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Rudrapal M, Kirboga KK, Abdalla M, Maji S. Explainable artificial intelligence-assisted virtual screening and bioinformatics approaches for effective bioactivity prediction of phenolic cyclooxygenase-2 (COX-2) inhibitors using PubChem molecular fingerprints. Mol Divers 2024:10.1007/s11030-023-10782-9. [PMID: 38200203 DOI: 10.1007/s11030-023-10782-9] [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: 07/11/2023] [Accepted: 11/22/2023] [Indexed: 01/12/2024]
Abstract
Cyclooxygenase-2 (COX-2) inhibitors are nonsteroidal anti-inflammatory drugs that treat inflammation, pain and fever. This study determined the interaction mechanisms of COX-2 inhibitors and the molecular properties needed to design new drug candidates. Using machine learning and explainable AI methods, the inhibition activity of 1488 molecules was modelled, and essential properties were identified. These properties included aromatic rings, nitrogen-containing functional groups and aliphatic hydrocarbons. They affected the water solubility, hydrophobicity and binding affinity of COX-2 inhibitors. The binding mode, stability and ADME properties of 16 ligands bound to the Cyclooxygenase active site of COX-2 were investigated by molecular docking, molecular dynamics simulation and MM-GBSA analysis. The results showed that ligand 339,222 was the most stable and effective COX-2 inhibitor. It inhibited prostaglandin synthesis by disrupting the protein conformation of COX-2. It had good ADME properties and high clinical potential. This study demonstrated the potential of machine learning and bioinformatics methods in discovering COX-2 inhibitors.
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Affiliation(s)
- Mithun Rudrapal
- Department of Pharmaceutical Sciences, School of Biotechnology and Pharmaceutical Sciences, Vignan's Foundation for Science, Technology & Research (Deemed to Be University), Guntur, 522213, India.
| | - Kevser Kübra Kirboga
- Informatics Institute, Istanbul Technical University, 34469, Maslak, Istanbul, Turkey.
- Bioengineering Department, BilecikSeyhEdebali University, 11230, Bilecik, Turkey.
| | - Mohnad Abdalla
- Pediatric Research Institute, Children's Hospital Affiliated to Shandong University, Jinan, 250022, Shandong, People's Republic of China
| | - Siddhartha Maji
- Department of Chemistry, Oklahoma State University, Stillwater, OK, USA
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Ease to Challenges in Achieving Successful Synthesized Schiff Base, Chirality, and Application as Antibacterial Agent. BIOMED RESEARCH INTERNATIONAL 2023. [DOI: 10.1155/2023/1626488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
This study reports how to overcome the challenges experienced in achieving successful synthesized Schiff base via types of Schiff base (chiral and achiral), synthesis, nature of products, and its antibacterial applications. Schiff base is a versatile ligand which is useful in asymmetric reactions to prepare chiral catalysts. It is also used in symmetric reactions to prepare achiral compounds. In line with the achiral compounds, conventional (room temperature and refluxing) and microwave irradiation methods are the two main types of methods to synthesize achiral Schiff base as reported in this review. Among various experimental approaches, this study supports the green chemistry microwave approach to synthesize Schiff base because of its benefits environmental sustainability. Problems relating to the nature of products formed from the synthesized Schiff bases were examined and resolved. Herein, the products could either be solid (crystals, powder, and precipitate), oily, or viscous (sticky) products. Some familiar characterization techniques used to identify and confirm the successful syntheses of Schiff bases, such as solubility test, melting point (MP), Fourier transform infrared (FTIR), ultraviolet-visible (UV-Vis), and nuclear magnetic resonance (NMR, 1H NMR, and 13C NMR), were discussed. In addition, the antibacterial studies on Schiff base and corresponding metal complexes confirmed their biological relevance to the human.
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Li J, Chen M, Jiang J, Huang J, Chen H, Pan L, Nesterov DS, Ma Z, Pombeiro AJL. A New Concept of Enhancing the Anticancer Activity of Manganese Terpyridine Complex by Oxygen-Containing Substituent Modification. Int J Mol Sci 2023; 24:ijms24043903. [PMID: 36835315 PMCID: PMC9963696 DOI: 10.3390/ijms24043903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 01/31/2023] [Accepted: 02/02/2023] [Indexed: 02/17/2023] Open
Abstract
Eleven manganese 4'-substituted-2,2':6',2″-terpyridine complexes (1a-1c and 2a-2h) with three non-oxygen-containing substituents (L1a-L1c: phenyl, naphthalen-2-yl and naphthalen-1-yl, L1a-L1c) and eight oxygen-containing substituents (L2a-L2h: 4-hydroxyl-phenyl, 3-hydroxyl-phenyl, 2-hydroxyl-phenyl, 4-methoxyl-phenyl, 4-carboxyl-phenyl, 4-(methylsulfonyl)phenyl, 4-nitrophenyl and furan-2-yl) were prepared and characterized by IR, elemental analysis or single crystal X-ray diffraction. In vitro data demonstrate that all of these show higher antiproliferative activities than cisplatin against five human carcinoma cell lines: A549, Bel-7402, Eca-109, HeLa and MCF-7. Compound 2d presents the strongest antiproliferative effect against A549 and HeLa cells, with IC50 values being 0.281 μM and 0.356 μM, respectively. The lowest IC50 values against Bel-7402 (0.523 μM) Eca-109 (0.514 μM) and MCF-7 (0.356 μM) were obtained for compounds 2h, 2g and 2c, respectively. Compound 2g with a nitro group showed the best results on the whole, with relevantly low IC50 values against all the tested tumor cells. The DNA interactions with these compounds were studied by circular dichroism spectroscopic and molecular modeling methods. Spectrophotometric results revealed that the compounds have strong affinities in binding with DNA as intercalators, and the binding induces DNA conformational transition. Molecular docking studies indicate that the binding is contributed by the π-π stacking and hydrogen bonds. The anticancer activities of the compounds are correlated with their DNA binding ability, and the modification of oxygen-containing substituents significantly enhanced the anticancer activity, which could provide a new rationale for the future design of terpyridine-based metal complexes with antitumor potential.
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Affiliation(s)
- Jiahe Li
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
- National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning 530007, China
- Centro de Química Estrutural, Institute of Molecular Sciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal
| | - Min Chen
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Jinzhang Jiang
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Jieyou Huang
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Hailan Chen
- School of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Lixia Pan
- National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning 530007, China
- Correspondence: (L.P.); or (Z.M.)
| | - Dmytro S. Nesterov
- Centro de Química Estrutural, Institute of Molecular Sciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal
| | - Zhen Ma
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
- Centro de Química Estrutural, Institute of Molecular Sciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal
- Correspondence: (L.P.); or (Z.M.)
| | - Armando J. L. Pombeiro
- Centro de Química Estrutural, Institute of Molecular Sciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal
- Research Institute of Chemistry, Peoples’ Friendship University of Russia (RUDN University), Moscow 117198, Russia
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Kumar A, Mishra R, Mazumder A, Mazumder R, Varshney S. Exploring Synthesis and Chemotherapeutic Potential of Thiosemicarbazide Analogs. Anticancer Agents Med Chem 2023; 23:60-75. [PMID: 35658880 DOI: 10.2174/1871520622666220603090626] [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: 02/16/2022] [Revised: 04/20/2022] [Accepted: 04/25/2022] [Indexed: 02/08/2023]
Abstract
BACKGROUND Cancer is a leading cause of death worldwide, accounting for nearly 10 million deaths in 2020. Researchers are continually finding new and more effective medications to battle the diseases. OBJECTIVE The objective of this study is to identify the emerging role of Thiosemicarbazide analogs for different types of cancer targets with a glance at different novel synthetic routes reported for their synthesis. METHODS A systematic literature review was conducted from various sources over the last 15 years with the inclusion of published research and review articles that involves the synthesis and use of thiosemicarbazide analogs for different targets of cancer. Data from the literature review for synthesis and anticancer potential for specific targets for cancer studies of thiosemicarbazide analogs are summarized in the paper. RESULTS There are several emerging studies for new synthetic routes of thiosemicarbazide derivatives with their role in various types of cancers. The main limitation is the lack of clinical trial of the key findings for the emergence of new anticancer medication with thiosemicarbazide moiety. CONCLUSION Emerging therapies exist for use of a limited number of medications for the treatment of cancer; results of the ongoing studies will provide more robust evidence in the future.
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Affiliation(s)
- Akhalesh Kumar
- Department of Pharmaceutical Chemistry, Noida Institute of Engineering and Technology (Pharmacy Institute), Knowledge park-2, Plot 19, Greater Noida, India
| | - Rakhi Mishra
- Department of Pharmaceutical Chemistry, Noida Institute of Engineering and Technology (Pharmacy Institute), Knowledge park-2, Plot 19, Greater Noida, India
| | - Avijit Mazumder
- Department of Pharmaceutical Chemistry, Noida Institute of Engineering and Technology (Pharmacy Institute), Knowledge park-2, Plot 19, Greater Noida, India
| | - Rupa Mazumder
- Department of Pharmaceutical Chemistry, Noida Institute of Engineering and Technology (Pharmacy Institute), Knowledge park-2, Plot 19, Greater Noida, India
| | - Shruti Varshney
- Department of Pharmaceutical Chemistry, Noida Institute of Engineering and Technology (Pharmacy Institute), Knowledge park-2, Plot 19, Greater Noida, India
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Chai Y, Li C, Zhang X, Chai L. Antimicrobial activities of two 1‐D, 2‐D and 3‐D mononuclear Mn (II) and dinuclear Bi (III) complexes: X‐ray structures, spectroscopic, ESP, HSA and TD/DFT studies. Appl Organomet Chem 2022. [DOI: 10.1002/aoc.6682] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Yong‐Mei Chai
- School of Chemistry and Chemical Engineering Lanzhou Jiaotong University Lanzhou China
| | - Cheng‐Guo Li
- School of Chemistry and Chemical Engineering Lanzhou Jiaotong University Lanzhou China
| | - Xiao‐Fang Zhang
- School of Chemistry and Chemical Engineering Lanzhou Jiaotong University Lanzhou China
| | - Lan‐Qin Chai
- School of Chemistry and Chemical Engineering Lanzhou Jiaotong University Lanzhou China
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Cherukumalli PKR, Tadiboina BR, Gulipalli KC, Bodige S, Badavath VN, Sridhar G, Gangarapu K. Design and synthesis of novel urea derivatives of pyrimidine-pyrazoles as anticancer agents. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131937] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Manganese(II) catalyzed synthesis of bis(N-cyclohexylthiourea) derived from thiosemicarbazide: Structural characterization, fluorescence, cyclic voltammetry, Hirshfeld surface analysis and DFT calculation. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.131060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Aita S, Badavath VN, Gundluru M, Sudileti M, Nemallapudi BR, Gundala S, Zyryanov GV, Chamarti NR, Cirandur SR. Novel α-Aminophosphonates of imatinib Intermediate: Synthesis, anticancer Activity, human Abl tyrosine kinase Inhibition, ADME and toxicity prediction. Bioorg Chem 2021; 109:104718. [PMID: 33618257 DOI: 10.1016/j.bioorg.2021.104718] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/13/2021] [Accepted: 02/01/2021] [Indexed: 02/07/2023]
Abstract
An efficient method for the synthesis of a new class of α-aminophosphonates of imatinib derivative has been developed in one-pot Kabachnik-Fields reaction of N-(5-amino-2-methyl phenyl)-4-(3-pyridyl)-2-pyrimidine amine with various aldehydes and diethyl phosphite under microwave irradiation and neat conditions using NiO nanoparticles as an reusable and heterogeneous catalyst, with 96% yield at 450 W within 15 min. All the compounds were evaluated for their in vitro cytotoxicity with various cancer cell lines by MTT assay method. Compounds with halo (4f, -4Br, IC50 = 1.068 ± 0.88 µM to 2.033 ± 0.97 µM), nitro substitution (4 h, -3NO2, IC50 = 1.380 ± 0.94 µM to 2.213 ± 0.64 µM), (4 g, -4NO2, IC50 = 1.402 ± 0.79 µM to 2.335 ± 0.73 µM) and (4i, 4-Cl, 3-NO2, IC50 = 1.437 ± 0.92 µM to 2.558 ± 0.76 µM) were showed better anticancer activity when compared with standard drugs Doxorubicin and Imatinib using MTT assay method. Further in silico target hunting reveals the anticancer activity of the designed compounds by inhibiting human ABL tyrosine kinase and all the designed compounds have shown significant drug-like characteristics.
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Affiliation(s)
- Saikiran Aita
- Department of Chemistry, Sri Venkateswara University, Tirupati 517 502, A.P., India.
| | - Vishnu Nayak Badavath
- Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem 9112001, Israel.
| | - Mohan Gundluru
- Department of Chemistry, Sri Venkateswara University, Tirupati 517 502, A.P., India; DST-PURSE Centre, Sri Venkateswara University, Tirupati-517502, A.P., India.
| | - Murali Sudileti
- Department of Chemistry, Sri Venkateswara University, Tirupati 517 502, A.P., India.
| | | | - Sravya Gundala
- Chemical Engineering Institute, Ural Federal University, Yekaterinburg 620002, Russian Federation.
| | - Grigoriy Vasilievich Zyryanov
- Chemical Engineering Institute, Ural Federal University, Yekaterinburg 620002, Russian Federation; Ural Division of the Russian Academy of Sciences, I. Ya. Postovskiy Institute of Organic Synthesis, 22 S. Kovalevskoy Street, Yekaterinburg 620219, Russian Federation.
| | - Naga Raju Chamarti
- Department of Chemistry, Sri Venkateswara University, Tirupati 517 502, A.P., India.
| | - Suresh Reddy Cirandur
- Department of Chemistry, Sri Venkateswara University, Tirupati 517 502, A.P., India.
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9
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Nasseri MA, Rezazadeh Z, Kazemnejadi M, Allahresani A. Cu-Mn Bimetallic Complex Immobilized on Magnetic NPs as an Efficient Catalyst for Domino One-Pot Preparation of Benzimidazole and Biginelli Reactions from Alcohols. Catal Letters 2020. [DOI: 10.1007/s10562-020-03371-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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10
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Gómez-Machuca H, Quiroga-Campano C, Zapata-Torres G, Jullian C. Influence of DMβCD on the Interaction of Copper(II) Complex of 6-Hydroxychromone-3-carbaldehyde-3-hydroxybenzoylhydrazine with ctDNA. ACS OMEGA 2020; 5:6928-6936. [PMID: 32258929 PMCID: PMC7114617 DOI: 10.1021/acsomega.0c00275] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 03/10/2020] [Indexed: 05/04/2023]
Abstract
The interaction mechanism between a scarcely soluble copper(II) complex of Cu(II)-6-hydroxychromone-3-carbaldehyde-(3'-hydroxy)benzoylhydrazone (CuCHz) in aqueous solution and its DMβCD complex was studied in the presence of ctDNA through spectroscopy and thermodynamic methods. The thermodynamic results indicate that the binding process of the CuCHz-DMβCD inclusion complex is a spontaneous process and the inclusion is enthalpy-driven. The binding constants of CuCHz and CuCHz-DMβCD with ctDNA are 2.69 × 103 and 14.7 × 103 L mol-1, respectively. The stoichiometry of the complex is 1:1, and the determined thermodynamic indicates that the process of binding is spontaneous and entropy-driven. A competitive binding titration with ethidium bromide revealed that CuCHz efficiently displaces EB from the EB-DNA system. In addition to the thermal denaturation experiments and docking studies, we can confirm that the mode of binding of this complex to ctDNA is intercalation mode. The presence of DMβCD enhances the aqueous solubility of CuCHz; nevertheless, the cyclodextrin did not affect the interaction of CuCHz with ctDNA because the inclusion complex breaks down when it binds with ctDNA.
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Affiliation(s)
- Horacio Gómez-Machuca
- Departamento
de Química Orgánica y Fisicoquímica,
Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Olivos 1007, Independencia, Santiago 8380492, Chile
| | - Cinthia Quiroga-Campano
- Departamento
de Química Orgánica y Fisicoquímica,
Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Olivos 1007, Independencia, Santiago 8380492, Chile
| | - Gerald Zapata-Torres
- Departamento
de Química Inorgánica y Analítica,
Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Olivos 1007, Independencia, Santiago 8380492, Chile
| | - Carolina Jullian
- Departamento
de Química Orgánica y Fisicoquímica,
Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Olivos 1007, Independencia, Santiago 8380492, Chile
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Reddy Gangireddy M, Mantipally M, Gundla R, Nayak Badavath V, Paidikondala K, Yamala A. Design and Synthesis of Piperazine‐Linked Imidazo[1,2‐
a
]pyridine Derivatives as Potent Anticancer Agents. ChemistrySelect 2019. [DOI: 10.1002/slct.201902955] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
| | - Manohar Mantipally
- Department of ChemistrySchool of TechnologyGITAM University Hyderabad 502329,Telangana India
| | - Rambabu Gundla
- Department of ChemistrySchool of TechnologyGITAM University Hyderabad 502329,Telangana India
| | - Vishnu Nayak Badavath
- Department of MicrobiologyFaculty of MedicineChulalongkorn University, Pathumwan Bangkok- 10330 Thailand
| | - Kalyani Paidikondala
- Department of ChemistrySchool of TechnologyGITAM University Hyderabad 502329,Telangana India
| | - Anilkumar Yamala
- School of Engineering Science and TechnologyUniversity of Hyderabad, Hyderabad India
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Saravanabhavan M, Badavath VN, Maji S, Muhammad S, Sekar M. Novel halogenated pyrido[2,3-a]carbazoles with enhanced aromaticity as potent anticancer and antioxidant agents: rational design and microwave assisted synthesis. NEW J CHEM 2019. [DOI: 10.1039/c8nj06504g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Design and synthesis a series of pyrido[2,3-a]carbazoles for their anticancer and antioxidant activity.
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Affiliation(s)
- Munusamy Saravanabhavan
- Department of Chemistry
- Sri Ramakrishna Mission Vidyalaya College of Arts and Science
- Coimbatore-641020
- India
- Department of Chemistry
| | - Vishnu Nayak Badavath
- Applied Medical Virology Research Unit
- Department of Microbiology
- Faculty of Medicine
- Chulalongkorn University
- Bangkok
| | - Siddhartha Maji
- Department of Pharmaceutical Sciences and Technology
- Birla Institute of Technology
- Ranchi
- India
| | - Shabbir Muhammad
- Department of Physics
- College of Science
- King Khalid University
- Abha
- Saudi Arabia
| | - Marimuthu Sekar
- Department of Chemistry
- Sri Ramakrishna Mission Vidyalaya College of Arts and Science
- Coimbatore-641020
- India
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