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Achiri R, Fouzia M, Benomari FZ, Djabou N, Boufeldja T, Muselli A, Dib MEA. Chemical composition/pharmacophore modelling- based, virtual screening, molecular docking and dynamic simulation studies for the discovery of novel superoxide dismutase ( SODs) of bioactive molecules from aerial parts of Inula Montana as antioxydant's agents. J Biomol Struct Dyn 2022; 40:12439-12460. [PMID: 34472418 DOI: 10.1080/07391102.2021.1971563] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The accumulation of free radicals in the body develops chronic and degenerative diseases such as cancer, autoimmune diseases, rheumatoid arthritis, cardiovascular and neurodegenerative diseases. The first aim of this work was to study the chemical composition of Inula Montana essential oil using GC-FID and GC/MS analysis and the antioxidant activities using radical scavenging (DPPH) and the Ferric -Reducing Antioxidant Power (FRAP) tests. The second aim was to describe the assess the antioxidant activity and computational study of Superoxide Dismutase (SODs) and ctDNA inhibition. Sixty-nine compounds were identified in the essential oil of the aerial part of Inula montana. Shyobunol and α-Cadinol were the major compounds in the essential oil. The antioxidant power of the essential oil showed an important antioxidant effect compared to ascorbic acid and the methionine co-crystallized inhibitor. The results of the docking simulation revealed that E, E-Farnesyl acetate has an affinity to interact with binding models and the antioxidant activities of the ctDNA sequence and Superoxide Dismutase target. The penetration through the Blood-Brain Barrier came out to be best for E, E-Farnesyl acetate and E-Nerolidolacetate and was significantly higher than the control molecule and Lref. Finally, the application of ADMET filters gives us positive information on the compound E, E-Farnesyl acetate, which appears as a new inhibitor potentially more active towards ctDNA and SODs target. The active compounds, E,E-Farnesyl acetate can be used as templates for further development of more potent antioxidative agents.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Radja Achiri
- Laboratoire des Substances Naturelles & Bioactives (LASNABIO), Département de Chimie, Faculté des Sciences, Université Abou BekrBelkaıd, Tlemcen, Algeria
| | - Mesli Fouzia
- Laboratoire des Substances Naturelles & Bioactives (LASNABIO), Département de Chimie, Faculté des Sciences, Université Abou BekrBelkaıd, Tlemcen, Algeria
| | - Fatima Zohra Benomari
- Laboratoire de Chimie Organique, Substances Naturelles et Analyses (COSNA), Faculte des Sciences, Universite Abou BekrBelkaıd, Tlemcen, Algeria
| | - Nassim Djabou
- Laboratoire de Chimie Organique, Substances Naturelles et Analyses (COSNA), Faculte des Sciences, Universite Abou BekrBelkaıd, Tlemcen, Algeria
| | - Tabti Boufeldja
- Laboratoire des Substances Naturelles & Bioactives (LASNABIO), Département de Chimie, Faculté des Sciences, Université Abou BekrBelkaıd, Tlemcen, Algeria
| | - Alain Muselli
- Laboratoire Chimie des Produits Naturels, Université de Corse, UMR CNRS 6134, Corté, France
| | - Mohammed El Amine Dib
- Laboratoire des Substances Naturelles & Bioactives (LASNABIO), Département de Chimie, Faculté des Sciences, Université Abou BekrBelkaıd, Tlemcen, Algeria
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Gowtham HG, Murali M, Singh SB, Shivamallu C, Pradeep S, Shivakumar CS, Anandan S, Thampy A, Achar RR, Silina E, Stupin V, Ortega-Castro J, Frau J, Flores-Holguín N, Amruthesh KN, Kollur SP, Glossman-Mitnik D. Phytoconstituents of Withania somnifera unveiled Ashwagandhanolide as a potential drug targeting breast cancer: Investigations through computational, molecular docking and conceptual DFT studies. PLoS One 2022; 17:e0275432. [PMID: 36201520 PMCID: PMC9536605 DOI: 10.1371/journal.pone.0275432] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 09/12/2022] [Indexed: 11/18/2022] Open
Abstract
Breast cancer is the second most common malignancy in females worldwide and poses a great challenge that necessitates the identification of novel therapeutic agents from several sources. This research aimed to study the molecular docking and molecular dynamics simulations of four proteins (such as PDB: 6CBZ, 1FDW, 5GWK and 2WTT) with the selected phytochemicals from Withania somnifera to identify the potential inhibitors for breast cancer. The molecular docking result showed that among 44 compounds, two of them, Ashwagandhanolide and Withanolide sulfoxide have the potential to inhibit estrogen receptor alpha (ERα), 17-beta-hydroxysteroid -dehydrogenase type 1 (17β-HSD1), topoisomerase II alpha (TOP2A) and p73 tetramerization domain that are expressed during breast cancer. The molecular dynamics (MD) simulations results suggested that Ashwagandhanolide remained inside the binding cavity of four targeted proteins and contributed favorably towards forming a stable protein-ligand complex throughout the simulation. Absorption, Distribution, Metabolism, Excretion and Toxicity (ADMET) properties confirmed that Ashwagandhanolide is hydrophobic and has moderate intestinal permeability, good intestinal absorption, and poor skin permeability. The compound has a relatively low VDss value (-1.652) and can be transported across ABC transporter and good central nervous system (CNS) permeability but did not easily cross the blood-brain barrier (BBB). This compound does not possess any mutagenicity, hepatotoxicity and skin sensitization. Based on the results obtained, the present study highlights the anticancer potential of Ashwagandhanolide, a compound from W. somnifera. Furthermore, in vitro and in vivo studies are necessary to perform before clinical trials to prove the potentiality of Ashwagandhanolide.
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Affiliation(s)
| | - Mahadevamurthy Murali
- Applied Plant Pathology Laboratory, Department of Studies in Botany, University of Mysore, Manasagangotri, Mysore, Karnataka, India
| | | | - Chandan Shivamallu
- Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru, Karnataka, India
| | - Sushma Pradeep
- Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru, Karnataka, India
| | - C. S. Shivakumar
- Department of Clinical Nutrition and Dietetics, Sri Devaraj Urs Academy of Higher Education and Research, Kolar, Karnataka, India
| | - Satish Anandan
- Department of Clinical Nutrition and Dietetics, Sri Devaraj Urs Academy of Higher Education and Research, Kolar, Karnataka, India
- * E-mail: (SA); (KNA); (SPK); (DGM)
| | - Anjana Thampy
- Department of Clinical Nutrition and Dietetics, Sri Devaraj Urs Academy of Higher Education and Research, Kolar, Karnataka, India
| | - Raghu Ram Achar
- Division of Biochemistry, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru, Karnataka, India
| | - Ekaterina Silina
- Department of Human Pathology, I. M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Victor Stupin
- Department of Hospital Surgery, N.I. Pirogov Russian National Research Medical University (RNRMU), Moscow, Russia
| | | | - Juan Frau
- Departament de Química, Universitat de les Illes Balears, Palma de Malllorca, Spain
| | - Norma Flores-Holguín
- Laboratorio Virtual NANOCOSMOS, Departamento de Medio Ambiente y Energía, Centro de Investigación en Materiales Avanzados, Chih, México
| | - Kestur Nagaraj Amruthesh
- Applied Plant Pathology Laboratory, Department of Studies in Botany, University of Mysore, Manasagangotri, Mysore, Karnataka, India
- * E-mail: (SA); (KNA); (SPK); (DGM)
| | - Shiva Prasad Kollur
- School of Agriculture, Geography, Environment, Ocean and Natural Sciences (SAGEONS), University of the South Pacific, Laucala Campus, Suva, Fiji
- Department of Sciences, Amrita School of Arts and Sciences, Amrita Vishwa Vidyapeetham, Mysuru Campus, Mysore, Karnataka, India
- * E-mail: (SA); (KNA); (SPK); (DGM)
| | - Daniel Glossman-Mitnik
- Laboratorio Virtual NANOCOSMOS, Departamento de Medio Ambiente y Energía, Centro de Investigación en Materiales Avanzados, Chih, México
- * E-mail: (SA); (KNA); (SPK); (DGM)
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Sing LC, Roy A, Hui LY, Mun CS, Rajak H, Karunakaran R, Ravichandran V. Multi-targeted molecular docking, drug-likeness and ADMET studies of derivatives of few quinoline- and acridine-based FDA-approved drugs for anti-breast cancer activity. Struct Chem 2022. [DOI: 10.1007/s11224-022-01878-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Li X, Wang Q, Wu Z, Zheng J, Ji L. Integrated Bioinformatics Analysis for Identification of the Hub Genes Linked with Prognosis of Ovarian Cancer Patients. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:5113447. [PMID: 35047055 PMCID: PMC8763496 DOI: 10.1155/2022/5113447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 10/22/2021] [Accepted: 11/17/2021] [Indexed: 11/17/2022]
Abstract
BACKGROUND One of the most usual gynecological state of tumor is ovarian cancer and is a major reason of gynecological tumor-related global mortality rate. There have been multiple risk elements related to ovarian cancer like the background of past cases associated with breast cancer or ovarian cancer, or excessive body weight issues, case history of smoking, and untimely menstruation or menopause. Because of unclear expressions, more than 70% of the ovarian cancer patient cases are determined during the early stage. Material and Methods. GSE38666, GSE40595, and GSE66957 were the three microarray datasets which were analyzed using GEO2R for screening the differentially expressed genes. GO, Kyoto Encyclopedia of Genes, and protein expression studies were performed for analysis of hub genes. Then, survival analysis was performed for all the hub genes. RESULTS From the dataset, a total of 199 differentially expressed genes (DEGs) were identified. Through the KEGG pathway study, it was noted that the DEGs are mainly linked with the AGE-RAGE signaling pathway, central carbon metabolism, and human papillomavirus infection. The survival analysis showed 4 highly expressed hub genes COL4A1, SDC1, CDKN2A, and TOP2A which correlated with overall survival in ovarian cancer patients. Moreover, the expression of the 4 hub genes was validated by the GEPIA database and the Human Protein Atlas. CONCLUSION The results have shown that all 4 hub genes were found to be upregulated in ovarian cancer tissues which predict poor prognosis in patients with ovarian cancer.
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Affiliation(s)
- Xiaofeng Li
- Department of Laboratory Medicine, Peking University Shenzhen Hospital, Shenzhen, China
| | - Qiu Wang
- Department of Laboratory Medicine, Peking University Shenzhen Hospital, Shenzhen, China
| | - Zhicheng Wu
- Department of Laboratory Medicine, Peking University Shenzhen Hospital, Shenzhen, China
| | | | - Ling Ji
- Department of Laboratory Medicine, Peking University Shenzhen Hospital, Shenzhen, China
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Majumder R, Das CK, Banerjee I, Chandra Jena B, Mandal A, Das P, Pradhan AK, Das S, Basak P, Das SK, Emdad L, Fisher PB, Mandal M. Screening of the Prime bioactive compounds from Aloe vera as potential anti-proliferative agents targeting DNA. Comput Biol Med 2021; 141:105052. [PMID: 34836625 DOI: 10.1016/j.compbiomed.2021.105052] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/31/2021] [Accepted: 11/16/2021] [Indexed: 11/27/2022]
Abstract
BACKGROUND Aloe vera extract and its bioactive compounds possess anti-proliferative properties against cancer cells. However, no detailed molecular mechanism of action studies has been reported. We have now employed a computational approach to scrutinize the molecular mechanism of lead bioactive compounds from Aloe vera that potentially inhibit DNA synthesis. METHODS Initially, the anti-proliferative activity of Aloe vera extract was examined in human breast cancer cells (in vitro/in vivo). Later on, computational screening of bioactive compounds from Aloe vera targeting DNA was performed by molecular docking and molecular dynamics simulation. RESULTS In-vitro and in-vivo studies confirm that Aloe vera extract effectively suppresses the growth of breast cancer cells without significant cytotoxicity towards non-cancerous normal immortal cells. Computational screening predicts that growth suppression may be due to the presence of DNA intercalating bioactive compounds (riboflavin, daidzin, aloin, etc.) contained in Aloe vera. MM/PBSA calculation showed that riboflavin has a higher binding affinity at the DNA binding sites compared to standard drug daunorubicin. CONCLUSIONS These observations support the hypothesis that riboflavin may be exploited as an anti-proliferative DNA intercalating agent to prevent cancer and is worthy of testing for the management of cancer by performing more extensive pre-clinical and if validated clinical trials.
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Affiliation(s)
- Ranabir Majumder
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, West Bengal, India
| | - Chandan Kanta Das
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, West Bengal, India
| | - Indranil Banerjee
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, West Bengal, India
| | - Bikash Chandra Jena
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, West Bengal, India
| | - Anik Mandal
- Electronics and Electrical Communication Engineering, Indian Institute of Technology Kharagpur, West Bengal, India
| | - Pratik Das
- School of Bioscience and Engineering, Jadavpur University, Kolkata, West Bengal, India
| | - Anjan Kumar Pradhan
- Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, VA, 23298, USA
| | - Subhasis Das
- Patient-Derived Models Core Lab, University of Illinois Cancer Center and Department of Surgery, College of Medicine, University of Illinois at Chicago, Chicago, 60612, USA
| | - Piyali Basak
- School of Bioscience and Engineering, Jadavpur University, Kolkata, West Bengal, India
| | - Swadesh K Das
- Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, VA, 23298, USA
| | - Luni Emdad
- Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, VA, 23298, USA
| | - Paul B Fisher
- Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, VA, 23298, USA
| | - Mahitosh Mandal
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, West Bengal, India.
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Hoque MM, Bari MA, Khan MW. Rh(II)‐mediated one‐pot synthesis of dihydrobenzofuran and spiro[2.5]oct‐1‐ene: Experimental and DFT studies. J PHYS ORG CHEM 2021. [DOI: 10.1002/poc.4300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Mohammad Mazharol Hoque
- Department of Chemistry Bangladesh University of Engineering and Technology Dhaka Bangladesh
| | - Md. Abdul Bari
- Department of Chemistry Bangladesh University of Engineering and Technology Dhaka Bangladesh
| | - Md. Wahab Khan
- Department of Chemistry Bangladesh University of Engineering and Technology Dhaka Bangladesh
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Mohamed AA, Elshafie HS, Sadeek SA, Camele I. Biochemical Characterization, Phytotoxic Effect and Antimicrobial Activity against Some Phytopathogens of New Gemifloxacin Schiff Base Metal Complexes. Chem Biodivers 2021; 18:e2100365. [PMID: 34288421 DOI: 10.1002/cbdv.202100365] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 06/29/2021] [Indexed: 01/03/2023]
Abstract
String of Fe(III), Cu(II), Zn(II) and Zr(IV) complexes were synthesized with tetradentateamino Schiff base ligand derived by condensation of ethylene diamine with gemifloxacin. The novel Schiff base (4E,4'E)-4,4'-(ethane-1,2-diyldiazanylylidene)bis{7-[(4Z)-3-(aminomethyl)-4-(methoxyimino)pyrrolidin-1-yl]-1-cyclopropyl-6-fluoro-1,4-dihydro-1,8-naphthyridine-3-carboxylic acid} (GMFX-en) and its metal complexes were identified and confirmed by elemental analyses, FT-IR, UV/VIS, 1 H-NMR spectra, magnetic susceptibility, conductometric measurements and thermal analyses. The FT-IR spectral data showed the chelation behavior of GMFX-en toward the metal ions through oxygen of carboxylate group and nitrogen of azomethine group. In the light of all spectral data, these complexes presumably have octahedral geometry configurations. Thermal analysis specified that the decaying of the metal complexes exist in two or three steps with the final residue metal oxides. Antimicrobial activity of the new prepared metal complexes was screened against some common phytopathogens and their mode of action has been also discussed. The potential phytotoxic effectiveness of the new complexes was furthermore inspected on two commonly experimental plants. The complexes showed significant antimicrobial and phytotoxic effects against the majority of tested phytopathogens and the two tested plants, respectively. The potential antimicrobial activity of the complexes proved their possibility to be used successfully in agropharmacutical industry to control many serious phytopathogens. The phytotoxicity of the studied complexes also indicated their possibility as potential bio-based herbicides alternatives to weed control in crop fields.
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Affiliation(s)
- Amira A Mohamed
- Department of Basic Science, Zagazig Higher Institute of Engineering and Technology, 44519, Zagazig, Egypt
| | - Hazem S Elshafie
- School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, Viale dell'Ateneo Lucano 10, 85100, Potenza, Italy
| | - Sadeek A Sadeek
- Department of Chemistry, Faculty of Science, Zagazig University, 44519, Zagazig, Egypt
| | - Ippolito Camele
- School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, Viale dell'Ateneo Lucano 10, 85100, Potenza, Italy
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Dhaiban S, Al-Ani M, Elemam NM, Maghazachi AA. Targeting Chemokines and Chemokine Receptors in Multiple Sclerosis and Experimental Autoimmune Encephalomyelitis. J Inflamm Res 2020; 13:619-633. [PMID: 33061527 PMCID: PMC7532903 DOI: 10.2147/jir.s270872] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 08/27/2020] [Indexed: 12/13/2022] Open
Abstract
Multiple sclerosis (MS) is an immune-mediated and neurodegenerative disorder that results in inflammation and demyelination of the central nervous system (CNS). MS symptoms include walking difficulties, visual weakening, as well as learning and memory impairment, thus affecting the quality of the patient's life. Chemokines and chemokine receptors are expressed on the immune cells as well as the CNS resident cells. Several sets of chemokine receptors and their ligands tend to be pathogenic players in MS, including CCL2, CCL3, CCL4, CCL5, CCL7, CCL8, CCL11, CCL17, CCL19, CCL21, CCL22, CXCL1, CXCL8, CXCL9, CXCL10, CXCL11, and CXCL16. Furthermore, current modulatory drugs that are used in the treatment of MS and its animal model, the experimental autoimmune encephalomyelitis (EAE), affect the expression of several chemokine and chemokine receptors. In this review, we highlight the pathogenic roles of chemokines and their receptors as well as utilizing them as potential therapeutic targets through selective agents, such as specific antibodies and receptor blockers, or indirectly through MS or EAE immunomodulatory drugs.
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Affiliation(s)
- Sarah Dhaiban
- College of Medicine and Immuno-Oncology Group, Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Mena Al-Ani
- College of Medicine and Immuno-Oncology Group, Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Noha Mousaad Elemam
- College of Medicine and Immuno-Oncology Group, Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Azzam A Maghazachi
- College of Medicine and Immuno-Oncology Group, Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
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Hoque MM, Hussen MS, Kumer A, Khan MW. Synthesis of 5, 6-diaroylisoindoline-1, 3-dione and computational approaches for investigation on structural and mechanistic insights by DFT. MOLECULAR SIMULATION 2020. [DOI: 10.1080/08927022.2020.1811866] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Mohammad Mazharol Hoque
- Department of Chemistry, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh
| | - Md. Sajib Hussen
- Department of Chemistry, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh
| | - Ajoy Kumer
- Department of Chemistry, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh
| | - Md. Wahab Khan
- Department of Chemistry, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh
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Radaeva M, Dong X, Cherkasov A. The Use of Methods of Computer-Aided Drug Discovery in the Development of Topoisomerase II Inhibitors: Applications and Future Directions. J Chem Inf Model 2020; 60:3703-3721. [DOI: 10.1021/acs.jcim.0c00325] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Mariia Radaeva
- Vancouver Prostate Centre, University of British Columbia, 2660 Oak Street, Vancouver, British Columbia V6H 3Z6, Canada
| | - Xuesen Dong
- Vancouver Prostate Centre, University of British Columbia, 2660 Oak Street, Vancouver, British Columbia V6H 3Z6, Canada
| | - Artem Cherkasov
- Vancouver Prostate Centre, University of British Columbia, 2660 Oak Street, Vancouver, British Columbia V6H 3Z6, Canada
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Sirazhetdinova NS, Savelyev VA, Frolova TS, Baev DS, Klimenko LS, Chernikov IV, Oleshko OS, Sarojan TA, Pokrovskii AG, Shults EE. 1-Hydroxyanthraquinones Containing Aryl Substituents as Potent and Selective Anticancer Agents. Molecules 2020; 25:molecules25112547. [PMID: 32486108 PMCID: PMC7321108 DOI: 10.3390/molecules25112547] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 05/27/2020] [Accepted: 05/28/2020] [Indexed: 12/16/2022] Open
Abstract
A series of 1,2-, 1,4-disubstituted or 1,2,4-trisubstituted anthraquinone-based compounds was designed, synthesized, characterized and biologically evaluated for anticancer efficacy. 2- or 4-arylated 1-hydroxy-9,10-antraquinones (anthracene-9,10-diones) were prepared by Suzuki–Miyaura cross-coupling reaction of 1-hydroxy-2-bromoanthraquinone, 1-hydroxy-4-iodoanthraquinone or 1-hydroxy-2,4-dibromoanthraquinone with arylboronic acids. The cross-coupling reaction of 2,4-dibromo-9,10-anthraquinone with arylboronic acids provide a convenient approach to 2,4-bis arylated 1-hydroxyanthraquinones with a variety of aryl substituent in the 2 and 4 position. The cytotoxicity of new anthraquinone derivatives was evaluated using the conventional MTT assays. The data revealed that six of the aryl substituted compounds among the entire series 3, 15, 16, 25, 27, 28 were comparable potent with the commercially available reference drug doxorubicin on the human glioblastoma cells SNB-19, prostate cancer DU-145 or breast cancer cells MDA-MB-231 and were relatively safe towards human telomerase (h-TERT)immortalized lung fibroblasts cells. The results suggested that the in vitro antitumor activity of synthesized 2-aryl, 4-aryl- and 2,4-diaryl substituted 1-hydroxyanthraquinones depends on the nature of the substituent within the cyclic backbone. Docking interaction of 2-, 4-substituted and 2,4-disubstituted 1-hydroxyanthraquinones indicates intercalative mode of binding of compounds with DNA topoisomerase. The interaction with the DNA of 4-aryl-13, 15, 16 and 4-(furan-3-yl)-23 1-hydroxyanthraquinones was experimentally confirmed through a change in electroforetic mobility. Further experiments with 1-hydroxy-4-phenyl-anthraquinone 13 demonstrated that the compound induced cell cycle arrest at sub-G1 phase in DU-145 cells in the concentration 1.1 μM, which is probably achieved by inducing apoptosis. 4-Arylsubstituted 1-hydroxyanthraquinones 13 and 16 induced the enhancement of DNA synthesis on SNB19 cell lines.
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Affiliation(s)
- Nafisa S. Sirazhetdinova
- Laboratory of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Ave, 9, 630090 Novosibirsk, Russia; (N.S.S.); (V.A.S.); (D.S.B.)
| | - Victor A. Savelyev
- Laboratory of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Ave, 9, 630090 Novosibirsk, Russia; (N.S.S.); (V.A.S.); (D.S.B.)
| | - Tatyana S. Frolova
- The Federal Research Center Institute of Cytology and Genetics, Acad. Lavrentyev Ave., 10, 630090 Novosibirsk, Russia;
- Novosibirsk State University, Pirogova Str. 1, 630090 Novosibirsk, Russia; (O.S.O.); (T.A.S.); (A.G.P.)
| | - Dmitry S. Baev
- Laboratory of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Ave, 9, 630090 Novosibirsk, Russia; (N.S.S.); (V.A.S.); (D.S.B.)
| | | | - Ivan V. Chernikov
- Institute of Chemical Biology and Fundamental Medicine Siberian Branch of the Russian Academy of Sciences, Lavrentyev Ave, 9, 630090 Novosibirsk, Russia;
| | - Olga S. Oleshko
- Novosibirsk State University, Pirogova Str. 1, 630090 Novosibirsk, Russia; (O.S.O.); (T.A.S.); (A.G.P.)
| | - Teresa A. Sarojan
- Novosibirsk State University, Pirogova Str. 1, 630090 Novosibirsk, Russia; (O.S.O.); (T.A.S.); (A.G.P.)
| | - Andrey G. Pokrovskii
- Novosibirsk State University, Pirogova Str. 1, 630090 Novosibirsk, Russia; (O.S.O.); (T.A.S.); (A.G.P.)
| | - Elvira E. Shults
- Laboratory of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Ave, 9, 630090 Novosibirsk, Russia; (N.S.S.); (V.A.S.); (D.S.B.)
- Correspondence: ; Fax: +7-383-330-9752
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Molecular docking, dynamics simulation and ADMET prediction of Acetaminophen and its modified derivatives based on quantum calculations. SN APPLIED SCIENCES 2019. [DOI: 10.1007/s42452-019-1442-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
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Costa PJ, Nunes R, Vila-Viçosa D. Halogen bonding in halocarbon-protein complexes and computational tools for rational drug design. Expert Opin Drug Discov 2019; 14:805-820. [PMID: 31131651 DOI: 10.1080/17460441.2019.1619692] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Introduction: Halogens have a prominent role in drug design. Often used as a mean to improve ADME properties, they are also becoming a tool in protein-ligand recognition given their ability to form a non-covalent interaction, termed halogen bond, where halogens act as electrophilic species interacting with electron-rich partners. Rational drug design of halogen-bonding lead molecules requires an accurate description of halocarbon-protein complexes by computational tools though not all methods are able to tackle this non-covalent interaction. Areas covered: The authors present a review of computational methodologies that can be used to properly describe halogen bonds in the context of protein-ligand complexes, providing also insights on how these methods can be used in the context of computer-aided drug design. Expert opinion: Although in the last few years many computational tools, ranging from fast screening methods to the more expensive QM calculations, have been developed to tackle the halogen bonding phenomenon, they are not yet standard in the literature. This will eventually change as official software distributions are including support for halogen bonding in their methods. Tackling desolvation of halogenated species seems to be a good strategy to improve the accuracy of computational methods, that will be more commonly used prior to laboratory work in the future.
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Affiliation(s)
- Paulo J Costa
- a Centro de Quı́mica e Bioquı́mica, Departamento de Quı́mica e Bioquı́mica , Faculdade de Ciências da Universidade de Lisboa, Campo Grande , Lisboa , Portugal.,b University of Lisboa, Faculty of Sciences , BioISI - Biosystems & Integrative Sciences Institute , Lisboa , Portugal
| | - Rafael Nunes
- a Centro de Quı́mica e Bioquı́mica, Departamento de Quı́mica e Bioquı́mica , Faculdade de Ciências da Universidade de Lisboa, Campo Grande , Lisboa , Portugal.,b University of Lisboa, Faculty of Sciences , BioISI - Biosystems & Integrative Sciences Institute , Lisboa , Portugal
| | - Diogo Vila-Viçosa
- a Centro de Quı́mica e Bioquı́mica, Departamento de Quı́mica e Bioquı́mica , Faculdade de Ciências da Universidade de Lisboa, Campo Grande , Lisboa , Portugal.,b University of Lisboa, Faculty of Sciences , BioISI - Biosystems & Integrative Sciences Institute , Lisboa , Portugal
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15
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Uddin N, Ahmed S, Khan AM, Mazharol Hoque M, Halim MA. Halogenated derivatives of methotrexate as human dihydrofolate reductase inhibitors in cancer chemotherapy. J Biomol Struct Dyn 2019; 38:901-917. [PMID: 30938661 DOI: 10.1080/07391102.2019.1591302] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Methotrexate is a widely used anti-metabolite in cancer chemotherapy. A series of halogenated drugs is designed from Methotrexate to assess their interactions with human dihydrofolate reductase. The aim of this study is to evaluate the performance of the modified drugs compared to the parent Methotrexate. Density Functional Theory is employed to optimize these drugs. Molecular docking calculation of these optimized drugs against dihydrofolate reductase is performed to find out binding affinity. In addition, molecular dynamics simulation is considered for the complexes of best two modified drugs with their receptors. Modifications by the halogens show significant changes in the charge distribution, dipole moment, thermodynamic stability, enthalpy and free energy. The highest binding affinity value (-36.401 KJ/mol) was obtained for M14. Hybrid quantum mechanics/molecular mechanics calculation shows a binding energy of -255.140 KJ/mol. Modified drugs have significant hydrogen and non-covalent bonding interactions with amino acids of the receptor. Molecular dynamics simulation disclosed that the root-mean-square-deviation of the alpha carbon associated with M6-1KMV and M14-1KMV complexes is 2.367 Å and 2.622 Å, respectively. Moreover, the interactions between modified drugs and receptor are mostly persevered in 25 nanosecond molecular dynamics simulation. Ensemble-based docking also confirmed that modified drugs show strong non-bonding interactions with different crystallographic and molecular dynamics based conformers. The best scored drugs show considerable pharmacokinetic properties. Modified derivatives M5, M6, M8, M10, M13 and M14 show the better binding affinity and a good number of hydrogen and other non-bonding interactions with the target protein which are similar to other anticancer drugs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Nizam Uddin
- Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh.,Department of Pharmacy, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Sinthyia Ahmed
- Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh
| | - Akib Mahmud Khan
- Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh
| | - Mohammad Mazharol Hoque
- Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh
| | - Mohammad A Halim
- Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh
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16
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Al-Otaibi JS, Wasli Y, ELGogary TM. Theoretical and experimental studies on anticancer drug mitoxantrone. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.07.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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17
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Li W, Liu Z, Liang B, Chen S, Zhang X, Tong X, Lou W, Le L, Tang X, Fu F. Identification of core genes in ovarian cancer by an integrative meta-analysis. J Ovarian Res 2018; 11:94. [PMID: 30453999 PMCID: PMC6240943 DOI: 10.1186/s13048-018-0467-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 10/30/2018] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Epithelial ovarian cancer is one of the most severe public health threats in women. Since it is still challenging to screen in early stages, identification of core genes that play an essential role in epithelial ovarian cancer initiation and progression is of vital importance. RESULTS Seven gene expression datasets (GSE6008, GSE18520, GSE26712, GSE27651, GSE29450, GSE36668, and GSE52037) containing 396 ovarian cancer samples and 54 healthy control samples were analyzed to identify the significant differentially expressed genes (DEGs). We identified 563 DEGs, including 245 upregulated and 318 downregulated genes. Enrichment analysis based on the gene ontology (GO) functions and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways showed that the upregulated genes were significantly enriched in cell division, cell cycle, tight junction, and oocyte meiosis, while the downregulated genes were associated with response to endogenous stimuli, complement and coagulation cascades, the cGMP-PKG signaling pathway, and serotonergic synapse. Two significant modules were identified from a protein-protein interaction network by using the Molecular Complex Detection (MCODE) software. Moreover, 12 hub genes with degree centrality more than 29 were selected from the protein-protein interaction network, and module analysis illustrated that these 12 hub genes belong to module 1. Furthermore, Kaplan-Meier analysis for overall survival indicated that 9 of these hub genes was correlated with poor prognosis of epithelial ovarian cancer patients. CONCLUSION The present study systematically validates the results of previous studies and fills the gap regarding a large-scale meta-analysis in the field of epithelial ovarian cancer. Furthermore, hub genes that could be used as a novel biomarkers to facilitate early diagnosis and therapeutic approaches are evaluated, providing compelling evidence for future genomic-based individualized treatment of epithelial ovarian cancer.
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Affiliation(s)
- Wenyu Li
- The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330031, People's Republic of China
| | - Zheran Liu
- Queen Mary School, Medical College of Nanchang University, Nanchang, Jiangxi, 330031, People's Republic of China
| | - Bowen Liang
- School of Public Health, Nanchang University, Nanchang, Jiangxi, 330031, People's Republic of China
| | - Siyang Chen
- School of Public Health, Nanchang University, Nanchang, Jiangxi, 330031, People's Republic of China
| | - Xinping Zhang
- School of Public Health, Nanchang University, Nanchang, Jiangxi, 330031, People's Republic of China
| | - Xiaoqin Tong
- School of Public Health, Nanchang University, Nanchang, Jiangxi, 330031, People's Republic of China
| | - Weiming Lou
- School of Public Health, Nanchang University, Nanchang, Jiangxi, 330031, People's Republic of China
| | - Lulu Le
- The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330031, People's Republic of China
| | - Xiaoli Tang
- School of Basic Medical Science, Nanchang University, Nanchang, Jiangxi, 330031, People's Republic of China.
| | - Fen Fu
- The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330031, People's Republic of China.
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Rahman MS, Hossain SM, Rahman MT, Halim MA, Ishtiak MN, Kabir M. Determination of trace metal concentration in compost, DAP, and TSP fertilizers by neutron activation analysis (NAA) and insights from density functional theory calculations. ENVIRONMENTAL MONITORING AND ASSESSMENT 2017; 189:618. [PMID: 29119383 DOI: 10.1007/s10661-017-6328-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 10/24/2017] [Indexed: 06/07/2023]
Abstract
Leaching of toxic metals from fertilizers is a growing concern in an agricultural country like Bangladesh due to the serious consequences in health and food chain. Fertilizers used in farming fields and nurseries (plant sales outlet) in the mid-southern part of Bangladesh were collected for the determination of toxic metals. This study employed the neutron activation method and a relative standardization approach. Three standard/certified reference materials, namely NIST coal fly ash 1633b, IAEA-Soil-7, and IAEA-SL-1 (lake sediment), were considered for elemental quantification. Concentration of As (2.63-16.73 mg/kg), Cr (40.93-261.77 mg/kg), Sb (0.47-63.58 mg/kg), Th (1.44-19.16 mg/kg), and U (1.90-209.41 mg/kg) were determined in fertilizers. High concentrations of Cr, Sb, and U were detected in some compost and phosphate fertilizers (TSP and diammonium phosphate (DAP)) in comparison with the IAEA/European market standard and other studies. Quantum mechanical calculations were performed to understand the molecular level interaction of CrO3, Sb2O3, and AsO3, with DAP by employing density functional theory with the B3LYP/SDD level of theory. Our results indicated that CrO3 and Sb2O3 have strong binding affinity with DAP compared to AsO3, which supports the experimental results. These compounds attached to the phosphate group through covalent-like bonding with oxygen. The frontier molecular orbital calculation indicated that HOMO-LUMO gap of the AsO3-DAP (5.46 eV) and Sb2O3-DAP (6.48 eV) complexes are relatively lower than the CrO3-DAP, which indicates that As and Sb oxides are chemically more prone to attach with the phosphate group of DAP fertilizer.
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Affiliation(s)
- Md Sajjadur Rahman
- Department of Chemistry and Biochemistry, South Dakota State University, Brookings, SD, 57007, USA
| | - Syed Mohammod Hossain
- Reactor and Neutron Physics Division, INST, Atomic Energy Research Establishment, Savar, GPO Box-3787, Dhaka, 1000, Bangladesh
| | - Mir Tamzid Rahman
- Department of Chemistry, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh.
| | - Mohammad A Halim
- Division of Quantum Chemistry, Green Research Centre, BICCB, 38 Green Road West, Dhaka, 1205, Bangladesh
| | - Mohammad Niaz Ishtiak
- Division of Quantum Chemistry, Green Research Centre, BICCB, 38 Green Road West, Dhaka, 1205, Bangladesh
| | - Mahbub Kabir
- Department of Chemistry, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh
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19
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Khan AM, Shawon J, Halim MA. Multiple receptor conformers based molecular docking study of fluorine enhanced ethionamide with mycobacterium enoyl ACP reductase (InhA). J Mol Graph Model 2017; 77:386-398. [DOI: 10.1016/j.jmgm.2017.09.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 09/07/2017] [Accepted: 09/09/2017] [Indexed: 01/11/2023]
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20
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Tonry C, Armstrong J, Pennington S. Probing the prostate tumour microenvironment II: Impact of hypoxia on a cell model of prostate cancer progression. Oncotarget 2017; 8:15307-15337. [PMID: 28410543 PMCID: PMC5362488 DOI: 10.18632/oncotarget.14574] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 11/22/2016] [Indexed: 12/21/2022] Open
Abstract
Approximately one in six men are diagnosed with Prostate Cancer every year in the Western world. Although it can be well managed and non-life threatening in the early stages, over time many patients cease to respond to treatment and develop castrate resistant prostate cancer (CRPC). CRPC represents a clinically challenging and lethal form of prostate cancer. Progression of CRPC is, in part, driven by the ability of cancer cells to alter their metabolic profile during the course of tumourgenesis and metastasis so that they can survive in oxygen and nutrient-poor environments and even withstand treatment. This work was carried out as a continuation of a study aimed towards gaining greater mechanistic understanding of how conditions within the tumour microenvironment impact on both androgen sensitive (LNCaP) and androgen independent (LNCaP-abl and LNCaP-abl-Hof) prostate cancer cell lines. Here we have applied technically robust and reproducible label-free liquid chromatography mass spectrometry analysis for comprehensive proteomic profiling of prostate cancer cell lines under hypoxic conditions. This led to the identification of over 4,000 proteins - one of the largest protein datasets for prostate cancer cell lines established to date. The biological and clinical significance of proteins showing a significant change in expression as result of hypoxic conditions was established. Novel, intuitive workflows were subsequently implemented to enable robust, reproducible and high throughput verification of selected proteins of interest. Overall, these data suggest that this strategy supports identification of protein biomarkers of prostate cancer progression and potential therapeutic targets for CRPC.
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Affiliation(s)
- Claire Tonry
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Ireland
| | | | - Stephen Pennington
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Ireland
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