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Ullah S, Ullah A, Waqas M, Halim SA, Pasha AR, Shafiq Z, Mali SN, Jawarkar RD, Khan A, Khalid A, Abdalla AN, Kashtoh H, Al-Harrasi A. Structural, dynamic behaviour, in-vitro and computational investigations of Schiff's bases of 1,3-diphenyl urea derivatives against SARS-CoV-2 spike protein. Sci Rep 2024; 14:12588. [PMID: 38822113 PMCID: PMC11143201 DOI: 10.1038/s41598-024-63345-9] [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: 12/15/2023] [Accepted: 05/28/2024] [Indexed: 06/02/2024] Open
Abstract
The COVID-19 has had a significant influence on people's lives across the world. The viral genome has undergone numerous unanticipated changes that have given rise to new varieties, raising alarm on a global scale. Bioactive phytochemicals derived from nature and synthetic sources possess lot of potential as pathogenic virus inhibitors. The goal of the recent study is to report new inhibitors of Schiff bases of 1,3-dipheny urea derivatives against SARS COV-2 spike protein through in-vitro and in-silico approach. Total 14 compounds were evaluated, surprisingly, all the compounds showed strong inhibition with inhibitory values between 79.60% and 96.00% inhibition. Here, compounds 3a (96.00%), 3d (89.60%), 3e (84.30%), 3f (86.20%), 3g (88.30%), 3h (86.80%), 3k (82.10%), 3l (90.10%), 3m (93.49%), 3n (85.64%), and 3o (81.79%) exhibited high inhibitory potential against SARS COV-2 spike protein. While 3c also showed significant inhibitory potential with 79.60% inhibition. The molecular docking of these compounds revealed excellent fitting of molecules in the spike protein receptor binding domain (RBD) with good interactions with the key residues of RBD and docking scores ranging from - 4.73 to - 5.60 kcal/mol. Furthermore, molecular dynamics simulation for 150 ns indicated a strong stability of a complex 3a:6MOJ. These findings obtained from the in-vitro and in-silico study reflect higher potency of the Schiff bases of 1,3-diphenyl urea derivatives. Furthermore, also highlight their medicinal importance for the treatment of SARS COV-2 infection. Therefore, these small molecules could be a possible drug candidate.
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Affiliation(s)
- Saeed Ullah
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Nizwa, Sultanate of Oman
| | - Atta Ullah
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Nizwa, Sultanate of Oman
| | - Muhammad Waqas
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Nizwa, Sultanate of Oman
| | - Sobia Ahsan Halim
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Nizwa, Sultanate of Oman
| | - Anam Rubbab Pasha
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Nizwa, Sultanate of Oman
- Institute of Chemical Sciences, Bahauddin Zakariya University, Multan, 60800, Pakistan
| | - Zahid Shafiq
- Institute of Chemical Sciences, Bahauddin Zakariya University, Multan, 60800, Pakistan.
| | - Suraj N Mali
- School of Pharmacy, D.Y. Patil University (Deemed to be University), Sector 7, Nerul, Navi Mumbai, 400706, India
| | - Rahul D Jawarkar
- Department of Medicinal Chemistry and Drug Discovery, Dr. Rajendra Gode Institute of Pharmacy, University Mardi Road, Amravati, 444603, India
| | - Ajmal Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Nizwa, Sultanate of Oman.
| | - Asaad Khalid
- Substance Abuse and Toxicology Research Center, Jazan University, P.O. Box: 114, 45142, Jazan, Saudi Arabia
| | - Ashraf N Abdalla
- Department of Pharmacology and Toxicology, College of Pharmacy, Umm Al-Qura University, 21955, Makkah, Saudi Arabia
| | - Hamdy Kashtoh
- Department of Biotechnology, Yeungnam University, Gyeongsan, 38541, Gyeongbuk, Republic of Korea.
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Nizwa, Sultanate of Oman.
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2
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Comesse S, Alahyen I, Benhamou L, Dalla V, Taillier C. 20 Years of Forging N-Heterocycles from Acrylamides through Domino/Cascade Reactions. SYNTHESIS-STUTTGART 2021. [DOI: 10.1055/a-1503-7932] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
AbstractAcrylamides are versatile building blocks that are easily obtained from readily available starting materials. During the last 20 years, these valuable substrates bearing a nucleophilic nitrogen atom and an electrophilic double bond have proven to be efficient domino partners, leading to a wide variety of complex aza-heterocycles of synthetic relevance. In this non-exhaustive review, metal-free and metal-triggered reactions followed by an annulation will be presented; these two approaches allow good modulation of the reactivity of the polyvalent acrylamides.1 Introduction2 Metal-Free Annulations2.1 Domino Reactions Triggered by a Michael Addition2.2 Domino Reactions Triggered by an Aza-Michael Addition2.3 Domino Processes Triggered by an Acylation Reaction2.4 Domino Reactions Triggered by a Baylis–Hillman Reaction2.5 Cycloadditions and Domino Reactions2.6 Miscellaneous Domino Reactions3 Metal-Triggered/Mediated Annulations3.1 Zinc-Promoted Transformations3.2 Rhodium-Catalyzed Functionalization/Annulation Cascades3.3 Cobalt-Catalyzed Functionalization/Annulation Cascades3.4 Ruthenium-Catalyzed Functionalization/Annulation Cascades3.5 Iron-Catalyzed Functionalization/Annulation Cascades3.6 Palladium-Catalyzed Functionalization/Annulation Cascades3.7 Copper-Catalyzed Transformations3.8 Transition Metals Acting in Tandem in Domino Processes4 Radical Cascade Reactions5 Conclusion
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Li LH, Niu ZJ, Li YX, Liang YM. Transition-metal-free multinitrogenation of amides by C-C bond cleavage: a new approach to tetrazoles. Chem Commun (Camb) 2018; 54:11148-11151. [PMID: 30225493 DOI: 10.1039/c8cc06324a] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A metal-free brand-new one-pot multinitrogenation of amides for the chemo- and regioselective synthesis of 1,5-disubstituted tetrazoles has been developed. By means of electrophilic amide activation, and further C-C bond cleavage and rearrangement, a diverse set of functionalized 1,5-DST derivatives were selectively constructed under mild conditions. As showcased in the mechanisms, the chemoselectivity is easily switched by the selection of the starting materials in the reaction.
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Affiliation(s)
- Lian-Hua Li
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, P. R. China.
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Moon SH, Latif M, Qasim M, Choi SW, Lee JY, Byun BJ, Saeed A, Kim SH. Synthesis, Characterization, and Biological Evaluation of Oxadiazole Derivatives Bearing 5-Phenyl-tetrazole as Osteoclast Differentiation Inhibitors. B KOREAN CHEM SOC 2015. [DOI: 10.1002/bkcs.10436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Seong-Hee Moon
- Laboratory of Translational Therapeutics; Korea Research Institute of Chemical Technology; Daejeon 305-600 Republic of Korea
| | - Muhammad Latif
- Center for Catalytic Hydrocarbon Functionalization; Institute for Basic Science (IBS) and Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST); Daejeon 305-701 Korea
| | - Muhammad Qasim
- Department of Chemistry; Quaid-I-Azam University; Islamabad 45320 Pakistan
| | - Sik-Won Choi
- Laboratory of Translational Therapeutics; Korea Research Institute of Chemical Technology; Daejeon 305-600 Republic of Korea
| | - Joo Yun Lee
- Drug Discovery Platform Technology Group; Korea Research Institute of Chemical Technology; Daejeon 305-600 Republic of Korea
| | - Byung Jin Byun
- Drug Discovery Platform Technology Group; Korea Research Institute of Chemical Technology; Daejeon 305-600 Republic of Korea
| | - Aamer Saeed
- Department of Chemistry; Quaid-I-Azam University; Islamabad 45320 Pakistan
| | - Seong Hwan Kim
- Laboratory of Translational Therapeutics; Korea Research Institute of Chemical Technology; Daejeon 305-600 Republic of Korea
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Pyrrolidinyl phenylurea derivatives as novel CCR3 antagonists. Bioorg Med Chem Lett 2012; 22:6876-81. [DOI: 10.1016/j.bmcl.2012.09.035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Revised: 09/04/2012] [Accepted: 09/12/2012] [Indexed: 11/21/2022]
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Nitta A, Iura Y, Tomioka H, Sato I, Morihira K, Kubota H, Morokata T, Takeuchi M, Ohta M, Tsukamoto SI, Imaoka T, Takahashi T. Discovery and structure–activity relationships of urea derivatives as potent and novel CCR3 antagonists. Bioorg Med Chem Lett 2012; 22:4951-4. [DOI: 10.1016/j.bmcl.2012.06.042] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Revised: 06/06/2012] [Accepted: 06/13/2012] [Indexed: 10/28/2022]
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Jain V, Saravanan P, Arvind A, Mohan CG. First pharmacophore model of CCR3 receptor antagonists and its homology model-assisted, stepwise virtual screening. Chem Biol Drug Des 2011; 77:373-87. [PMID: 21284830 DOI: 10.1111/j.1747-0285.2011.01088.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
CCR3, a G protein-coupled receptor, plays a central role in allergic inflammation and is an important drug target for inflammatory diseases. To understand the structure-function relationship of CCR3 receptor, different computational techniques were employed, which mainly include: (i) homology modeling of CCR3 receptor, (ii) 3D-quantitative pharmacophore model of CCR3 antagonists, (iii) virtual screening of small compound databases, and (iv) finally, molecular docking at the binding site of the CCR3 receptor homology model. Pharmacophore model was developed for the first time, on a training data set of 22 CCR3 antagonists, using CATALYST HypoRefine program. Best hypothesis (Hypo1) has three different chemical features: two hydrogen-bond acceptors, one hydrophobic, and one ring aromatic. Hypo1 model was further validated using (i) 87 test set CCR3 antagonists, (ii) Cat Scramble randomization technique, and (iii) Decoy data set. Molecular docking studies were performed on modeled CCR3 receptor using 303 virtually screened hits, obtained from small compound database virtual screening. Finally, five hits were identified as potential leads against CCR3 receptor, which exhibited good estimated activities, favorable binding interactions, and high docking scores. These studies provided useful information on the structurally vital residues of CCR3 receptor involved in the antagonist binding, and their unexplored potential for the future development of potent CCR3 receptor antagonists.
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Affiliation(s)
- Vaibhav Jain
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar- 160 062, Punjab, India
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8
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Willems LI, Ijzerman AP. Small molecule antagonists for chemokine CCR3 receptors. Med Res Rev 2011; 30:778-817. [PMID: 19967721 DOI: 10.1002/med.20181] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The chemokine receptor CCR3 is believed to play a role in the development of allergic diseases such as asthma, atopic dermatitis, and allergic rhinitis. Despite the conflicting results that have been reported regarding the importance of eosinophils and CCR3 in allergic inflammation, inhibition of this receptor with small molecule antagonists is thought to provide a valuable approach for the treatment of these diseases. This review describes the structure-activity relationships (SAR) of small molecule CCR3 antagonists as reported in the scientific and patent literature. Various chemical classes of small molecule CCR3 antagonists have been described so far, including (bi)piperidine and piperazine derivatives, N-arylalkylpiperidine urea derivatives and (N-ureidoalkyl)benzylpiperidines, phenylalanine derivatives, morpholinyl derivatives, pyrrolidinohydroquinazolines, arylsulfonamides, amino-alkyl amides, imidazole- and pyrimidine-based antagonists, and bicyclic diamines. The (N-ureidoalkyl)benzylpiperidines are the best studied class in view of their generally high affinity and antagonizing potential. For many of these antagonists subnanomolar IC(50) values were reported for binding to CCR3 along with the ability to effectively inhibit intracellular calcium mobilization and eosinophil chemotaxis induced by CCR3 agonist ligands in vitro.
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Affiliation(s)
- Lianne I Willems
- Leiden/Amsterdam Center for Drug Research, Division of Medicinal Chemistry, PO Box 9502, 2300RA Leiden, The Netherlands
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9
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Gong L, Wilhelm RS. CCR3 antagonists: a survey of the patent literature. Expert Opin Ther Pat 2009; 19:1109-32. [DOI: 10.1517/13543770903008544] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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10
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Caramori G, Groneberg D, Ito K, Casolari P, Adcock IM, Papi A. New drugs targeting Th2 lymphocytes in asthma. J Occup Med Toxicol 2008; 3 Suppl 1:S6. [PMID: 18315837 PMCID: PMC2259400 DOI: 10.1186/1745-6673-3-s1-s6] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Asthma represents a profound worldwide public health problem. The most effective anti-asthmatic drugs currently available include inhaled beta2-agonists and glucocorticoids and control asthma in about 90-95% of patients. The current asthma therapies are not cures and symptoms return soon after treatment is stopped even after long term therapy. Although glucocorticoids are highly effective in controlling the inflammatory process in asthma, they appear to have little effect on the lower airway remodelling processes that appear to play a role in the pathophysiology of asthma at currently prescribed doses. The development of novel drugs may allow resolution of these changes. In addition, severe glucocorticoid-dependent and resistant asthma presents a great clinical burden and reducing the side-effects of glucocorticoids using novel steroid-sparing agents is needed. Furthermore, the mechanisms involved in the persistence of inflammation are poorly understood and the reasons why some patients have severe life threatening asthma and others have very mild disease are still unknown. Drug development for asthma has been directed at improving currently available drugs and findings new compounds that usually target the Th2-driven airway inflammatory response. Considering the apparently central role of T lymphocytes in the pathogenesis of asthma, drugs targeting disease-inducing Th2 cells are promising therapeutic strategies. However, although animal models of asthma suggest that this is feasible, the translation of these types of studies for the treatment of human asthma remains poor due to the limitations of the models currently used. The myriad of new compounds that are in development directed to modulate Th2 cells recruitment and/or activation will clarify in the near future the relative importance of these cells and their mediators in the complex interactions with the other pro-inflammatory/anti-inflammatory cells and mediators responsible of the different asthmatic phenotypes. Some of these new Th2-oriented strategies may in the future not only control symptoms and modify the natural course of asthma, but also potentially prevent or cure the disease.
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Affiliation(s)
- Gaetano Caramori
- Dipartimento di Medicina Clinica e Sperimentale, Centro di Ricerca su Asma e BPCO, Università di Ferrara, Ferrara, Italy
| | - David Groneberg
- Institute of Occupational Medicine, Charité- Universitätsmedizin Berlin, Free University and Humboldt University, Berlin, Germany
| | - Kazuhiro Ito
- Airway Disease Section, National Heart and Lung Institute, Imperial College of London, London, UK
| | - Paolo Casolari
- Dipartimento di Medicina Clinica e Sperimentale, Centro di Ricerca su Asma e BPCO, Università di Ferrara, Ferrara, Italy
| | - Ian M Adcock
- Airway Disease Section, National Heart and Lung Institute, Imperial College of London, London, UK
| | - Alberto Papi
- Dipartimento di Medicina Clinica e Sperimentale, Centro di Ricerca su Asma e BPCO, Università di Ferrara, Ferrara, Italy
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Blakeney JS, Reid RC, Le GT, Fairlie DP. Nonpeptidic Ligands for Peptide-Activated G Protein-Coupled Receptors. Chem Rev 2007; 107:2960-3041. [PMID: 17622179 DOI: 10.1021/cr050984g] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jade S Blakeney
- Centre for Drug Design and Development, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
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12
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Pruitt JR, Batt DG, Wacker DA, Bostrom LL, Booker SK, McLaughlin E, Houghton GC, Varnes JG, Christ DD, Covington M, Das AM, Davies P, Graden D, Kariv I, Orlovsky Y, Stowell NC, Vaddi KG, Wadman EA, Welch PK, Yeleswaram S, Solomon KA, Newton RC, Decicco CP, Carter PH, Ko SS. CC chemokine receptor-3 (CCR3) antagonists: Improving the selectivity of DPC168 by reducing central ring lipophilicity. Bioorg Med Chem Lett 2007; 17:2992-7. [PMID: 17418570 DOI: 10.1016/j.bmcl.2007.03.065] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2007] [Revised: 03/20/2007] [Accepted: 03/21/2007] [Indexed: 11/21/2022]
Abstract
DPC168, a benzylpiperidine-substituted aryl urea CCR3 antagonist evaluated in clinical trials, was a relatively potent inhibitor of the 2D6 isoform of cytochrome P-450 (CYP2D6). Replacement of the cyclohexyl central ring with saturated heterocycles provided potent CCR3 antagonists with improved selectivity against CYP2D6. The favorable preclinical profile of DPC168 was maintained in an acetylpiperidine derivative, BMS-570520.
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Affiliation(s)
- James R Pruitt
- Bristol-Myers Squibb Pharmaceutical Research Institute, PO Box 4000, Princeton, NJ 08543-4000, USA
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13
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Myznikov LV, Hrabalek A, Koldobskii GI. Drugs in the tetrazole series. (Review). Chem Heterocycl Compd (N Y) 2007. [DOI: 10.1007/s10593-007-0001-5] [Citation(s) in RCA: 198] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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14
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Ting PC, Umland SP, Aslanian R, Cao J, Garlisi CG, Huang Y, Jakway J, Liu Z, Shah H, Tian F, Wan Y, Shih NY. The synthesis of substituted bipiperidine amide compounds as CCR3 ligands: antagonists versus agonists. Bioorg Med Chem Lett 2005; 15:3020-3. [PMID: 15908209 DOI: 10.1016/j.bmcl.2005.04.054] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2005] [Revised: 04/19/2005] [Accepted: 04/19/2005] [Indexed: 11/28/2022]
Abstract
Structure-activity relationship study of bipiperidine amide 1 has identified the reverse bipiperidine amide 4a as a CC chemokine-3 (CCR3) receptor antagonist. Optimization of the structure-activity relationship of compound 4a has resulted in the identification of a CCR3 antagonist 4i as well as a CCR3 agonist 13.
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Affiliation(s)
- Pauline C Ting
- Schering Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA.
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