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Rasmussen M, Tolone A, Paquet-Durand F, Welinder C, Schwede F, Ekström P. The photoreceptor protective cGMP-analog Rp-8-Br-PET-cGMPS interacts with cGMP-interactors PKGI, PDE1, PDE6, and PKAI in the degenerating mouse retina. J Comp Neurol 2023; 531:935-951. [PMID: 36989379 DOI: 10.1002/cne.25475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 07/12/2022] [Accepted: 03/06/2023] [Indexed: 03/31/2023]
Abstract
The inherited eye disease retinitis pigmentosa (RP) causes the loss of photoreceptors by a still unknown cell death mechanism. During this degeneration, cyclic guanosine-3',5'-monophosphate (cGMP) levels become elevated, leading to over-activation of the cGMP-binding protein cGMP-dependent protein kinase (PKG). cGMP analogs selectively modified to have inhibitory actions on PKG have aided in impeding photoreceptor death, and one such cGMP analog is Rp-8-Br-PET-cGMPS. However, cGMP analogs have previously been shown to interact with numerous targets, so to better understand the therapeutic action of Rp-8-Br-PET-cGMPS, it is necessary to elucidate its target-selectivity and hence what potential cellular mechanism(s) it may affect within the photoreceptors. Here, we, therefore, applied affinity chromatography together with mass spectrometry to isolate and identify Rp-8-Br-PET-cGMPS interactors from retinas derived from three different murine RP models (i.e., rd1, rd2, and rd10 mice). Our findings revealed that Rp-8-Br-PET-cGMPS bound seven known cGMP-binding proteins, including PKG1β, PDE1β, PDE1c, PDE6α, and PKA1α. Furthermore, an additional 28 proteins were found to be associated with Rp-8-Br-PET-cGMPS. This latter group included MAPK1/3, which is known to connect with cGMP/PKG in other systems. However, in organotypic retinal cultures, Rp-8-Br-PET-cGMPS had no effect on photoreceptor MAPK1/3 expression or activity. To summarize, Rp-8-Br-PET-cGMPS is more target specific compared to regular cGMP.
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Affiliation(s)
- Michel Rasmussen
- Faculty of Medicine, Department of Clinical Sciences Lund, Lund University, Ophthalmology, Lund, Sweden
| | - Arianna Tolone
- Insitute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | | | - Charlotte Welinder
- Faculty of Medicine, Department of Clinical Sciences Lund, Mass Spectrometry, Lund University, Lund, Sweden
| | - Frank Schwede
- BIOLOG Life Science Institute GmbH & Co. KG, Bremen, Germany
| | - Per Ekström
- Faculty of Medicine, Department of Clinical Sciences Lund, Lund University, Ophthalmology, Lund, Sweden
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2
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Byun JA, VanSchouwen B, Huang J, Baryar U, Melacini G. Divergent allostery reveals critical differences between structurally homologous regulatory domains of Plasmodium falciparum and human protein kinase G. J Biol Chem 2022; 298:101691. [PMID: 35143840 PMCID: PMC8931422 DOI: 10.1016/j.jbc.2022.101691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/01/2022] [Accepted: 02/02/2022] [Indexed: 11/24/2022] Open
Abstract
Malaria is a life-threatening infectious disease primarily caused by the Plasmodium falciparum parasite. The increasing resistance to current antimalarial drugs and their side effects has led to an urgent need for novel malaria drug targets, such as the P. falciparum cGMP-dependent protein kinase (pfPKG). However, PKG plays an essential regulatory role also in the human host. Human PKG (hPKG) and pfPKG are controlled by structurally homologs cGMP-binding domains (CBDs). Here, we show that despite the structural similarities between the essential CBDs in pfPKG and hPKG, their respective allosteric networks differ significantly. Through comparative analyses of CHESCA, molecular dynamics simulations, and backbone internal dynamics measurements, we found that conserved allosteric elements within the essential CBDs are wired differently in pfPKG and hPKG to implement cGMP-dependent kinase activation. Such pfPKG vs. hPKG rewiring of allosteric networks was unexpected due to the structural similarity between the two essential CBDs. Yet, such finding provides crucial information on which elements to target for selective inhibition of pfPKG vs. hPKG, which may potentially reduce undesired side-effects in malaria treatments.
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Affiliation(s)
- Jung Ah Byun
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main St. W. Hamilton, Canada
| | - Bryan VanSchouwen
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main St. W. Hamilton, Canada
| | - Jinfeng Huang
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main St. W. Hamilton, Canada
| | - Ubaidullah Baryar
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main St. W. Hamilton, Canada
| | - Giuseppe Melacini
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main St. W. Hamilton, Canada; Department of Chemistry and Chemical Biology, McMaster University, 1280 Main St. W. Hamilton, Canada.
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3
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Rasmussen M, Welinder C, Schwede F, Ekström P. The stereospecific interaction sites and target specificity of cGMP analogs in mouse cortex. Chem Biol Drug Des 2021; 99:206-221. [PMID: 34687134 DOI: 10.1111/cbdd.13976] [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: 08/01/2021] [Revised: 09/29/2021] [Accepted: 10/16/2021] [Indexed: 11/30/2022]
Abstract
cGMP interactors play a role in several pathologies and may be targets for cGMP analog-based drugs, but the success of targeting depends on the biochemical stereospecificity between the cGMP-analog and the interactor. The stereospecificity between general cGMP analogs-or such that are selectivity-modified to obtain, for example, inhibitory actions on a specific target, like the cGMP-dependent protein kinase-have previously been investigated. However, the importance of stereospecificity for cGMP-analog binding to interactors is not known. We, therefore, applied affinity chromatography on mouse cortex proteins utilizing analogs with cyclic phosphate (8-AET-cGMP, 2-AH-cGMP, 2'-AHC-cGMP) and selectivity-modified analogs with sulfur-containing cyclic phosphorothioates (Rp/Sp-8-AET-cGMPS, Rp/Sp-2'-AHC-cGMPS) immobilized to agaroses. The results illustrate the cGMP analogs' stereospecific binding for PKG, PKA regulatory subunits and PKA catalytic subunits, PDEs, and EPAC2 and the involvement of these in various KEGG pathways. For the seven agaroses, PKG, PKA regulatory subunits, and PKA catalytic subunits were more prone to be enriched by 2-AH-, 8-AET-, Rp-8-AET-, and Sp-8-AET-cGMP, whereas PDEs and EPAC2 were more likely to be enriched by 2-AH-, Rp-2'-AHC-, and Rp-8-AET-cGMP. Our findings help elucidate the stereospecific-binding sites essential for the interaction between individual cGMP analogs and cGMP-binding proteins, as well as the cGMP analogs' target specificity, which are two crucial parameters in drug design.
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Affiliation(s)
- Michel Rasmussen
- Faculty of Medicine, Department of Clinical Sciences Lund, Ophthalmology, Lund University, Lund, Sweden
| | - Charlotte Welinder
- Faculty of Medicine, Department of Clinical Sciences Lund, Oncology, Lund University, Lund, Sweden
| | - Frank Schwede
- BIOLOG Life Science Institute GmbH & Co. KG, Bremen, Germany
| | - Per Ekström
- Faculty of Medicine, Department of Clinical Sciences Lund, Ophthalmology, Lund University, Lund, Sweden
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Estrada K, Froelich S, Wuster A, Bauer CR, Sterling T, Clark WT, Ru Y, Trinidad M, Nguyen HP, Luu AR, Wendt DJ, Yogalingam G, Yu GK, LeBowitz JH, Cardon LR. Identifying therapeutic drug targets using bidirectional effect genes. Nat Commun 2021; 12:2224. [PMID: 33850126 PMCID: PMC8044152 DOI: 10.1038/s41467-021-21843-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 02/12/2021] [Indexed: 01/15/2023] Open
Abstract
Prioritizing genes for translation to therapeutics for common diseases has been challenging. Here, we propose an approach to identify drug targets with high probability of success by focusing on genes with both gain of function (GoF) and loss of function (LoF) mutations associated with opposing effects on phenotype (Bidirectional Effect Selected Targets, BEST). We find 98 BEST genes for a variety of indications. Drugs targeting those genes are 3.8-fold more likely to be approved than non-BEST genes. We focus on five genes (IGF1R, NPPC, NPR2, FGFR3, and SHOX) with evidence for bidirectional effects on stature. Rare protein-altering variants in those genes result in significantly increased risk for idiopathic short stature (ISS) (OR = 2.75, p = 3.99 × 10-8). Finally, using functional experiments, we demonstrate that adding an exogenous CNP analog (encoded by NPPC) rescues the phenotype, thus validating its potential as a therapeutic treatment for ISS. Our results show the value of looking for bidirectional effects to identify and validate drug targets.
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Affiliation(s)
| | | | | | | | | | | | - Yuanbin Ru
- BioMarin Pharmaceutical Inc., Novato, CA, USA
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5
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Kim C, Sharma R. Cyclic nucleotide selectivity of protein kinase G isozymes. Protein Sci 2020; 30:316-327. [PMID: 33271627 DOI: 10.1002/pro.4008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 11/25/2020] [Accepted: 12/01/2020] [Indexed: 11/07/2022]
Abstract
The intrinsic activity of the C-terminal catalytic (C) domain of cyclic guanosine monophosphate (cGMP)-dependent protein kinases (PKG) is inhibited by interactions with the N-terminal regulatory (R) domain. Selective binding of cGMP to cyclic nucleotide binding (CNB) domains within the R-domain disrupts the inhibitory R-C interaction, leading to the release and activation of the C-domain. Affinity measurements of mammalian and plasmodium PKG CNB domains reveal different degrees of cyclic nucleotide affinity and selectivity; the CNB domains adjacent to the C-domain are more cGMP selective and therefore critical for cGMP-dependent activation. Crystal structures of isolated CNB domains in the presence and absence of cyclic nucleotides reveal isozyme-specific contacts that explain cyclic nucleotide selectivity and conformational changes that accompany CNB. Crystal structures of tandem CNB domains identify two types of CNB-mediated dimeric contacts that indicate cGMP-driven reorganization of domain-domain interfaces that include large conformational changes. Here, we review the available structural and functional information of PKG CNB domains that further advance our understanding of cGMP mediated regulation and activation of PKG isozymes.
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Affiliation(s)
- Choel Kim
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas, USA.,Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Rajesh Sharma
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas, USA
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Qin L, Sankaran B, Aminzai S, Casteel DE, Kim C. Structural basis for selective inhibition of human PKG Iα by the balanol-like compound N46. J Biol Chem 2018; 293:10985-10992. [PMID: 29769318 PMCID: PMC6052212 DOI: 10.1074/jbc.ra118.002427] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 05/11/2018] [Indexed: 12/18/2022] Open
Abstract
Activation of protein kinase G (PKG) Iα in nociceptive neurons induces long-term hyperexcitability that causes chronic pain. Recently, a derivative of the fungal metabolite balanol, N46, has been reported to inhibit PKG Iα with high potency and selectivity and attenuate thermal hyperalgesia and osteoarthritic pain. Here we determined co-crystal structures of the PKG Iα C-domain and cAMP-dependent protein kinase (PKA) Cα, each bound with N46, at 1.98 Å and 2.65 Å, respectively. N46 binds the active site with its external phenyl ring, specifically interacting with the glycine-rich loop and the αC helix. Phe-371 at the PKG Iα glycine-rich loop is oriented parallel to the phenyl ring of N46, forming a strong π-stacking interaction, whereas the analogous Phe-54 in PKA Cα rotates 30° and forms a weaker interaction. Structural comparison revealed that steric hindrance between the preceding Ser-53 and the propoxy group of the phenyl ring may explain the weaker interaction with PKA Cα. The analogous Gly-370 in PKG Iα, however, causes little steric hindrance with Phe-371. Moreover, Ile-406 on the αC helix forms a hydrophobic interaction with N46 whereas its counterpart in PKA, Thr-88, does not. Substituting these residues in PKG Iα with those in PKA Cα increases the IC50 values for N46, whereas replacing these residues in PKA Cα with those in PKG Iα reduces the IC50, consistent with our structural findings. In conclusion, our results explain the structural basis for N46-mediated selective inhibition of human PKG Iα and provide a starting point for structure-guided design of selective PKG Iα inhibitors.
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Affiliation(s)
- Liying Qin
- From the Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030
| | - Banumathi Sankaran
- the Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Sahar Aminzai
- the Department of Medicine, University of California, San Diego, La Jolla, California 92093, and
| | - Darren E Casteel
- the Department of Medicine, University of California, San Diego, La Jolla, California 92093, and
| | - Choel Kim
- From the Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030,
- the Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas 77030
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Gerlits O, Campbell JC, Blakeley MP, Kim C, Kovalevsky A. Neutron Crystallography Detects Differences in Protein Dynamics: Structure of the PKG II Cyclic Nucleotide Binding Domain in Complex with an Activator. Biochemistry 2018. [PMID: 29517905 DOI: 10.1021/acs.biochem.8b00010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
As one of the main receptors of a second messenger, cGMP, cGMP-dependent protein kinase (PKG) isoforms I and II regulate distinct physiological processes. The design of isoform-specific activators is thus of great biomedical importance and requires detailed structural information about PKG isoforms bound with activators, including accurate positions of hydrogen atoms and a description of the hydrogen bonding and water architecture. Here, we determined a 2.2 Å room-temperature joint X-ray/neutron (XN) structure of the human PKG II carboxyl cyclic nucleotide binding (CNB-B) domain bound with a potent PKG II activator, 8-pCPT-cGMP. The XN structure directly visualizes intermolecular interactions and reveals changes in hydrogen bonding patterns upon comparison to the X-ray structure determined at cryo-temperatures. Comparative analysis of the backbone hydrogen/deuterium exchange patterns in PKG II:8-pCPT-cGMP and previously reported PKG Iβ:cGMP XN structures suggests that the ability of these agonists to activate PKG is related to how effectively they quench dynamics of the cyclic nucleotide binding pocket and the surrounding regions.
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Affiliation(s)
- Oksana Gerlits
- Bredesen Center , University of Tennessee , Knoxville , Tennessee 37996 , United States
| | - James C Campbell
- Department of Pharmacology and Chemical Biology , Baylor College of Medicine , Houston , Texas 77030 , United States
| | - Matthew P Blakeley
- Large-Scale Structures Group , Institut Laue Langevin , 38042 Grenoble Cedex 9, France
| | - Choel Kim
- Department of Pharmacology and Chemical Biology , Baylor College of Medicine , Houston , Texas 77030 , United States.,Verna and Marrs McLean Department of Biochemistry and Molecular Biology , Baylor College of Medicine , Houston , Texas 77030 , United States
| | - Andrey Kovalevsky
- Neutron Scattering Division, Neutron Sciences Directorate , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37831 , United States
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Bubis J, Martínez JC, Calabokis M, Ferreira J, Sanz-Rodríguez CE, Navas V, Escalona JL, Guo Y, Taylor SS. The gene product of a Trypanosoma equiperdum ortholog of the cAMP-dependent protein kinase regulatory subunit is a monomeric protein that is not capable of binding cyclic nucleotides. Biochimie 2017; 146:166-180. [PMID: 29288679 DOI: 10.1016/j.biochi.2017.12.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 12/23/2017] [Indexed: 02/03/2023]
Abstract
The full gene sequence encoding for the Trypanosoma equiperdum ortholog of the cAMP-dependent protein kinase (PKA) regulatory (R) subunits was cloned. A poly-His tagged construct was generated [TeqR-like(His)8], and the protein was expressed in bacteria and purified to homogeneity. The size of the purified TeqR-like(His)8 was determined to be ∼57,000 Da by molecular exclusion chromatography indicating that the parasite protein is a monomer. Limited proteolysis with various proteases showed that the T. equiperdum R-like protein possesses a hinge region very susceptible to proteolysis. The recombinant TeqR-like(His)8 did not bind either [3H] cAMP or [3H] cGMP up to concentrations of 0.40 and 0.65 μM, respectively, and neither the parasite protein nor its proteolytically generated carboxy-terminal large fragments were capable of binding to a cAMP-Sepharose affinity column. Bioinformatics analyses predicted that the carboxy-terminal region of the trypanosomal R-like protein appears to fold similarly to the analogous region of all known PKA R subunits. However, the protein amino-terminal portion seems to be unrelated and shows homology with proteins that contained Leu-rich repeats, a folding motif that is particularly appropriate for protein-protein interactions. In addition, the three-dimensional structure of the T. equiperdum protein was modeled using the crystal structure of the bovine PKA RIα subunit as template. Molecular docking experiments predicted critical changes in the environment of the two putative nucleotide binding clefts of the parasite protein, and the resulting binding energy differences support the lack of cyclic nucleotide binding in the trypanosomal R-like protein.
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Affiliation(s)
- José Bubis
- Departamento de Biología Celular, Universidad Simón Bolívar, Caracas 1081-A, Venezuela.
| | - Juan Carlos Martínez
- Dirección de Salud, Fundación Instituto de Estudios Avanzados IDEA, Caracas 1015-A, Venezuela.
| | - Maritza Calabokis
- Departamento de Biología Celular, Universidad Simón Bolívar, Caracas 1081-A, Venezuela.
| | - Joilyneth Ferreira
- Dirección de Salud, Fundación Instituto de Estudios Avanzados IDEA, Caracas 1015-A, Venezuela; Postgrado en Ciencias Biológicas, Universidad Simón Bolívar, Caracas 1081-A, Venezuela.
| | | | - Victoria Navas
- Departamento de Biología Celular, Universidad Simón Bolívar, Caracas 1081-A, Venezuela; Dirección de Salud, Fundación Instituto de Estudios Avanzados IDEA, Caracas 1015-A, Venezuela; Escuela de Biología, Facultad de Ciencias, Universidad Central de Venezuela, Caracas 1041-A, Venezuela.
| | | | - Yurong Guo
- Department of Chemistry, Biochemistry and Pharmacology, University of California San Diego, La Jolla, CA 92093-0654, USA.
| | - Susan S Taylor
- Department of Chemistry, Biochemistry and Pharmacology, University of California San Diego, La Jolla, CA 92093-0654, USA.
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New cGMP analogues restrain proliferation and migration of melanoma cells. Oncotarget 2017; 9:5301-5320. [PMID: 29435180 PMCID: PMC5797051 DOI: 10.18632/oncotarget.23685] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 12/18/2017] [Indexed: 12/14/2022] Open
Abstract
Melanoma is one of the most aggressive cancers and displays high resistance to conventional chemotherapy underlining the need for new therapeutic strategies. The cGMP/PKG signaling pathway was detected in melanoma cells and shown to reduce migration, proliferation and to increase apoptosis in different cancer types. In this study, we evaluated the effects on cell viability, cell death, proliferation and migration of novel dimeric cGMP analogues in two melanoma cell lines (MNT1 and SkMel28). These new dimeric cGMP analogues, by activating PKG with limited effects on PKA, significantly reduced proliferation, migration and increased cell death. No decrease in cell viability was observed in non-tumor cells suggesting a tumor-specific effect. These effects observed in melanoma are possibly mediated by PKG2 activation based on the decreased toxic effects in tumor cell lines not expressing PKG2. Finally, PKG-associated phosphorylation of vasodilator-stimulated-phosphoprotein (VASP), linked to cell death, proliferation and migration was found increased and with a change of subcellular localization. Increased phosphorylation of RhoA induced by activation of PKG may also contribute to reduced migration ability of the SkMel28 melanoma cell line when treated with cGMP analogues. These findings suggest that the cGMP/PKG pathway can be envisaged as a therapeutic target of novel dimeric cGMP analogues for the treatment of melanoma.
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