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Yıldırır Y, Özel S, Doyduk D, Kartal Y, Sabuncuoğlu S. Synthesis of Apigenin and Quercetin‐Like Compounds, Molecular Docking Simulation, and Investigation of Their Bioactivity on A549 Cell Lines. ChemistrySelect 2022. [DOI: 10.1002/slct.202203121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Yılmaz Yıldırır
- Department of Chemistry Faculty of Science Gazi University 06500 Ankara Turkey
| | - Selinay Özel
- Department of Chemistry Faculty of Science Gazi University 06500 Ankara Turkey
| | - Doğukan Doyduk
- Department of Chemistry Faculty of Science Gazi University 06500 Ankara Turkey
| | - Yasemin Kartal
- Department of Physiology Faculty of Medicine Kırklareli University 39000 Kırklareli Turkey
| | - Suna Sabuncuoğlu
- Department of Toxicology Faculty of Pharmacy Hacettepe University Ankara, 06100 Turkey
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2
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Patterson JR, Graves AP, Stoy P, Cheung M, Desai TA, Fries H, Gatto GJ, Holt DA, Shewchuk L, Totoritis R, Wang L, Kallander LS. Identification of Diarylurea Inhibitors of the Cardiac-Specific Kinase TNNI3K by Designing Selectivity Against VEGFR2, p38α, and B-Raf. J Med Chem 2021; 64:15651-15670. [PMID: 34699203 DOI: 10.1021/acs.jmedchem.1c00700] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A series of diarylurea inhibitors of the cardiac-specific kinase TNNI3K were developed to elucidate the biological function of TNNI3K and evaluate TNNI3K as a therapeutic target for the treatment of cardiovascular diseases. Utilizing a structure-based design, enhancements in kinase selectivity were engineered into the series, capitalizing on the established X-ray crystal structures of TNNI3K, VEGFR2, p38α, and B-Raf. Our efforts culminated in the discovery of an in vivo tool compound 47 (GSK329), which exhibited desirable TNNI3K potency and rat pharmacokinetic properties as well as promising kinase selectivity against VEGFR2 (40-fold), p38α (80-fold), and B-Raf (>200-fold). Compound 47 demonstrated positive cardioprotective outcomes in a mouse model of ischemia/reperfusion cardiac injury, indicating that optimized exemplars from this series, such as 47, are favorable leads for discovering novel medicines for cardiac diseases.
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Affiliation(s)
- Jaclyn R Patterson
- Heart Failure Discovery Performance Unit, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Alan P Graves
- Platform Technology and Sciences, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Patrick Stoy
- Heart Failure Discovery Performance Unit, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Mui Cheung
- Heart Failure Discovery Performance Unit, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Tina A Desai
- Heart Failure Discovery Performance Unit, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Harvey Fries
- Heart Failure Discovery Performance Unit, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Gregory J Gatto
- Heart Failure Discovery Performance Unit, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Dennis A Holt
- Heart Failure Discovery Performance Unit, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Lisa Shewchuk
- Platform Technology and Sciences, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Rachel Totoritis
- Platform Technology and Sciences, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Liping Wang
- Platform Technology and Sciences, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Lara S Kallander
- Heart Failure Discovery Performance Unit, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
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3
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Pham C, Muñoz-Martín N, Lodder EM. The Diverse Roles of TNNI3K in Cardiac Disease and Potential for Treatment. Int J Mol Sci 2021; 22:6422. [PMID: 34203974 PMCID: PMC8232738 DOI: 10.3390/ijms22126422] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/11/2021] [Accepted: 06/14/2021] [Indexed: 12/25/2022] Open
Abstract
In the two decades since the discovery of TNNI3K it has been implicated in multiple cardiac phenotypes and physiological processes. TNNI3K is an understudied kinase, which is mainly expressed in the heart. Human genetic variants in TNNI3K are associated with supraventricular arrhythmias, conduction disease, and cardiomyopathy. Furthermore, studies in mice implicate the gene in cardiac hypertrophy, cardiac regeneration, and recovery after ischemia/reperfusion injury. Several new papers on TNNI3K have been published since the last overview, broadening the clinical perspective of TNNI3K variants and our understanding of the underlying molecular biology. We here provide an overview of the role of TNNI3K in cardiomyopathy and arrhythmia covering both a clinical perspective and basic science advancements. In addition, we review the potential of TNNI3K as a target for clinical treatments in different cardiac diseases.
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Affiliation(s)
| | | | - Elisabeth M. Lodder
- Department of Clinical and Experimental Cardiology, Heart Center, University of Amsterdam, Amsterdam UMC, 1105 AZ Amsterdam, The Netherlands; (C.P.); (N.M.-M.)
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Pang H, Wang N, Chai J, Wang X, Zhang Y, Bi Z, Wu W, He G. Discovery of novel TNNI3K inhibitor suppresses pyroptosis and apoptosis in murine myocardial infarction injury. Eur J Med Chem 2020; 197:112314. [PMID: 32344181 DOI: 10.1016/j.ejmech.2020.112314] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/06/2020] [Accepted: 04/06/2020] [Indexed: 02/08/2023]
Abstract
Myocardial infarction (MI) injury is a highly lethal syndrome that has, until recently, suffered from a lack of clinically efficient targeted therapeutics. The cardiac troponin I interacting kinase (TNNI3K) exacerbates ischemia-reperfusion (IR) injury via oxidative stress, thereby promoting cardiomyocyte death. In this current study, we designed and synthesized 35 novel TNNI3K inhibitors with a pyrido[4,5]thieno[2,3-d] pyrimidine scaffold. In vitro results indicated that some of the inhibitors exhibited sub-micromolar TNNI3K inhibitory capacity and good kinase selectivity, as well as cytoprotective activity, in an oxygen-glucose deprivation (OGD) injury cardiomyocyte model. Furthermore, investigation of the mechanism of the representative derivative compound 6o suggested it suppresses pyroptosis and apoptosis in cardiomyocytes by interfering with p38MAPK activation, which was further confirmed in a murine myocardial infarction injury model. In vivo results indicate that compound 6o can markedly reduce myocardial infarction size and alleviate cardiac tissue damage in rats. In brief, our results provide the basis for further development of novel TNNI3K inhibitors for targeted MI therapy.
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Affiliation(s)
- Haiying Pang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, 610041, PR China
| | - Ning Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, 610041, PR China
| | - Jinlong Chai
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, 610041, PR China
| | - Xiaoyun Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, 610041, PR China
| | - Yuehua Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, 610041, PR China
| | - Zhiang Bi
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, 610041, PR China
| | - Wenbin Wu
- Department of Neurology, Chongzhou People's Hospital, Chengdu, 611230, PR China
| | - Gu He
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, 610041, PR China.
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New Insights into 4-Anilinoquinazolines as Inhibitors of Cardiac Troponin I-Interacting Kinase (TNNi3K). Molecules 2020; 25:molecules25071697. [PMID: 32272798 PMCID: PMC7180948 DOI: 10.3390/molecules25071697] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 04/03/2020] [Accepted: 04/03/2020] [Indexed: 11/16/2022] Open
Abstract
We report the synthesis of several related 4-anilinoquinazolines as inhibitors of cardiac troponin I-interacting kinase (TNNi3K). These close structural analogs of 3-((6,7-dimethoxyquinazolin-4-yl)amino)-4-(dimethylamino)-N-methylbenzenesulfonamide (GSK114) provide new understanding of structure-activity relationships between the 4-anilinoquinazoline scaffold and TNNi3K inhibition. Through a small focused library of inhibitors, we observed that the N-methylbenzenesulfonamide was driving the potency in addition to the more traditional quinazoline hinge-binding motif. We also identified a compound devoid of TNNi3K kinase activity due to the addition of a methyl group in the hinge binding region. This compound could serve as a negative control in the study of TNNi3K biology. Small molecule crystal structures of several quinazolines have been solved, supporting observations made about overall conformation and TNNi3K inhibition.
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Skalic M, Sabbadin D, Sattarov B, Sciabola S, De Fabritiis G. From Target to Drug: Generative Modeling for the Multimodal Structure-Based Ligand Design. Mol Pharm 2019; 16:4282-4291. [PMID: 31437001 DOI: 10.1021/acs.molpharmaceut.9b00634] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Chemical space is impractically large, and conventional structure-based virtual screening techniques cannot be used to simply search through the entire space to discover effective bioactive molecules. To address this shortcoming, we propose a generative adversarial network to generate, rather than search, diverse three-dimensional ligand shapes complementary to the pocket. Furthermore, we show that the generated molecule shapes can be decoded using a shape-captioning network into a sequence of SMILES enabling directly the structure-based de novo drug design. We evaluate the quality of the method by both structure- (docking) and ligand-based [quantitative structure-activity relationship (QSAR)] virtual screening methods. For both evaluation approaches, we observed enrichment compared to random sampling from initial chemical space of ZINC drug-like compounds.
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Affiliation(s)
- Miha Skalic
- Computational Science Laboratory , Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB) , C Dr Aiguader 88 , 08003 Barcelona , Spain
| | - Davide Sabbadin
- Computational Science Laboratory , Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB) , C Dr Aiguader 88 , 08003 Barcelona , Spain
| | - Boris Sattarov
- Computational Science Laboratory , Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB) , C Dr Aiguader 88 , 08003 Barcelona , Spain
| | - Simone Sciabola
- Biogen Chemistry and Molecular Therapeutics , 115 Broadway Street , Cambridge , Massachusetts 02142 , United States
| | - Gianni De Fabritiis
- Computational Science Laboratory , Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB) , C Dr Aiguader 88 , 08003 Barcelona , Spain.,Acellera, Barcelona Biomedical Research Park (PRBB) , C Dr. Aiguader 88 , 08003 Barcelona , Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA) , Passeig Lluis Companys 23 , 08010 Barcelona , Spain
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Dittmann S, Schulze-Bahr E. Nonsynonymous TNNI3K mutations and phenotypes: More than a "simple" cardiomyopathy. Heart Rhythm 2019; 16:106-107. [PMID: 30063992 DOI: 10.1016/j.hrthm.2018.07.033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Indexed: 12/14/2022]
Affiliation(s)
- Sven Dittmann
- Institute for Genetics of Heart Diseases (IfGH), University Hospital Münster, Münster, Germany
| | - Eric Schulze-Bahr
- Institute for Genetics of Heart Diseases (IfGH), University Hospital Münster, Münster, Germany.
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Ramírez D, Caballero J. Is It Reliable to Take the Molecular Docking Top Scoring Position as the Best Solution without Considering Available Structural Data? Molecules 2018; 23:molecules23051038. [PMID: 29710787 PMCID: PMC6102569 DOI: 10.3390/molecules23051038] [Citation(s) in RCA: 228] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 04/21/2018] [Accepted: 04/26/2018] [Indexed: 12/13/2022] Open
Abstract
Molecular docking is the most frequently used computational method for studying the interactions between organic molecules and biological macromolecules. In this context, docking allows predicting the preferred pose of a ligand inside a receptor binding site. However, the selection of the “best” solution is not a trivial task, despite the widely accepted selection criterion that the best pose corresponds to the best energy score. Here, several rigid-target docking methods were evaluated on the same dataset with respect to their ability to reproduce crystallographic binding orientations, to test if the best energy score is a reliable criterion for selecting the best solution. For this, two experiments were performed: (A) to reconstruct the ligand-receptor complex by performing docking of the ligand in its own crystal structure receptor (defined as self-docking), and (B) to reconstruct the ligand-receptor complex by performing docking of the ligand in a crystal structure receptor that contains other ligand (defined as cross-docking). Root-mean square deviation (RMSD) was used to evaluate how different the obtained docking orientation is from the corresponding co-crystallized pose of the same ligand molecule. We found that docking score function is capable of predicting crystallographic binding orientations, but the best ranked solution according to the docking energy is not always the pose that reproduces the experimental binding orientation. This happened when self-docking was achieved, but it was critical in cross-docking. Taking into account that docking is typically used with predictive purposes, during cross-docking experiments, our results indicate that the best energy score is not a reliable criterion to select the best solution in common docking applications. It is strongly recommended to choose the best docking solution according to the scoring function along with additional structural criteria described for analogue ligands to assure the selection of a correct docking solution.
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Affiliation(s)
- David Ramírez
- Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, 5 Poniente No. 1670, 3460000 Talca, Chile.
| | - Julio Caballero
- Centro de Bioinformática y Simulación Molecular (CBSM), Universidad de Talca. 1 Poniente No. 1141, 3460000 Talca, Chile.
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Philp J, Lawhorn BG, Graves AP, Shewchuk L, Rivera KL, Jolivette LJ, Holt DA, Gatto GJ, Kallander LS. 4,6-Diaminopyrimidines as Highly Preferred Troponin I-Interacting Kinase (TNNI3K) Inhibitors. J Med Chem 2018; 61:3076-3088. [PMID: 29561151 DOI: 10.1021/acs.jmedchem.8b00125] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Structure-guided progression of a purine-derived series of TNNI3K inhibitors directed design efforts that produced a novel series of 4,6-diaminopyrimidine inhibitors, an emerging kinase binding motif. Herein, we report a detailed understanding of the intrinsic conformational preferences of the scaffold, which impart high specificity for TNNI3K. Further manipulation of the template based on the conformational analysis and additional structure-activity relationship studies provided enhancements in kinase selectivity and pharmacokinetics that furnished an advanced series of potent inhibitors. The optimized compounds (e.g., GSK854) are suitable leads for identifying new cardiac medicines and have been employed as in vivo tools in investigational studies aimed at defining the role of TNNI3K within heart failure.
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van der Kemp J, van der Schouw YT, Asselbergs FW, Onland-Moret NC. Women-specific risk factors for heart failure: A genetic approach. Maturitas 2018; 109:104-111. [DOI: 10.1016/j.maturitas.2017.12.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 12/22/2017] [Accepted: 12/29/2017] [Indexed: 02/07/2023]
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11
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Johnston JR, Chase PB, Pinto JR. Troponin through the looking-glass: emerging roles beyond regulation of striated muscle contraction. Oncotarget 2017; 9:1461-1482. [PMID: 29416706 PMCID: PMC5787451 DOI: 10.18632/oncotarget.22879] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 11/20/2017] [Indexed: 01/03/2023] Open
Abstract
Troponin is a heterotrimeric Ca2+-binding protein that has a well-established role in regulating striated muscle contraction. However, mounting evidence points to novel cellular functions of troponin, with profound implications in cancer, cardiomyopathy pathogenesis and skeletal muscle aging. Here, we highlight the non-canonical roles and aberrant expression patterns of troponin beyond the sarcomeric milieu. Utilizing bioinformatics tools and online databases, we also provide pathway, subcellular localization, and protein-protein/DNA interaction analyses that support a role for troponin in multiple subcellular compartments. This emerging knowledge challenges the conventional view of troponin as a sarcomere-specific protein exclusively involved in muscle contraction and may transform the way we think about sarcomeric proteins, particularly in the context of human disease and aging.
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Affiliation(s)
- Jamie R Johnston
- Department of Biomedical Sciences, The Florida State University College of Medicine, Tallahassee, FL, 32306-4300, USA
| | - P Bryant Chase
- Department of Biological Science, The Florida State University, Tallahassee, FL, 32306-4370, USA
| | - Jose Renato Pinto
- Department of Biomedical Sciences, The Florida State University College of Medicine, Tallahassee, FL, 32306-4300, USA
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12
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Lawhorn BG, Philp J, Graves AP, Holt DA, Gatto GJ, Kallander LS. Substituent Effects on Drug–Receptor H-bond Interactions: Correlations Useful for the Design of Kinase Inhibitors. J Med Chem 2016; 59:10629-10641. [DOI: 10.1021/acs.jmedchem.6b01342] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Brian G. Lawhorn
- Heart Failure Discovery Performance Unit and ‡Platform Technology
and Sciences, GlaxoSmithKline, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Joanne Philp
- Heart Failure Discovery Performance Unit and ‡Platform Technology
and Sciences, GlaxoSmithKline, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Alan P. Graves
- Heart Failure Discovery Performance Unit and ‡Platform Technology
and Sciences, GlaxoSmithKline, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Dennis A. Holt
- Heart Failure Discovery Performance Unit and ‡Platform Technology
and Sciences, GlaxoSmithKline, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Gregory J. Gatto
- Heart Failure Discovery Performance Unit and ‡Platform Technology
and Sciences, GlaxoSmithKline, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Lara S. Kallander
- Heart Failure Discovery Performance Unit and ‡Platform Technology
and Sciences, GlaxoSmithKline, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
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