy
| | - Massimo Coletta
- a Department of Clinical Sciences and Translation Medicine , University of Roma Tor Vergata , Roma , Italy.,b CIRCMSB , Bari , Italy.,c Center for TeleInfrastructures, University of Roma Tor Vergata , Roma , Italy
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33
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Kurochkin IV, Guarnera E, Wong JH, Eisenhaber F, Berezovsky IN. Toward Allosterically Increased Catalytic Activity of Insulin-Degrading Enzyme against Amyloid Peptides. Biochemistry 2016; 56:228-239. [PMID: 27982586 DOI: 10.1021/acs.biochem.6b00783] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The physiological role of insulin-degrading enzyme (IDE) in the intracytosolic clearance of amyloid β (Aβ) and other amyloid-like peptides supports a hypothesis that human IDE hyperactivation could be therapeutically beneficial for the treatment of late-onset Alzheimer's disease (AD). The major challenge standing in the way of this goal is increasing the specific catalytic activity of IDE against the Aβ substrate. There were previous indications that the allosteric mode of IDE activity regulation could potentially provide a highly specific path toward degradation of amyloid-like peptides, while not dramatically affecting activity against other substrates. Recently developed theoretical concepts are used here to explore potential allosteric modulation of the IDE activity as a result of single-residue mutations. Five candidates are selected for experimental follow-up and allosteric free energy calculations: Ser137Ala, Lys396Ala, Asp426Ala, Phe807Ala, and Lys898Ala. Our experiments show that three mutations (Ser137Ala, Phe807Ala, and Lys898Ala) decrease the Km of the Aβ substrate. Mutation Lys898Ala results in increased catalytic activity of IDE; on the other hand, Lys364Ala does not change the activity and Asp426Ala diminishes it. Quantifying effects of mutations in terms of allosteric free energy, we show that favorable mutations lead to stabilization of the catalytic sites and other function-relevant distal sites as well as increased dynamics of the IDE-N and IDE-C halves that allow efficient substrate entrance and cleavage. A possibility for intramolecular upregulation of IDE activity against amyloid peptides via allosteric mutations calls for further investigations in this direction. Ultimately, we are hopeful it will lead to the development of IDE-based drugs for the treatment of the late-onset form of AD characterized by an overall impairment of Aβ clearance.
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Affiliation(s)
- Igor V Kurochkin
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR) , 30 Biopolis Street, #07-01, Matrix, Singapore 138671
| | - Enrico Guarnera
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR) , 30 Biopolis Street, #07-01, Matrix, Singapore 138671
| | - Jin H Wong
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR) , 30 Biopolis Street, #07-01, Matrix, Singapore 138671
| | - Frank Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR) , 30 Biopolis Street, #07-01, Matrix, Singapore 138671.,Department of Biological Sciences (DBS), National University of Singapore (NUS) , 8 Medical Drive, Singapore 117579.,School of Computer Engineering (SCE), Nanyang Technological University (NTU) , 50 Nanyang Drive, Singapore 637553
| | - Igor N Berezovsky
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR) , 30 Biopolis Street, #07-01, Matrix, Singapore 138671.,Department of Biological Sciences (DBS), National University of Singapore (NUS) , 8 Medical Drive, Singapore 117579
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34
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Ma B, Zhao J, Nussinov R. Conformational selection in amyloid-based immunotherapy: Survey of crystal structures of antibody-amyloid complexes. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1860:2672-81. [PMID: 27266343 PMCID: PMC5610039 DOI: 10.1016/j.bbagen.2016.05.040] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 05/05/2016] [Accepted: 05/31/2016] [Indexed: 11/27/2022]
Abstract
BACKGROUND The dominant feature in neurodegenerative diseases is protein aggregations that lead to neuronal loss. Immunotherapies using antibodies or antibody fragments to target the aggregations are a highly perused approach. The molecular mechanisms underlying the amyloid-based immunotherapy are complex. Deciphering the properties of amyloidogenic proteins responsible for these diseases is essential to obtain insights into antibody recognition of the amyloid antigens. SCOPE OF REVIEW We systematically explore all available crystal structures of antibody-amyloid complexes related to neurodegenerative diseases, including antibodies that recognize the Aβ peptide, tau protein, prion protein, alpha-synuclein, huntingtin protein (mHTT), and polyglutamine. MAJOR CONCLUSIONS We found that antibodies mostly use the conformational selection mechanism to recognize the highly flexible amyloid antigens. In particular, solanezumab bound to Aβ12-28 tripeptide motif conformation (F19F20A21), which is shared with the Aβ42 fibril. This motif, which is trapped by the antibody, may provide the missing link in amyloid formation. Water molecules often bridge between the antibody and amyloid, contributing to the recognition. GENERAL SIGNIFICANCE This paper provides the structural basis for antibody recognition of amyloidogenic proteins. The analysis and discussion of known structures are expected to help in the design and optimization of antibodies in neurodegenerative diseases. This article is part of a Special Issue entitled "System Genetics" Guest Editor: Dr. Yudong Cai and Dr. Tao Huang.
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Affiliation(s)
- Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, MD 21702, United States.
| | - Jun Zhao
- Cancer and Inflammation Program, National Cancer Institute, Frederick, MD 21702, United States
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, MD 21702, United States; Sackler Inst. of Molecular Medicine, Department of Human Genetics and Molecular Medicine Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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35
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Camberos MDC, Pérez AA, Passicot GA, Martucci LC, Wanderley MI, Udrisar DP, Cresto JC. II - Insulin processing in mitochondria. J Bioenerg Biomembr 2016; 48:469-482. [PMID: 27796771 DOI: 10.1007/s10863-016-9682-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 10/12/2016] [Indexed: 11/29/2022]
Abstract
Our objective was to know how insulin is processing in mitochondria; if IDE is the only participant in mitochondrial insulin degradation and the role of insulin degradation on IDE accumulation in mitoplasts. Mitochondria and its fractions were isolated as described by Greenwalt. IDE was purified and detected in immunoblot with specific antibodies. High insulin degradation was obtained through addition to rat's diet of 25 g/rat of apple and 10 g/rat of hard-boiled eggs, 3 days a week. Mitochondrial insulin degradation was assayed with 5 % TCA, insulin antibody or Sephadex G50 chromatography. Degradation was also assayed 60 min at 37 °C in mitochondrial fractions (IMS and Mx) with diet or not and without IDE. Degradation in fractions precipitated with ammonium sulfates (60-80 %) were studied after mitochondrial insulin incubation (1 ng. insulin during 15 min, at 30 °C) or with addition of 2.5 mM ATP. Supplementary diet increased insulin degradation. High insulin did not increase mitoplasts accumulation and did not decrease mitochondrial degradation. High insulin and inhibition of degradation evidence insulin competition for a putative transport system. Mitochondrial incubation with insulin increased IDE in matrix as observed in immunoblot. ATP decreased degradation in Mx and increased it in IMS. Chromatography of IMS demonstrated an ATP-dependent protease that degraded insulin, similar to described by Sitte et al. Mitochondria participate in insulin degradation and the diet increased it. High insulin did not accomplish mitochondrial decrease of degradation or its accumulation in mitoplasts. Mitochondrial incubation with insulin increased IDE in matrix. ATP suggested being a regulator of mitochondrial insulin degradation.
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Affiliation(s)
- María Del Carmen Camberos
- Endocrinology Research Center "Dr. Cesar Bergada" (CEDIE-CONICET), Endocrinology Division, Children Hospital. R. Gutierrez, Gallo 1330 (C1425), Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina.
| | - Adriana A Pérez
- Department Genetic and Evolution, School of Natural and Exact Sciences, University of Buenos Aires (UBA), Buenos Aires, Argentina
| | - Gisel A Passicot
- Endocrinology Research Center "Dr. Cesar Bergada" (CEDIE-CONICET), Endocrinology Division, Children Hospital. R. Gutierrez, Gallo 1330 (C1425), Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Lucía C Martucci
- Endocrinology Research Center "Dr. Cesar Bergada" (CEDIE-CONICET), Endocrinology Division, Children Hospital. R. Gutierrez, Gallo 1330 (C1425), Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - María I Wanderley
- Laboratory of Endocrinology and Metabolism, Department of Physiology and Pharmacology, University of Pernambuco, Recife, Pernambuco, Brazil
| | - Daniel P Udrisar
- Laboratory of Endocrinology and Metabolism, Department of Physiology and Pharmacology, University of Pernambuco, Recife, Pernambuco, Brazil
| | - Juan C Cresto
- Endocrinology Research Center "Dr. Cesar Bergada" (CEDIE-CONICET), Endocrinology Division, Children Hospital. R. Gutierrez, Gallo 1330 (C1425), Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
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36
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Tundo GR, Di Muzio E, Ciaccio C, Sbardella D, Di Pierro D, Polticelli F, Coletta M, Marini S. Multiple allosteric sites are involved in the modulation of insulin-degrading-enzyme activity by somatostatin. FEBS J 2016; 283:3755-3770. [PMID: 27579517 DOI: 10.1111/febs.13841] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 07/18/2016] [Accepted: 08/30/2016] [Indexed: 11/30/2022]
Abstract
Somatostatin is a cyclic peptide, released in the gastrointestinal system and the central nervous system, where it is involved in the regulation of cognitive and sensory functions, motor activity and sleep. It is a substrate of insulin-degrading enzyme (IDE), as well as a modulator of its activity and expression. In the present study, we have investigated the modulatory role of somatostatin on IDE activity at 37 °C and pH 7.3 for various substrates [i.e. insulin, β-amyloid (Aβ)1-40 and bradykinin], aiming to quantitatively characterize the correlation between the specific features of the substrates and the regulatory mechanism. Functional data indicate that somatostatin, in addition to the catalytic site of IDE (being a substrate), is also able to bind to two additional exosites, which play different roles according to the size of the substrate and its binding mode to the IDE catalytic cleft. In particular, one exosite, which displays high affinity for somatostatin, regulates only the interaction of IDE with larger substrates (such as insulin and Aβ1-40 ) in a differing fashion according to their various modes of binding to the enzyme. A second exosite, which is involved in the regulation of enzymatic processing by IDE of all substrates investigated (including a 10-25 amino acid long amyloid-like peptide, bradykinin and somatostatin itself, which had been studied previously), probably acts through the alteration of an 'open-closed' equilibrium.
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Affiliation(s)
- Grazia R Tundo
- Department of Clinical Sciences and Translational Medicine, University of Roma Tor Vergata, Italy.,Interuniversity Consortium for the Research on Chemistry of Metals in Biological Systems, Bari, Italy
| | | | - Chiara Ciaccio
- Department of Clinical Sciences and Translational Medicine, University of Roma Tor Vergata, Italy.,Interuniversity Consortium for the Research on Chemistry of Metals in Biological Systems, Bari, Italy
| | - Diego Sbardella
- Department of Clinical Sciences and Translational Medicine, University of Roma Tor Vergata, Italy.,Interuniversity Consortium for the Research on Chemistry of Metals in Biological Systems, Bari, Italy
| | - Donato Di Pierro
- Department of Clinical Sciences and Translational Medicine, University of Roma Tor Vergata, Italy
| | - Fabio Polticelli
- Department of Sciences, University of Roma Tre, Italy.,National Institute of Nuclear Physics, Roma Tre Section, Italy
| | - Massimo Coletta
- Department of Clinical Sciences and Translational Medicine, University of Roma Tor Vergata, Italy.,Interuniversity Consortium for the Research on Chemistry of Metals in Biological Systems, Bari, Italy
| | - Stefano Marini
- Department of Clinical Sciences and Translational Medicine, University of Roma Tor Vergata, Italy. .,Interuniversity Consortium for the Research on Chemistry of Metals in Biological Systems, Bari, Italy.
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37
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Wei Q, Ran T, Ma C, He J, Xu D, Wang W. Crystal Structure and Function of PqqF Protein in the Pyrroloquinoline Quinone Biosynthetic Pathway. J Biol Chem 2016; 291:15575-87. [PMID: 27231346 PMCID: PMC4957043 DOI: 10.1074/jbc.m115.711226] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 05/23/2016] [Indexed: 01/10/2023] Open
Abstract
Pyrroloquinoline quinone (PQQ) has received considerable attention due to its numerous important physiological functions. PqqA is a precursor peptide of PQQ with two conserved residues: glutamate and tyrosine. After linkage of the Cγ of glutamate and Cϵ of tyrosine by PqqE, these two residues are hypothesized to be cleaved from PqqA by PqqF. The linked glutamate and tyrosine residues are then used to synthesize PQQ. Here, we demonstrated that the pqqF gene is essential for PQQ biosynthesis as deletion of it eliminated the inhibition of prodigiosin production by glucose. We further determined the crystal structure of PqqF, which has a closed clamshell-like shape. The PqqF consists of two halves composed of an N- and a C-terminal lobe. The PqqF-N and PqqF-C lobes form a chamber with the volume of the cavity of ∼9400 Å(3) The PqqF structure conforms to the general structure of inverzincins. Compared with the most thoroughly characterized inverzincin insulin-degrading enzyme, the size of PqqF chamber is markedly smaller, which may define the specificity for its substrate PqqA. Furthermore, the 14-amino acid-residue-long tag formed by the N-terminal tag from expression vector precisely protrudes into the counterpart active site; this N-terminal tag occupies the active site and stabilizes the closed, inactive conformation. His-48, His-52, Glu-129 and His-14 from the N-terminal tag coordinate with the zinc ion. Glu-51 acts as a base catalyst. The observed histidine residue-mediated inhibition may be applicable for the design of a peptide for the inhibition of M16 metalloproteases.
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Affiliation(s)
- Qiaoe Wei
- From the Department of microbiology, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, China and
| | - Tingting Ran
- From the Department of microbiology, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, China and
| | - Chencui Ma
- From the Department of microbiology, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, China and
| | - Jianhua He
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, 201204 Shanghai, China
| | - Dongqing Xu
- From the Department of microbiology, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, China and
| | - Weiwu Wang
- From the Department of microbiology, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, China and
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38
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Hubin E, Cioffi F, Rozenski J, van Nuland NAJ, Broersen K. Characterization of insulin-degrading enzyme-mediated cleavage of Aβ in distinct aggregation states. Biochim Biophys Acta Gen Subj 2016; 1860:1281-90. [PMID: 26968463 DOI: 10.1016/j.bbagen.2016.03.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 02/19/2016] [Accepted: 03/07/2016] [Indexed: 12/15/2022]
Abstract
To enhance our understanding of the potential therapeutic utility of insulin-degrading enzyme (IDE) in Alzheimer's disease (AD), we studied in vitro IDE-mediated degradation of different amyloid-beta (Aβ) peptide aggregation states. Our findings show that IDE activity is driven by the dynamic equilibrium between Aβ monomers and higher ordered aggregates. We identify Met(35)-Val(36) as a novel IDE cleavage site in the Aβ sequence and show that Aβ fragments resulting from IDE cleavage form non-toxic amorphous aggregates. These findings need to be taken into account in therapeutic strategies designed to increase Aβ clearance in AD patients by modulating IDE activity.
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Affiliation(s)
- Ellen Hubin
- Nanobiophysics Group, MIRA Institute for Biomedical Technology and Technical Medicine, Faculty of Science and Technology, Universiteit Twente, Enschede, The Netherlands; Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Federica Cioffi
- Nanobiophysics Group, MIRA Institute for Biomedical Technology and Technical Medicine, Faculty of Science and Technology, Universiteit Twente, Enschede, The Netherlands
| | - Jef Rozenski
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium
| | - Nico A J van Nuland
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium.
| | - Kerensa Broersen
- Nanobiophysics Group, MIRA Institute for Biomedical Technology and Technical Medicine, Faculty of Science and Technology, Universiteit Twente, Enschede, The Netherlands.
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39
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Tang WJ. Targeting Insulin-Degrading Enzyme to Treat Type 2 Diabetes Mellitus. Trends Endocrinol Metab 2016; 27:24-34. [PMID: 26651592 PMCID: PMC4698235 DOI: 10.1016/j.tem.2015.11.003] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 11/03/2015] [Accepted: 11/04/2015] [Indexed: 10/22/2022]
Abstract
Insulin-degrading enzyme (IDE) selectively degrades peptides, such as insulin, amylin, and amyloid β (Aβ) that form toxic aggregates, to maintain proteostasis. IDE defects are linked to the development of type 2 diabetes mellitus (T2DM) and Alzheimer's disease (AD). Structural and biochemical analyses revealed the molecular basis for IDE-mediated destruction of amyloidogenic peptides and this information has been exploited to develop promising inhibitors of IDE to improve glucose homeostasis. However, the inhibition of IDE can also lead to glucose intolerance. In this review, I focus on recent advances regarding our understanding of the structure and function of IDE and the discovery of IDE inhibitors, as well as challenges in developing IDE-based therapy for human diseases, particularly T2DM.
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Affiliation(s)
- Wei-Jen Tang
- Ben-May Department for Cancer Research, the University of Chicago, Chicago, IL, USA.
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40
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Novel Druggable Sites of Insulin-Degrading Enzyme Identified through Applied Structural Bioinformatics Analysis. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.procs.2016.05.419] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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41
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Catalytic site inhibition of insulin-degrading enzyme by a small molecule induces glucose intolerance in mice. Nat Commun 2015; 6:8250. [PMID: 26394692 PMCID: PMC4580987 DOI: 10.1038/ncomms9250] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 07/31/2015] [Indexed: 01/22/2023] Open
Abstract
Insulin-degrading enzyme (IDE) is a protease that cleaves insulin and other bioactive peptides such as amyloid-β. Knockout and genetic studies have linked IDE to Alzheimer's disease and type-2 diabetes. As the major insulin-degrading protease, IDE is a candidate drug target in diabetes. Here we have used kinetic target-guided synthesis to design the first catalytic site inhibitor of IDE suitable for in vivo studies (BDM44768). Crystallographic and small angle X-ray scattering analyses show that it locks IDE in a closed conformation. Among a panel of metalloproteases, BDM44768 selectively inhibits IDE. Acute treatment of mice with BDM44768 increases insulin signalling and surprisingly impairs glucose tolerance in an IDE-dependent manner. These results confirm that IDE is involved in pathways that modulate short-term glucose homeostasis, but casts doubt on the general usefulness of the inhibition of IDE catalytic activity to treat diabetes. Inhibiting insulin-degrading enzyme (IDE) has been proposed as a potential therapeutic strategy for the treatment of patients with diabetes. Here, the authors develop a novel IDE inhibitor but find that, surprisingly, IDE inhibition has negative effects on glucose tolerance in mice.
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42
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Sharma SK, Chorell E, Steneberg P, Vernersson-Lindahl E, Edlund H, Wittung-Stafshede P. Insulin-degrading enzyme prevents α-synuclein fibril formation in a nonproteolytical manner. Sci Rep 2015; 5:12531. [PMID: 26228656 PMCID: PMC4521159 DOI: 10.1038/srep12531] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 06/29/2015] [Indexed: 11/25/2022] Open
Abstract
The insulin-degrading enzyme (IDE) degrades amyloidogenic proteins such as Amyloid β (Αβ) and Islet Amyloid Polypeptide (IAPP), i.e. peptides associated with Alzheimer’s disease and type 2 diabetes, respectively. In addition to the protease activity normally associated with IDE function an additional activity involving the formation of stable, irreversible complexes with both Αβ and α-synuclein, an amyloidogenic protein involved in Parkinson’s disease, was recently proposed. Here, we have investigated the functional consequences of IDE-α-synuclein interactions in vitro. We demonstrate that IDE in a nonproteolytic manner and at sub-stoichiometric ratios efficiently inhibits α-synuclein fibril formation by binding to α-synuclein oligomers making them inert to amyloid formation. Moreover, we show that, within a defined range of α-synuclein concentrations, interaction with α-synuclein oligomers increases IDE’s proteolytic activity on a fluorogenic substrate. We propose that the outcomes of IDE-α-synuclein interactions, i.e. protection against α-synuclein amyloid formation and stimulated IDE protease activity, may be protective in vivo.
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Affiliation(s)
| | - Erik Chorell
- Department of Chemistry, Umeå University, 90187 Umeå, Sweden
| | - Pär Steneberg
- Umeå Center for Molecular Medicine, Umeå University, 90187 Umeå, Sweden
| | | | - Helena Edlund
- Umeå Center for Molecular Medicine, Umeå University, 90187 Umeå, Sweden
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43
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Grasso G, Satriano C, Milardi D. A neglected modulator of insulin-degrading enzyme activity and conformation: The pH. Biophys Chem 2015; 203-204:33-40. [PMID: 26025789 DOI: 10.1016/j.bpc.2015.05.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 05/19/2015] [Accepted: 05/21/2015] [Indexed: 12/16/2022]
Abstract
Insulin-degrading enzyme (IDE), a ubiquitously expressed zinc metalloprotease, has multiple activities in addition to insulin degradation and its malfunction is believed to connect type 2 diabetes with Alzheimer's disease. IDE has been found in many different cellular compartments, where it may experience significant physio-pathological pH variations. However, the exact role of pH variations on the interplay between enzyme conformations, stability, oligomerization state and catalysis is not understood. Here, we use ESI mass spectrometry, atomic force microscopy, surface plasmon resonance and circular dichroism to investigate the structure-activity relationship of IDE at different pH values. We show that acidic pH affects the ability of the enzyme to bind the substrate and decrease the stability of the protein by inducing an α-helical bundle conformation with a concomitant dissociation of multi-subunit IDE assemblies into monomeric units and loss of activity. These effects suggest a major role played by electrostatic forces in regulating multi-subunit enzyme assembly and function. Our results clearly indicate a pH dependent coupling among enzyme conformation, assembly and stability and suggest that cellular acidosis can have a large effect on IDE oligomerization state, inducing an enzyme inactivation and an altered insulin degradation that could have an impact on insulin signaling.
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Affiliation(s)
- Giuseppe Grasso
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale Andrea Doria 6, 95125 Catania, Italy.
| | - Cristina Satriano
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Danilo Milardi
- Istituto Biostrutture e Bioimmagini, CNR, Via P. Gaifami 18, 95126 Catania, Italy
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44
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Liang WG, Ren M, Zhao F, Tang WJ. Structures of human CCL18, CCL3, and CCL4 reveal molecular determinants for quaternary structures and sensitivity to insulin-degrading enzyme. J Mol Biol 2015; 427:1345-1358. [PMID: 25636406 PMCID: PMC4355285 DOI: 10.1016/j.jmb.2015.01.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 01/07/2015] [Accepted: 01/21/2015] [Indexed: 11/23/2022]
Abstract
CC chemokine ligands (CCL) are 8-14 kDa signaling proteins involved in diverse immune functions. While CCLs share similar tertiary structures, oligomerization produces highly diverse quaternary structures that protect chemokines from proteolytic degradation and modulate their functions. CCL18 is closely related to CCL3 and CCL4 with respect to both protein sequence and genomic location, yet CCL18 has distinct biochemical and biophysical properties. Here, we report a crystal structure of human CCL18 and its oligomerization states in solution based on crystallographic and small angle X-ray scattering (SAXS) analyses. Our data shows that CCL18 adopts an α-helical conformation at its N-terminus that weakens its dimerization, explaining CCL18’s preference for the monomeric state. Multiple contacts between monomers allow CCL18 to reversibly form a unique open-ended oligomer different from those of CCL3, CCL4, and CCL5. Furthermore, these differences hinge on proline 8, which is conserved in CCL3 and CCL4, but is replaced by lysine in human CCL18. Our structural analyses suggest that a proline 8 to alanine mutation stabilizes a type I β-turn at the N-terminus of CCL4 to prevent dimerization but prevents dimers from making key contacts with each other in CCL3. Thus, the P8A mutation induces depolymerization of CCL3 and CCL4 by distinct mechanisms. Finally, we used structural, biochemical, and functional analyses to unravel why insulin-degrading enzyme (IDE) degrades CCL3 and CCL4 but not CCL18. Our results elucidate the molecular basis for the oligomerization of three closely related CC chemokines and suggest how oligomerization shapes CCL chemokine function.
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Affiliation(s)
- Wenguang G Liang
- Ben May Department for Cancer Research, The University of Chicago, IL 60637, USA
| | - Min Ren
- Ben May Department for Cancer Research, The University of Chicago, IL 60637, USA
| | - Fan Zhao
- Ben May Department for Cancer Research, The University of Chicago, IL 60637, USA
| | - Wei-Jen Tang
- Ben May Department for Cancer Research, The University of Chicago, IL 60637, USA.
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45
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Huang L, Liu X, Cheng B, Huang K. How our bodies fight amyloidosis: effects of physiological factors on pathogenic aggregation of amyloidogenic proteins. Arch Biochem Biophys 2015; 568:46-55. [PMID: 25615529 DOI: 10.1016/j.abb.2015.01.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 01/08/2015] [Accepted: 01/11/2015] [Indexed: 12/15/2022]
Abstract
The process of protein aggregation from soluble amyloidogenic proteins to insoluble amyloid fibrils plays significant roles in the onset of over 30 human amyloidogenic diseases, such as Prion disease, Alzheimer's disease and type 2 diabetes mellitus. Amyloid deposits are commonly found in patients suffered from amyloidosis; however, such deposits are rarely seen in healthy individuals, which may be largely attributed to the self-regulation in vivo. A vast number of physiological factors have been demonstrated to directly affect the process of amyloid formation in vivo. In this review, physiological factors that influence amyloidosis, including biological factors (chaperones, natural antibodies, enzymes, lipids and saccharides) and physicochemical factors (metal ions, pH environment, crowding and pressure, etc.), together with the mechanisms underlying these proteostasis effects, are summarized.
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Affiliation(s)
- Lianqi Huang
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan, Hubei 430030, PR China
| | - Xinran Liu
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan, Hubei 430030, PR China
| | - Biao Cheng
- Department of Pharmacy, Central Hospital of Wuhan, Wuhan, Hubei 430014, PR China
| | - Kun Huang
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan, Hubei 430030, PR China; Centre for Biomedicine Research, Wuhan Institute of Biotechnology, Wuhan, Hubei 430075, PR China.
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46
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Structure-activity relationships of imidazole-derived 2-[N-carbamoylmethyl-alkylamino]acetic acids, dual binders of human insulin-degrading enzyme. Eur J Med Chem 2014; 90:547-67. [PMID: 25489670 DOI: 10.1016/j.ejmech.2014.12.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 08/19/2014] [Accepted: 12/03/2014] [Indexed: 12/19/2022]
Abstract
Insulin degrading enzyme (IDE) is a zinc metalloprotease that degrades small amyloid peptides such as amyloid-â and insulin. So far the dearth of IDE-specific pharmacological inhibitors impacts the understanding of its role in the physiopathology of Alzheimer's disease, amyloid-â clearance, and its validation as a potential therapeutic target. Hit 1 was previously discovered by high-throughput screening. Here we describe the structure-activity study, that required the synthesis of 48 analogues. We found that while the carboxylic acid, the imidazole and the tertiary amine were critical for activity, the methyl ester was successfully optimized to an amide or a 1,2,4-oxadiazole. Along with improving their activity, compounds were optimized for solubility, lipophilicity and stability in plasma and microsomes. The docking or co-crystallization of some compounds at the exosite or the catalytic site of IDE provided the structural basis for IDE inhibition. The pharmacokinetic properties of best compounds 44 and 46 were measured in vivo. As a result, 44 (BDM43079) and its methyl ester precursor 48 (BDM43124) are useful chemical probes for the exploration of IDE's role.
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47
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Vestergaard B, Sayers Z. Investigating increasingly complex macromolecular systems with small-angle X-ray scattering. IUCRJ 2014; 1:523-9. [PMID: 25485132 PMCID: PMC4224470 DOI: 10.1107/s2052252514020843] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2014] [Accepted: 09/17/2014] [Indexed: 05/04/2023]
Abstract
The biological solution small-angle X-ray scattering (BioSAXS) field has undergone tremendous development over recent decades. This means that increasingly complex biological questions can be addressed by the method. An intricate synergy between advances in hardware and software development, data collection and evaluation strategies and implementations that readily allow integration with complementary techniques result in significant results and a rapidly growing user community with ever increasing ambitions. Here, a review of these developments, by including a selection of novel BioSAXS method-ologies and recent results, is given.
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Affiliation(s)
- Bente Vestergaard
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, Copenhagen, DK-2100, Denmark
- Correspondence e-mail:
| | - Zehra Sayers
- Faculty of Engineering and Natural Science, Sabanci University, Orhanli, Istanbul Tuzla 34956, Turkey
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48
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Grasso G, Mielczarek P, Niedziolka M, Silberring J. Metabolism of cryptic peptides derived from neuropeptide FF precursors: the involvement of insulin-degrading enzyme. Int J Mol Sci 2014; 15:16787-99. [PMID: 25247577 PMCID: PMC4200852 DOI: 10.3390/ijms150916787] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 09/03/2014] [Accepted: 09/09/2014] [Indexed: 11/16/2022] Open
Abstract
The term “cryptome” refers to the subset of cryptic peptides with bioactivities that are often unpredictable and very different from the parent protein. These cryptic peptides are generated by proteolytic cleavage of proteases, whose identification in vivo can be very challenging. In this work, we show that insulin-degrading enzyme (IDE) is able to degrade specific amino acid sequences present in the neuropeptide pro-NPFFA (NPFF precursor), generating some cryptic peptides that are also observed after incubation with rat brain cortex homogenate. The reported experimental findings support the increasingly accredited hypothesis, according to which, due to its wide substrate selectivity, IDE is involved in a wide variety of physiopathological processes.
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Affiliation(s)
- Giuseppe Grasso
- Department of Chemical Sciences, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy.
| | - Przemyslaw Mielczarek
- Department of Biochemistry and Neurobiology, AGH University of Science and Technology, Mickiewicza 30, 30-059 Krakow, Poland.
| | - Magdalena Niedziolka
- Department of Biochemistry and Neurobiology, AGH University of Science and Technology, Mickiewicza 30, 30-059 Krakow, Poland.
| | - Jerzy Silberring
- Department of Biochemistry and Neurobiology, AGH University of Science and Technology, Mickiewicza 30, 30-059 Krakow, Poland.
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49
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Webster CI, Burrell M, Olsson LL, Fowler SB, Digby S, Sandercock A, Snijder A, Tebbe J, Haupts U, Grudzinska J, Jermutus L, Andersson C. Engineering neprilysin activity and specificity to create a novel therapeutic for Alzheimer's disease. PLoS One 2014; 9:e104001. [PMID: 25089527 PMCID: PMC4121237 DOI: 10.1371/journal.pone.0104001] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 07/05/2014] [Indexed: 02/07/2023] Open
Abstract
Neprilysin is a transmembrane zinc metallopeptidase that degrades a wide range of peptide substrates. It has received attention as a potential therapy for Alzheimer’s disease due to its ability to degrade the peptide amyloid beta. However, its broad range of peptide substrates has the potential to limit its therapeutic use due to degradation of additional peptides substrates that tightly regulate many physiological processes. We sought to generate a soluble version of the ectodomain of neprilysin with improved activity and specificity towards amyloid beta as a potential therapeutic for Alzheimer’s disease. Extensive amino acid substitutions were performed at positions surrounding the active site and inner surface of the enzyme and variants screened for activity on amyloid beta 1–40, 1–42 and a variety of other physiologically relevant peptides. We identified several mutations that modulated and improved both enzyme selectivity and intrinsic activity. Neprilysin variant G399V/G714K displayed an approximately 20-fold improved activity on amyloid beta 1–40 and up to a 3,200-fold reduction in activity on other peptides. Along with the altered peptide substrate specificity, the mutant enzyme produced a markedly altered series of amyloid beta cleavage products compared to the wild-type enzyme. Crystallisation of the mutant enzyme revealed that the amino acid substitutions result in alteration of the shape and size of the pocket containing the active site compared to the wild-type enzyme. The mutant enzyme offers the potential for the more efficient degradation of amyloid beta in vivo as a therapeutic for the treatment of Alzheimer’s disease.
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Affiliation(s)
- Carl I. Webster
- Antibody Discovery and Protein Engineering, MedImmune, Cambridge, United Kingdom
- * E-mail:
| | - Matthew Burrell
- Antibody Discovery and Protein Engineering, MedImmune, Cambridge, United Kingdom
| | | | - Susan B. Fowler
- Antibody Discovery and Protein Engineering, MedImmune, Cambridge, United Kingdom
| | - Sarah Digby
- Antibody Discovery and Protein Engineering, MedImmune, Cambridge, United Kingdom
| | - Alan Sandercock
- Antibody Discovery and Protein Engineering, MedImmune, Cambridge, United Kingdom
| | - Arjan Snijder
- Discovery Sciences, AstraZeneca R & D, Mölndal, Sweden
| | - Jan Tebbe
- Global Drug Discovery, Global Biologics, Bayer HealthCare AG, Cologne, Germany
| | - Ulrich Haupts
- Global Drug Discovery, Global Biologics, Bayer HealthCare AG, Cologne, Germany
| | - Joanna Grudzinska
- Global Drug Discovery, Global Biologics, Bayer HealthCare AG, Cologne, Germany
| | - Lutz Jermutus
- Antibody Discovery and Protein Engineering, MedImmune, Cambridge, United Kingdom
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King JV, Liang WG, Scherpelz KP, Schilling AB, Meredith SC, Tang WJ. Molecular basis of substrate recognition and degradation by human presequence protease. Structure 2014; 22:996-1007. [PMID: 24931469 DOI: 10.1016/j.str.2014.05.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Revised: 04/12/2014] [Accepted: 05/01/2014] [Indexed: 01/17/2023]
Abstract
Human presequence protease (hPreP) is an M16 metalloprotease localized in mitochondria. There, hPreP facilitates proteostasis by utilizing an ∼13,300-Å(3) catalytic chamber to degrade a diverse array of potentially toxic peptides, including mitochondrial presequences and β-amyloid (Aβ), the latter of which contributes to Alzheimer disease pathogenesis. Here, we report crystal structures for hPreP alone and in complex with Aβ, which show that hPreP uses size exclusion and charge complementation for substrate recognition. These structures also reveal hPreP-specific features that permit a diverse array of peptides, with distinct distributions of charged and hydrophobic residues, to be specifically captured, cleaved, and have their amyloidogenic features destroyed. SAXS analysis demonstrates that hPreP in solution exists in dynamic equilibrium between closed and open states, with the former being preferred. Furthermore, Aβ binding induces the closed state and hPreP dimerization. Together, these data reveal the molecular basis for flexible yet specific substrate recognition and degradation by hPreP.
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Affiliation(s)
- John V King
- Ben May Department for Cancer Research, The University of Chicago, 929 E. 57(th) Street, Chicago, IL 60637, USA
| | - Wenguang G Liang
- Ben May Department for Cancer Research, The University of Chicago, 929 E. 57(th) Street, Chicago, IL 60637, USA
| | - Kathryn P Scherpelz
- Department of Biochemistry and Molecular Biophysics, The University of Chicago, Chicago, IL 60637, USA
| | - Alexander B Schilling
- Mass Spectrometry, Metabolomics, and Proteomics Facility, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Stephen C Meredith
- Department of Pathology, The University of Chicago, Chicago, IL 60637, USA
| | - Wei-Jen Tang
- Ben May Department for Cancer Research, The University of Chicago, 929 E. 57(th) Street, Chicago, IL 60637, USA.
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