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Marques SM, Daniel L, Buryska T, Prokop Z, Brezovsky J, Damborsky J. Enzyme Tunnels and Gates As Relevant Targets in Drug Design. Med Res Rev 2016; 37:1095-1139. [PMID: 27957758 DOI: 10.1002/med.21430] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 10/11/2016] [Accepted: 11/07/2016] [Indexed: 12/28/2022]
Abstract
Many enzymes contain tunnels and gates that are essential to their function. Gates reversibly switch between open and closed conformations and thereby control the traffic of small molecules-substrates, products, ions, and solvent molecules-into and out of the enzyme's structure via molecular tunnels. Many transient tunnels and gates undoubtedly remain to be identified, and their functional roles and utility as potential drug targets have received comparatively little attention. Here, we describe a set of general concepts relating to the structural properties, function, and classification of these interesting structural features. In addition, we highlight the potential of enzyme tunnels and gates as targets for the binding of small molecules. The different types of binding that are possible and the potential pharmacological benefits of such targeting are discussed. Twelve examples of ligands bound to the tunnels and/or gates of clinically relevant enzymes are used to illustrate the different binding modes and to explain some new strategies for drug design. Such strategies could potentially help to overcome some of the problems facing medicinal chemists and lead to the discovery of more effective drugs.
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Affiliation(s)
- Sergio M Marques
- Loschmidt Laboratories, Faculty of Science, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment, RECETOX, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Lukas Daniel
- Loschmidt Laboratories, Faculty of Science, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment, RECETOX, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital, Pekarska 53, 656 91, Brno, Czech Republic
| | - Tomas Buryska
- Loschmidt Laboratories, Faculty of Science, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment, RECETOX, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital, Pekarska 53, 656 91, Brno, Czech Republic
| | - Zbynek Prokop
- Loschmidt Laboratories, Faculty of Science, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment, RECETOX, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital, Pekarska 53, 656 91, Brno, Czech Republic
| | - Jan Brezovsky
- Loschmidt Laboratories, Faculty of Science, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment, RECETOX, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital, Pekarska 53, 656 91, Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Faculty of Science, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment, RECETOX, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital, Pekarska 53, 656 91, Brno, Czech Republic
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Hu P, Li B, Zhang W, Li Y, Li G, Jiang X, Wdzieczak-Bakala J, Liu J. AcSDKP regulates cell proliferation through the PI3KCA/Akt signaling pathway. PLoS One 2013; 8:e79321. [PMID: 24244481 PMCID: PMC3820705 DOI: 10.1371/journal.pone.0079321] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 09/20/2013] [Indexed: 12/15/2022] Open
Abstract
The natural tetrapeptide acetyl-N-Ser-Asp-Lys-Pro (AcSDKP) is generated from the N-terminus of thymosin-β4 through enzymatic cleavage by prolyl oligopeptidase (POP). AcSDKP regulation of proliferation of different cells is implicated in hematopoiesis and angiogenesis. This tetrapeptide present in almost all cells was recently detected at elevated concentrations in neoplastic diseases. However, previously reported in vitro and in vivo studies indicate that AcSDKP does not contribute to the pathogenesis of cancers. Here we show that exogenous AcSDKP exerts no effect on the proliferation of actively dividing malignant cells. Using S17092, a specific POP inhibitor (POPi), to suppress the biosynthesis of AcSDKP in U87-MG glioblastoma cells characterized by high intracellular levels of this peptide, we found that all tested doses of POPi resulted in an equally effective depletion of AcSDKP, which was not correlated with the dose-dependent decreases in the proliferation rate of treated cells. Interestingly, addition of exogenous AcSDKP markedly reversed the reduction in the proliferation of U87-MG cells treated with the highest dose of POPi, and this effect was associated with activation of the phosphatidylinositol-3 kinase (PI3K)/Akt pathway. However, extracellular-regulated protein kinase (ERK) activation was unaltered by S17092 and AcSDKP co-treatment. Knockdown of individual PI3K catalytic subunits revealed that p110α and p110β contributed differently to AcSDKP regulation of U87-MG cell proliferation. Disruption of p110α expression by small interfering RNA (siRNA) abrogated AcSDKP-stimulated Akt phosphorylation, whereas knockdown of p110β expression exhibited no such effect. Our findings indicate for the first time that the PI3KCA/Akt pathway mediates AcSDKP regulation of cell proliferation and suggest a role for this ubiquitous intracellular peptide in cell survival.
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Affiliation(s)
- Ping Hu
- Sino-France Laboratory for Drug Screening, Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Bin Li
- Sino-France Laboratory for Drug Screening, Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Wenhua Zhang
- Sino-France Laboratory for Drug Screening, Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yijian Li
- Sino-France Laboratory for Drug Screening, Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Guang Li
- Sino-France Laboratory for Drug Screening, Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xinnong Jiang
- Sino-France Laboratory for Drug Screening, Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | | | - Jianmiao Liu
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Gif sur Yvette, France
- * E-mail:
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Peptide POP inhibitors for the treatment of the cognitive symptoms of schizophrenia. Future Med Chem 2013; 5:1509-23. [DOI: 10.4155/fmc.13.135] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Schizophrenia is a serious life-long disease that affects a significant part of the adult population. Although there is considerably effective medication for the positive symptoms of the disease, none are available for the associated cognitive deficits. These deficits are a core feature of schizophrenia, and they severely impair the functionality and social integration of patients. POP is a promising target for the treatment of the cognitive deficits of schizophrenia. Inhibitors of this peptidase show cognition-enhancing properties, act through a complex mechanism and have suitable pharmacological properties. Nevertheless, several studies must be carried out in order to improve the design and clinical evaluation of these substances. Permeability to the brain, appropriate animal models and suitable indications are the main issues that must be addressed. However, current information supports the potential of POP as an interesting drug target for the treatment of the cognitive deficits related to schizophrenia.
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Hannula M, Myöhänen T, Tenorio-Laranga J, Männistö P, Garcia-Horsman J. Prolyl oligopeptidase colocalizes with α-synuclein, β-amyloid, tau protein and astroglia in the post-mortem brain samples with Parkinson’s and Alzheimer’s diseases. Neuroscience 2013; 242:140-50. [DOI: 10.1016/j.neuroscience.2013.03.049] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Revised: 03/20/2013] [Accepted: 03/21/2013] [Indexed: 11/15/2022]
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Kaushik S, Sowdhamini R. Structural analysis of prolyl oligopeptidases using molecular docking and dynamics: insights into conformational changes and ligand binding. PLoS One 2011; 6:e26251. [PMID: 22132071 PMCID: PMC3223163 DOI: 10.1371/journal.pone.0026251] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Accepted: 09/23/2011] [Indexed: 11/28/2022] Open
Abstract
Prolyl oligopeptidase (POP) is considered as an important pharmaceutical target for the treatment of numerous diseases. Despite enormous studies on various aspects of POPs structure and function still some of the questions are intriguing like conformational dynamics of the protein and interplay between ligand entry/egress. Here, we have used molecular modeling and docking based approaches to unravel questions like differences in ligand binding affinities in three POP species (porcine, human and A. thaliana). Despite high sequence and structural similarity, they possess different affinities for the ligands. Interestingly, human POP was found to be more specific, selective and incapable of binding to a few planar ligands which showed extrapolation of porcine POP in human context is more complicated. Possible routes for substrate entry and product egress were also investigated by detailed analyses of molecular dynamics (MD) simulations for the three proteins. Trajectory analysis of bound and unbound forms of three species showed differences in conformational dynamics, especially variations in β-propeller pore size, which was found to be hidden by five lysine residues present on blades one and seven. During simulation, β-propeller pore size was increased by ∼2 Å in porcine ligand-bound form which might act as a passage for smaller product movement as free energy barrier was reduced, while there were no significant changes in human and A. thaliana POPs. We also suggest that these differences in pore size could lead to fundamental differences in mode of product egress among three species. This analysis also showed some functionally important residues which can be used further for in vitro mutagenesis and inhibitor design. This study can help us in better understanding of the etiology of POPs in several neurodegenerative diseases.
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Affiliation(s)
- Swati Kaushik
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Ramanathan Sowdhamini
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
- * E-mail:
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Inhibition of prolyl oligopeptidase with a synthetic unnatural dipeptide. Bioorg Med Chem 2010; 18:4775-82. [DOI: 10.1016/j.bmc.2010.05.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2010] [Revised: 04/30/2010] [Accepted: 05/04/2010] [Indexed: 11/20/2022]
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Lawandi J, Gerber-Lemaire S, Juillerat-Jeanneret L, Moitessier N. Inhibitors of prolyl oligopeptidases for the therapy of human diseases: defining diseases and inhibitors. J Med Chem 2010; 53:3423-38. [PMID: 20058865 DOI: 10.1021/jm901104g] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Janice Lawandi
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 2K6, Canada
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Brandt I, Scharpé S, Lambeir AM. Suggested functions for prolyl oligopeptidase: a puzzling paradox. Clin Chim Acta 2006; 377:50-61. [PMID: 17034776 DOI: 10.1016/j.cca.2006.09.001] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2006] [Revised: 08/29/2006] [Accepted: 09/01/2006] [Indexed: 10/24/2022]
Abstract
Prolyl oligopeptidase (PO, E.C. 3.4.21.26) is a post-proline cleaving enzyme with endopeptidase activity towards peptides not longer than 30 amino acids. It has been purified and characterized from various mammalian and bacterial sources, but despite its thorough enzymological and structural characterization, the exact function of PO remains obscure. Many investigations have addressed the physiological role of this enzyme, mainly by the use of specific PO inhibitors, activity measurements in clinical samples and (neuro)peptide degradation studies. From the combined results emerges a puzzling paradox: how can an intracellular, cytoplasmatic oligopeptidase affect not only the amount of extracellular neuropeptides but also signal transduction and secretion? This report provides a review of the literature on the suggested functions for PO, highlighting possible pitfalls and contradictions.
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Affiliation(s)
- Inger Brandt
- Laboratory of Medical Biochemistry, Department of Pharmaceutical Sciences University of Antwerp, Universiteitsplein 1, Blg S6 B-2610 Antwerp (Wilrijk), Belgium
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Brandt I, De Vriendt K, Devreese B, Van Beeumen J, Van Dongen W, Augustyns K, De Meester I, Scharpé S, Lambeir AM. Search for substrates for prolyl oligopeptidase in porcine brain. Peptides 2005; 26:2536-46. [PMID: 15996789 DOI: 10.1016/j.peptides.2005.05.016] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2005] [Revised: 05/23/2005] [Accepted: 05/23/2005] [Indexed: 11/17/2022]
Abstract
The function of prolyl oligopeptidase (PO) has been associated with several disorders of the central nervous system. The purpose of this study was to identify endogenous substrates for recombinant porcine PO in porcine brain. The smaller polypeptides were extracted from total brain homogenates and fractionated by two-dimensional chromatography prior to incubation with PO. Shifts in the mass spectrum between the control and the incubated sample, marked potential substrates. Using MSMS peptide sequencing techniques, we identified several fragments of intracellular proteins as potential substrates, which opens new perspectives for finding the function of PO in the intracellular space.
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Affiliation(s)
- Inger Brandt
- Laboratory of Medical Biochemistry, Department of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
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Ahmed MM, Yamamoto M, Chikuma T, Rahman MK, Kato T. Dose-dependent effect of MK-801 on the levels of neuropeptides processing enzymes in rat brain regions. Neurosci Res 2003; 47:177-89. [PMID: 14512142 DOI: 10.1016/s0168-0102(03)00197-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The appropriate levels of neuropeptides and their processing enzyme activities are required to continue a normal cell life, and the dysfunction of these peptides and enzymes are responsible for many neuronal abnormalities. Systemic administration of (+) MK-801 (dizocilpine maleate), a noncompetitive N-methyl-[D]-aspartate (NMDA) receptor antagonist, causes both neuroprotective and neurotoxic activities depending on doses and conditions. In the present study, we investigated the dose dependent effect of (+) MK-801 on prolyl endopeptidase (PEP), endopeptidase EC 24.15 (EP 24.15) and beta-D-glucuronidase activities as well as the protein levels of EP 24.15 and neuron specific enolase (NSE) in the posterior cingulate/retrosplenial cortices (PC/RSC), hippocampus, frontal cortex and striatum of female rats 3 days after the treatment. The activity of PEP was significantly increased compared with controls (saline) in the PC/RSC at 1.0 and 5.0 mg/kg doses, and in the frontal cortex at 5.0 mg/kg dose. beta-D-Glucuronidase activity was dose-dependently increased in all brain regions examined. The activity of EP 24.15 was unchanged in all regions after the treatment, whereas the Western blot analysis for EP 24.15 showed the increased protein level in the PC/RSC. These results suggest that a low dose treatment with MK-801 causes neurotoxicity in the PC/RSC and hippocampus, and the high dose treatment causes neurotoxicity in all the brain regions examined.
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Affiliation(s)
- Md Mahiuddin Ahmed
- Laboratory of Natural Information Science, Graduate School of Integrated Science, Yokohama City University, 22-2 Seto, Kanazawa-Ku, Yokohama 236-0027, Japan
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Bellemère G, Morain P, Vaudry H, Jégou S. Effect of S 17092, a novel prolyl endopeptidase inhibitor, on substance P and alpha-melanocyte-stimulating hormone breakdown in the rat brain. J Neurochem 2003; 84:919-29. [PMID: 12603817 DOI: 10.1046/j.1471-4159.2003.01536.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In the present study, we have investigated the effects of a novel prolyl endopeptidase (EC 3.4.21.26, PEP) inhibitor, compound S 17092, on substance P (SP) and alpha-melanocyte-stimulating hormone (alpha-MSH) metabolism in the rat brain. In vitro experiments revealed that S 17092 inhibits in a dose-dependent manner PEP activity in rat cortical extracts (IC50 = 8.3 nm). In addition, S 17092 totally abolished the degradation of SP and alpha-MSH induced by bacterial PEP. In vivo, a significant decrease in PEP activity was observed in the medulla oblongata after a single oral administration of S 17092 at doses of 10 and 30 mg/kg (-78% and -82%, respectively) and after chronic oral treatment with S 17092 at doses of 10 and 30 mg/kg per day (-75% and -88%, respectively). Concurrently, a single administration of S 17092 (30 mg/kg) caused a significant increase in SP- and alpha-MSH-like immunoreactivity (LI) in the frontal cortex (+41% and +122%, respectively) and hypothalamus (+84% and +49%, respectively). In contrast, chronic treatment with S 17092 did not significantly modify SP- and alpha-MSH-LI in the frontal cortex and hypothalamus. Collectively, the present results show that S 17092 elevates SP and alpha-MSH concentrations in the rat brain by inhibiting PEP activity. These data suggest that the effect of S 17092 on memory impairment can be accounted for, at least in part, by inhibition of catabolism of promnesic neuropeptides such as SP and alpha-MSH.
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Affiliation(s)
- Gaëlle Bellemère
- European Institute for Peptide Research (IFRMP23), Laboratory of Cellular and Molecular Neuroendocrinology, INSERM U 413, CNRS, University of Rouen, 76821 Mont-Saint-Aignan, France
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Odaka C, Mizuochi T, Shirasawa T, Morain P, Checler F. Murine T cells expressing high activity of prolyl endopeptidase are susceptible to activation-induced cell death. FEBS Lett 2002; 512:163-7. [PMID: 11852073 DOI: 10.1016/s0014-5793(02)02249-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Prolyl endopeptidase (PEP) is widely distributed and thought to play an important role in the degradation of peptide hormones and neuropeptides, but its biological role is totally unknown. In this study, we examined PEP activity in subpopulations of murine T cells and found that PEP activity was significantly higher in immature thymocytes than in mature thymocytes or in peripheral T cells. Stimulation of murine peripheral T cells time-dependently increased PEP activity. Although murine T cell hybridomas exhibited high PEP activity, the PEP activity was fully inhibited by treatment with PEP inhibitor. The pretreated T cells were found to be resistant to activation-induced cell death (AICD). Similar results were obtained in murine thymocytes as well as in activated peripheral T cells. PEP activity in T cell hybridomas remained unchanged during AICD. These results suggest that T cells expressing high PEP activity are susceptible to ACID.
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Affiliation(s)
- Chikako Odaka
- Department of Bacterial and Blood Products, National Institute of Infectious Diseases, 1-23-1, Toyama, Shinjuku-ku, 162-8640, Tokyo, Japan.
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Laitinen KS, van Groen T, Tanila H, Venäläinen J, Männistö PT, Alafuzoff I. Brain prolyl oligopeptidase activity is associated with neuronal damage rather than beta-amyloid accumulation. Neuroreport 2001; 12:3309-12. [PMID: 11711876 DOI: 10.1097/00001756-200110290-00032] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Prolyl oligopeptidase (POP) have been suggested to participate in the pathogenesis of Alzheimer's disease (AD). In this study the activity of POP is evaluated in AD patients and in transgenic mice with substantial deposits of beta-amyloid (Abeta). In AD cases, the POP activity displayed a significant negative correlation with the scores of senile/neuritic plaques and neurofibrillary tangles but not with Abeta-load. The transgenic mice with high levels of Abeta did not have altered POP activity compared to wild type mice. Based on our results, the low POP activity in AD seems to be associated with neuronal degeneration rather than to Abeta accumulation.
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Affiliation(s)
- K S Laitinen
- Department of Pharmacology, University of Kuopio, P.O.Box 1627, Fin-70211, Kuopio, Finland
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