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Massey I, Yadav S, Kumar D, Maharia RS, Kumari K, Singh P. An insight for the inhibition of anxiolytic and anti-convulsant effects in zebrafish using the curcumins via exploring molecular docking and molecular dynamics simulations. Mol Divers 2024:10.1007/s11030-024-10865-1. [PMID: 38758508 DOI: 10.1007/s11030-024-10865-1] [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: 02/21/2024] [Accepted: 03/28/2024] [Indexed: 05/18/2024]
Abstract
In the contemporary landscape, anxiety and seizures stand as major areas of concern, prompting researchers to explore potential drugs against them. While numerous drugs have shown the potential to treat these two neurological conditions, certain adverse effects emphasize the need for development of safer alternatives. This study seeks to employ an in silico approach to evaluate natural compounds, particularly curcumins, as potential inhibitors of GABA-AT to mitigate anxiety and seizures. The proposed methodology includes generating a compound library, minimizing energy, conducting molecular docking using AutoDock, molecular dynamics simulations using Amber, and MM-GBSA calculations. Remarkably, CMPD50 and CMPD88 exhibited promising binding affinities of - 9.0 kcal/mol and - 9.1 kcal/mol with chains A and C of GABA-AT, respectively. Further, MM-GBSA calculations revealed binding free energies of - 10.88 kcal/mol and - 10.72 kcal/mol in CMPD50 and CMPD88, respectively. ADME analysis showed that these compounds contain drug-likeness properties and might be considered as potential drug candidates. The findings from this study will have practical applications in the field of drug discovery for the development of safer and effective drugs for treatment of anxiety and seizures. Overall, this study will lay the groundwork for providing valuable insights into the potential therapeutic effects of curcumins in alleviating anxiety and seizures, establishing a computational framework for future experimental validation.
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Affiliation(s)
- Iona Massey
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, Delhi, India
- Amity Institute of Biotechnology, Amity University, Noida, India
| | - Sandeep Yadav
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, Delhi, India
- Department of Chemistry, Faculty of Engineering and Technology, SRM Institute of Science and Technology, NCR Campus, Ghaziabad, Uttar Pradesh, India
| | - Durgesh Kumar
- Department of Chemistry, Maitreyi College, University of Delhi, Delhi, India.
| | - Ram Swaroop Maharia
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, Delhi, India
| | - Kamlesh Kumari
- Department of Zoology, University of Delhi, Delhi, India.
| | - Prashant Singh
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, Delhi, India.
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Chen T, Shi Y, Shi W. Huangqi Guizhi Wuwu decoction in peripheral neurotoxicity treatment using network pharmacology and molecular docking. Medicine (Baltimore) 2022; 101:e31281. [PMID: 36281162 PMCID: PMC9592446 DOI: 10.1097/md.0000000000031281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In this study, we predicted the core active compounds of Huangqi Guizhi Wuwu decoction in treatment of oxaliplatin-induced peripheral neuropathy and the related potential mechanism. Corresponding database was used to complete the interaction (PPI) network of key targets and the enrichment analysis of corresponding genmes. Molecular docking of key targets and key compounds was carried out using relevant software. The 60 chemical components corresponding to the oral absorption of Huangqi Guizhi Wuwu decoction correspond to 157 unique targets, and the 233 chemical components corresponding to percutaneous absorption in vitro correspond to 155 unique targets. There were 1074 unique targets for chemotherapy-induced peripheral neuropathy. Finally, three common key targets (SLC6A2, SLC6A3, and SLC6A4) and two key compounds (6-Gingerol and nuciferin) were screened according to the above three target datasets. The results showed that The PPI network of common key targets involved 23 associated proteins. In the related GO enrichment results, there were 33 items related to biological processes, 13 items related to cell composition, 21 items related to molecular function, and four KEGG pathway enrichments. L1000 kinase and GPCR perturbation analysis showed that the associated protein had an effect on the expression of multiple groups of kinase genes. HPA revealed that the enrichment of three common key targets was tissue-specific. The docking results showed that the 6 groups were structurally stable. The oral and topical use of Huangqi Guizhi Wuwu decoction can prevent and control peripheral neurotoxicity. The prevention and control effects may be related to its participation in the regulation of neurotransmitter transport, sympathetic activity, and transport. The histological parts of the mechanism are mainly distributed in the adrenal gland, placenta, brain, intestine, and lung, the blood is not specific. According to the prediction results of molecular docking, 6-Gingerol and nuciferin can closely bind to three common key targets.
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Affiliation(s)
- Tingting Chen
- School of the First Clinical Medical, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yabo Shi
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Wenchuan Shi
- Technology Transfer Center, Nanjing University of Chinese Medicine, Nanjing, China
- * Correspondence: Wenchuan Shi, Technology Transfer Center, Nanjing University of Chinese Medicine, Nanjing, China ()
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Ahmad Mir S, Alaidarous M, Alshehri B, Ahmad Mir B, Aziz Bin D A, Banawas S, Firoz A, A. Alsagab S, Awaji Madk Y, Jahan S, Kashoo F, Iqbal D, Ahmad Gana S, Kumar Chou R, Shaker Alb K, Naseem A. Identification of Mycobacterial RNA Polymerase Inhibitors from the Main Phytochemicals of Nigella sativa: An in silico Study. INT J PHARMACOL 2022. [DOI: 10.3923/ijp.2022.1015.1025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Vardhan S, Sahoo SK. Exploring the therapeutic nature of limonoids and triterpenoids against SARS-CoV-2 by targeting nsp13, nsp14, and nsp15 through molecular docking and dynamic simulations. J Tradit Complement Med 2021; 12:44-54. [PMID: 34926189 PMCID: PMC8666293 DOI: 10.1016/j.jtcme.2021.12.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 12/06/2021] [Accepted: 12/10/2021] [Indexed: 12/28/2022] Open
Abstract
Background and aim The ongoing global pandemic due to SARS-CoV-2 caused a medical emergency. Since December 2019, the COVID-19 disease is spread across the globe through physical contact and respiratory droplets. Coronavirus caused a severe effect on the human immune system where some of the non-structural proteins (nsp) are involved in virus-mediated immune response and pathogenesis. To suppress the viral RNA replication mechanism and immune-mediated responses, we aimed to identify limonoids and triterpenoids as antagonists by targeting helicases (nsp13), exonuclease (nsp14), and endoribonuclease (nsp15) of SARS-CoV-2 as therapeutic proteins. Experimental procedure In silico molecular docking and drug-likeness of a library of 369 phytochemicals from limonoids and triterpenoids were performed to screen the potential hits that binds effectively at the active site of the proteins target. In addition, the molecular dynamics simulations of the proteins and their complexes with the potential hits were performed for 100 ns by using GROMACS. Results and conclusion The potential compounds 26-deoxyactein and 25-O-anhydrocimigenol 3-O-beta-d-xylopyranoside posing strong interactions with a minimum binding energy of -10.1 and -9.5 kcal/mol, respectively and sustained close contact with nsp13 for 100 ns. The nsp14 replication fork activity was hindered by the tomentosolic acid, timosaponin A-I, and shizukaol A with the binding affinity score of -9.2, -9.2, and -9.0 kcal/mol, respectively. The nsp15 endoribonuclease catalytic residues were inhibited potentially by limonin, 25-O-anhydrocimigenol 3-O-alpha-l-arabinopyranoside, and asperagenin posing strong binding affinity scores of -9.0, -8.8, and -8.7 kcal/mol, respectively. Computationally predicted potential phytochemicals for SARS-CoV-2 are known to possess various medicinal properties.
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Affiliation(s)
- Seshu Vardhan
- Department of Chemistry, Sardar Vallabhbhai National Institute of Technology (SVNIT), Surat, 395007, Gujarat, India
| | - Suban K Sahoo
- Department of Chemistry, Sardar Vallabhbhai National Institute of Technology (SVNIT), Surat, 395007, Gujarat, India
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Guan S, Zhu K, Dong Y, Li H, Yang S, Wang S, Shan Y. Exploration of Binding Mechanism of a Potential Streptococcus pneumoniae Neuraminidase Inhibitor from Herbaceous Plants by Molecular Simulation. Int J Mol Sci 2020; 21:ijms21031003. [PMID: 32028720 PMCID: PMC7038148 DOI: 10.3390/ijms21031003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 01/28/2020] [Accepted: 02/01/2020] [Indexed: 01/11/2023] Open
Abstract
Streptococcus pneumoniae can cause diseases such as pneumonia. Broad-spectrum antibiotic therapy for Streptococcus pneumoniae is increasingly limited due to the emergence of drug-resistant strains. The development of novel drugs is still currently of focus. Abundant polyphenols have been demonstrated to have antivirus and antibacterial ability. Chlorogenic acid is one of the representatives that has been proven to have the potential to inhibit both the influenza virus and Streptococcus pneumoniae. However, for such a potential neuraminidase inhibitor, the interaction mechanism studies between chlorogenic acid and Streptococcus pneumoniae neuraminidase are rare. In the current study, the binding mechanism of chlorogenic acid and Streptococcus pneumoniae neuraminidase were investigated by molecular simulation. The results indicated that chlorogenic acid might establish the interaction with Streptococcus pneumoniae neuraminidase via hydrogen bonds, salt bridge, and cation-π. The vital residues involved Arg347, Ile348, Lys440, Asp372, Asp417, and Glu768. The side chain of Arg347 might form a cap-like structure to lock the chlorogenic acid to the active site. The results from binding energy calculation indicated that chlorogenic acid had strong binding potential with neuraminidase. The results predicted a detailed binding mechanism of a potential Streptococcus pneumoniae neuraminidase inhibitor, which will be provide a theoretical basis for the mechanism of new inhibitors.
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Affiliation(s)
- Shanshan Guan
- College of Food Engineering, Jilin Engineering Normal University, Changchun 130052, Jilin, China; (K.Z.); (Y.D.); (H.L.); (S.Y.)
- Key Laboratory of Molecular Nutrition at Universities of Jilin Province, Changchun 130052, Jilin, China
- Correspondence: (S.G.); (Y.S.); Tel.: +86-4318-172-1319 (S.G. & Y.S.)
| | - Ketong Zhu
- College of Food Engineering, Jilin Engineering Normal University, Changchun 130052, Jilin, China; (K.Z.); (Y.D.); (H.L.); (S.Y.)
- Key Laboratory of Molecular Nutrition at Universities of Jilin Province, Changchun 130052, Jilin, China
| | - Yanjiao Dong
- College of Food Engineering, Jilin Engineering Normal University, Changchun 130052, Jilin, China; (K.Z.); (Y.D.); (H.L.); (S.Y.)
- Key Laboratory of Molecular Nutrition at Universities of Jilin Province, Changchun 130052, Jilin, China
| | - Hao Li
- College of Food Engineering, Jilin Engineering Normal University, Changchun 130052, Jilin, China; (K.Z.); (Y.D.); (H.L.); (S.Y.)
- Key Laboratory of Molecular Nutrition at Universities of Jilin Province, Changchun 130052, Jilin, China
| | - Shuang Yang
- College of Food Engineering, Jilin Engineering Normal University, Changchun 130052, Jilin, China; (K.Z.); (Y.D.); (H.L.); (S.Y.)
- Key Laboratory of Molecular Nutrition at Universities of Jilin Province, Changchun 130052, Jilin, China
| | - Song Wang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, Jilin, China;
| | - Yaming Shan
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, Jilin, China
- Correspondence: (S.G.); (Y.S.); Tel.: +86-4318-172-1319 (S.G. & Y.S.)
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Investigation of the anti-TB potential of selected propolis constituents using a molecular docking approach. Sci Rep 2018; 8:12238. [PMID: 30116003 PMCID: PMC6095843 DOI: 10.1038/s41598-018-30209-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 06/26/2018] [Indexed: 01/09/2023] Open
Abstract
Human tuberculosis (TB), caused by Mycobacterium tuberculosis, is the leading bacterial killer disease worldwide and new anti-TB drugs are urgently needed. Natural remedies have long played an important role in medicine and continue to provide some inspiring templates for drug design. Propolis, a substance naturally-produced by bees upon collection of plant resins, is used in folk medicine for its beneficial anti-TB activity. In this study, we used a molecular docking approach to investigate the interactions between selected propolis constituents and four ‘druggable’ proteins involved in vital physiological functions in M. tuberculosis, namely MtPanK, MtDprE1, MtPknB and MtKasA. The docking score for ligands towards each protein was calculated to estimate the binding free energy, with the best docking score (lowest energy value) indicating the highest predicted ligand/protein affinity. Specific interactions were also explored to understand the nature of intermolecular bonds between the most active ligands and the protein binding site residues. The lignan (+)-sesamin displayed the best docking score towards MtDprE1 (−10.7 kcal/mol) while the prenylated flavonoid isonymphaeol D docked strongly with MtKasA (−9.7 kcal/mol). Both compounds showed docking scores superior to the control inhibitors and represent potentially interesting scaffolds for further in vitro biological evaluation and anti-TB drug design.
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Dharra R, Talwar S, Singh Y, Gupta R, Cirillo JD, Pandey AK, Kulharia M, Mehta PK. Rational design of drug-like compounds targeting Mycobacterium marinum MelF protein. PLoS One 2017; 12:e0183060. [PMID: 28873466 PMCID: PMC5584760 DOI: 10.1371/journal.pone.0183060] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 07/28/2017] [Indexed: 11/19/2022] Open
Abstract
The mycobacterial mel2 locus (mycobacterial enhanced infection locus, Rv1936-1941) is Mycobacterium marinum and M. tuberculosis specific, which can withstand reactive oxygen species (ROS) and reactive nitrogen species (RNS) induced stress. A library of over a million compounds was screened using in silico virtual ligand screening (VLS) to identify inhibitors against the modeled structure of MelF protein expressed by melF of mel2 locus so that M. marinum’s ability to withstand ROS/RNS stress could be reduced. The top ranked 1000 compounds were further screened to identify 178 compounds to maximize the scaffold diversity by manually evaluating the interaction of each compound with the target site. M. marinum melF was cloned, expressed and purified as maltose binding protein (MBP)-tagged recombinant protein in Escherichia coli. After establishing the flavin dependent oxidoreductase activity of MelF (~ 84 kDa), the inhibitors were screened for the inhibition of enzyme activity of whole cell lysate (WCL) and the purified MelF. Amongst these, 16 compounds could significantly inhibit the enzyme activity of purified MelF. For the six best inhibitory compounds, the minimal inhibitory concentration (MIC) was determined to be 3.4–19.4 μM and 13.5–38.8 μM for M. marinum and M. tuberculosis, respectively. Similarly, the minimal bactericidal concentration (MBC) was determined to be 6.8–38.8 μM and 27–38.8 μM against M. marinum and M. tuberculosis, respectively. One compound each in combination with isoniazid (INH) also showed synergistic inhibitory effect against M. marinum and M. tuberculosis with no cytotoxicity in HeLa cells. Interestingly, these inhibitors did not display any non-specific protein-structure destabilizing effect. Such inhibitors targeting the anti-ROS/RNS machinery may facilitate the efficient killing of replicating and nonreplicating mycobacteria inside the host cells.
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Affiliation(s)
- Renu Dharra
- Centre for Biotechnology, Maharshi Dayanand University (MDU), Rohtak, India
| | - Sakshi Talwar
- Translational Health Science and Technology Institute (THSTI), Faridabad, India
| | - Yogesh Singh
- Department of Microbiology, University of Delhi South Campus, New Delhi, India
| | - Rani Gupta
- Department of Microbiology, University of Delhi South Campus, New Delhi, India
| | - Jeffrey D. Cirillo
- Department of Microbial and Molecular Pathogenesis, Texas A&M Health Science Center, College Station, Texas, United States of America
| | - Amit K. Pandey
- Translational Health Science and Technology Institute (THSTI), Faridabad, India
| | - Mahesh Kulharia
- School of Basic and Applied Science, Central University of Punjab, Bathinda, India
- * E-mail: (MK); (PKM)
| | - Promod K. Mehta
- Centre for Biotechnology, Maharshi Dayanand University (MDU), Rohtak, India
- * E-mail: (MK); (PKM)
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Brindha S, Sundaramurthi JC, Velmurugan D, Vincent S, Gnanadoss JJ. Docking-based virtual screening of known drugs against murE of Mycobacterium tuberculosis towards repurposing for TB. Bioinformation 2016; 12:359-367. [PMID: 28275291 PMCID: PMC5312000 DOI: 10.6026/97320630012368] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 11/08/2016] [Indexed: 01/04/2023] Open
Abstract
Repurposing has gained momentum globally and become an alternative avenue for drug discovery because of its better success rate,
and reduced cost, time and issues related to safety than the conventional drug discovery process. Several drugs have already been
successfully repurposed for other clinical conditions including drug resistant tuberculosis (DR-TB). Though TB can be cured
completely with the use of currently available anti-tubercular drugs, emergence of drug resistant strains of Mycobacterium tuberculosis
and the huge death toll globally, together necessitate urgently newer and effective drugs for TB. Therefore, we performed virtual
screening of 1554 FDA approved drugs against murE, which is essential for peptidoglycan biosynthesis of M. tuberculosis. We used
Glide and AutoDock Vina for virtual screening and applied rigid docking algorithm followed by induced fit docking algorithm in
order to enhance the quality of the docking prediction and to prioritize drugs for repurposing. We found 17 drugs binding strongly
with murE and three of them, namely, lymecycline, acarbose and desmopressin were consistently present within top 10 ranks by both
Glide and AutoDock Vina in the induced fit docking algorithm, which strongly indicates that these three drugs are potential
candidates for further studies towards repurposing for TB.
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Affiliation(s)
| | | | - Devadasan Velmurugan
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai - 600025, Tamil Nadu, India
| | - Savariar Vincent
- Loyola College, Nungambakkam, Chennai - 600034, Tamil Nadu, India
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Lidor O, Al-Quntar A, Pesci EC, Steinberg D. Mechanistic analysis of a synthetic inhibitor of the Pseudomonas aeruginosa LasI quorum-sensing signal synthase. Sci Rep 2015; 5:16569. [PMID: 26593271 PMCID: PMC4655403 DOI: 10.1038/srep16569] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 10/14/2015] [Indexed: 01/24/2023] Open
Abstract
Pseudomonas aeruginosa is an opportunistic Gram-negative pathogen responsible for many human infections. LasI is an acyl-homoserine lactone synthase that produces a quorum-sensing (QS) signal that positively regulates numerous P. aeruginosa virulence determinants. The inhibition of the LasI protein is therefore an attractive drug target. In this study, a novel in silico to in vitro complementation was applied to screen thiazolidinedione-type compounds for their ability to inhibit biofilm formation at concentrations not affecting bacterial growth. The compound (z)-5-octylidenethiazolidine-2, 4-dione (TZD-C8) was a strong inhibitor of biofilm formation and chosen for further study. Structural exploration of in silico docking predicted that the compound had high affinity for the LasI activity pocket. The TZD-C8 compound was also predicted to create hydrogen bonds with residues Arg30 and Ile107. Site-directed mutagenesis (SDM) of these two sites demonstrated that TZD-C8 inhibition was abolished in the lasI double mutant PAO-R30D, I107S. In addition, in vitro swarming motility and quorum sensing signal production were affected by TZD-C 8, confirming this compound alters the cell to cell signalling circuitry. Overall, this novel inhibitor of P. aeruginosa quorum sensing shows great promise and validates our mechanistic approach to discovering inhibitors of LuxI-type acyl-homoserine lactone synthases.
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Affiliation(s)
- O. Lidor
- Biofilm Research Laboratory, Institute of Dental Sciences, Faculty of Dental Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - A. Al-Quntar
- Biofilm Research Laboratory, Institute of Dental Sciences, Faculty of Dental Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
- Institute of Drug Research, School of Pharmacy, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - E. C. Pesci
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, USA
| | - D. Steinberg
- Biofilm Research Laboratory, Institute of Dental Sciences, Faculty of Dental Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
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