1
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Morales N, Valdés-Muñoz E, González J, Valenzuela-Hormazábal P, Palma JM, Galarza C, Catagua-González Á, Yáñez O, Pereira A, Bustos D. Machine Learning-Driven Classification of Urease Inhibitors Leveraging Physicochemical Properties as Effective Filter Criteria. Int J Mol Sci 2024; 25:4303. [PMID: 38673888 PMCID: PMC11049951 DOI: 10.3390/ijms25084303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/03/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
Urease, a pivotal enzyme in nitrogen metabolism, plays a crucial role in various microorganisms, including the pathogenic Helicobacter pylori. Inhibiting urease activity offers a promising approach to combating infections and associated ailments, such as chronic kidney diseases and gastric cancer. However, identifying potent urease inhibitors remains challenging due to resistance issues that hinder traditional approaches. Recently, machine learning (ML)-based models have demonstrated the ability to predict the bioactivity of molecules rapidly and effectively. In this study, we present ML models designed to predict urease inhibitors by leveraging essential physicochemical properties. The methodological approach involved constructing a dataset of urease inhibitors through an extensive literature search. Subsequently, these inhibitors were characterized based on physicochemical properties calculations. An exploratory data analysis was then conducted to identify and analyze critical features. Ultimately, 252 classification models were trained, utilizing a combination of seven ML algorithms, three attribute selection methods, and six different strategies for categorizing inhibitory activity. The investigation unveiled discernible trends distinguishing urease inhibitors from non-inhibitors. This differentiation enabled the identification of essential features that are crucial for precise classification. Through a comprehensive comparison of ML algorithms, tree-based methods like random forest, decision tree, and XGBoost exhibited superior performance. Additionally, incorporating the "chemical family type" attribute significantly enhanced model accuracy. Strategies involving a gray-zone categorization demonstrated marked improvements in predictive precision. This research underscores the transformative potential of ML in predicting urease inhibitors. The meticulous methodology outlined herein offers actionable insights for developing robust predictive models within biochemical systems.
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Affiliation(s)
- Natalia Morales
- Magíster en Ciencias de la Computación, Universidad Católica del Maule, Talca 3460000, Chile; (N.M.); (J.G.)
| | - Elizabeth Valdés-Muñoz
- Doctorado en Biotecnología Traslacional, Centro de Biotecnología de los Recursos Naturales, Universidad Católica del Maule, Talca 3480094, Chile;
| | - Jaime González
- Magíster en Ciencias de la Computación, Universidad Católica del Maule, Talca 3460000, Chile; (N.M.); (J.G.)
| | - Paulina Valenzuela-Hormazábal
- Departamento de Farmacología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción 4030000, Chile;
| | - Jonathan M. Palma
- Facultad de Ingeniería, Universidad de Talca, Curicó 3344158, Chile;
| | - Christian Galarza
- Departamento de Matemáticas, Facultad de Ciencias Naturales y Matemáticas, Escuela Superior Politécnica del Litoral, Guayaquil EC090903, Ecuador; (C.G.); (Á.C.-G.)
| | - Ángel Catagua-González
- Departamento de Matemáticas, Facultad de Ciencias Naturales y Matemáticas, Escuela Superior Politécnica del Litoral, Guayaquil EC090903, Ecuador; (C.G.); (Á.C.-G.)
| | - Osvaldo Yáñez
- Núcleo de Investigación en Data Science, Facultad de Ingeniería y Negocios, Universidad de las Américas, Santiago 7500000, Chile;
| | - Alfredo Pereira
- Facultad de Ingeniería, Arquitectura y Diseño, Universidad San Sebastián, Bellavista 7, Santiago 8420524, Chile
| | - Daniel Bustos
- Laboratorio de Bioinformática y Química Computacional, Departamento de Medicina Traslacional, Facultad de Medicina, Universidad Católica del Maule, Talca 3480094, Chile
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2
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Khan Y, Khan S, Hussain R, Rehman W, Maalik A, Gulshan U, Attwa MW, Darwish HW, Ghabbour HA, Ali N. Identification of Indazole-Based Thiadiazole-Bearing Thiazolidinone Hybrid Derivatives: Theoretical and Computational Approaches to Develop Promising Anti-Alzheimer's Candidates. Pharmaceuticals (Basel) 2023; 16:1667. [PMID: 38139795 PMCID: PMC10747300 DOI: 10.3390/ph16121667] [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: 10/30/2023] [Revised: 11/18/2023] [Accepted: 11/28/2023] [Indexed: 12/24/2023] Open
Abstract
A hybrid library of compounds based on indazole-based thiadiazole containing thiazolidinone moieties (1-17) was synthesized. The synthesized compounds were screened in vitro for their inhibition profile against targetedacetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) activities. All the derivatives demonstrated a varied range of inhibitory activities having IC50 values ranging from 0.86 ± 0.33 μM to 26.73 ± 0.84 μM (AChE) and 0.89 ± 0.12 μM to 27.08 ± 0.19 μM (BuChE), respectively. The results obtained were compared with standard Donepezil drugs (IC50 = 1.26 ± 0.18 μM for AChE) and (1.35 ± 0.37 μM for BuChE), respectively. Specifically, the derivatives 1-17, 1, 9, and 14 were found to be significantly active, with IC50 values of 0.86 ± 0.30, 0.92 ± 0.10, and 1.10 ± 0.37 μM (against AChE) and 0.89 ± 0.12, 0.98 ± 0.48 and 1.19 ± 0.42 μM (against BuChE), respectively.The structure-activity relationship (SAR) studies revealed that derivatives bearing para-CF3, ortho-OH, and para-F substitutions on the phenyl ring attached to the thiadiazole skeleton, as well as meta-Cl, -NO2, and para-chloro substitutions on the phenyl ring, having a significant effect on inhibitory potential. The synthesized scaffolds have been further characterized by using 1H-NMR, 13C-NMR, and (HR-MS) to confirm the precise structures of the synthesized compounds. Additionally, the molecular docking approach was carried out for most active compounds to explore the binding interactions established by most active compounds, with the active sites of targeted enzymes and obtained results supporting the experimental data.
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Affiliation(s)
- Yousaf Khan
- Department of Chemistry, COMSATS University Islamabad, Islamabad 45550, Pakistan; (Y.K.); (U.G.)
| | - Shoaib Khan
- Department of Chemistry, Abbottabad University of Science and Technology (AUST), Abbottabad 22500, Pakistan;
| | - Rafaqat Hussain
- Department of Chemistry, Hazara University, Mansehra 21120, Pakistan;
| | - Wajid Rehman
- Department of Chemistry, Hazara University, Mansehra 21120, Pakistan;
| | - Aneela Maalik
- Department of Chemistry, COMSATS University Islamabad, Islamabad 45550, Pakistan; (Y.K.); (U.G.)
| | - Urooba Gulshan
- Department of Chemistry, COMSATS University Islamabad, Islamabad 45550, Pakistan; (Y.K.); (U.G.)
| | - Mohamed W. Attwa
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (M.W.A.); (H.W.D.)
| | - Hany W. Darwish
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (M.W.A.); (H.W.D.)
| | - Hazem A. Ghabbour
- School of Health and Biomedical Sciences, RMIT University, Melbourne 3083, Australia;
| | - Nawab Ali
- Shangai Key Laboratory of Functional Material Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Meilong Road 130, Shanghai 200237, China;
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3
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Phan THT, Hengphasatporn K, Shigeta Y, Xie W, Maitarad P, Rungrotmongkol T, Chavasiri W. Designing Potent α-Glucosidase Inhibitors: A Synthesis and QSAR Modeling Approach for Biscoumarin Derivatives. ACS OMEGA 2023; 8:26340-26350. [PMID: 37521599 PMCID: PMC10373460 DOI: 10.1021/acsomega.3c02868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 06/22/2023] [Indexed: 08/01/2023]
Abstract
Nineteen biscoumarins were synthesized, well-characterized, and evaluated against α-glucosidases in vitro. Of these, six compounds (10, 12, 16, and 17-19) were newly synthesized and not previously reported in the chemical literature. The majority of the synthesized derivatives demonstrated significant inhibitory activity. A quantitative structure-activity relationship (QSAR) model was developed, revealing a strong correlation between the anti-α-glucosidase activity and selected molecular descriptors. Based on this model, two new compounds (18 and 19) were designed, which exhibited the strongest inhibition with IC50 values of 0.62 and 1.21 μM, respectively, when compared to the positive control (acarbose) with an IC50 value of 93.63 μM. Enzyme kinetic studies of compounds 18 and 19 revealed their competitive inhibition with Ki values of 3.93 and 1.80 μM, respectively. Computational studies demonstrated that compound 18 could be inserted into the original binding site (OBS) of α-glucosidase MAL12 and form multiple hydrophobic interactions with nearby amino acids, with the bromo group playing an essential role in enhancing the binding strength and stability at the OBS of the enzyme based on the quantum mechanical calculations using the fragment molecular orbital method. These findings provide valuable insights into the design of potent α-glucosidase inhibitors, which may have potential therapeutic applications in the treatment of diabetes and related diseases.
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Affiliation(s)
- Thi-Hong-Truc Phan
- Center
of Excellence in Natural Products Chemistry, Department of Chemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand
| | - Kowit Hengphasatporn
- Center
for Computational Sciences, University of
Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Yasuteru Shigeta
- Center
for Computational Sciences, University of
Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Wanting Xie
- Research
Center of Nano Science and Technology, Shanghai
University, No. 99, Shangda Road, P.O. Box 111, Baoshan district, Shanghai 200444, People’s Republic of China
| | - Phornphimon Maitarad
- Research
Center of Nano Science and Technology, Shanghai
University, No. 99, Shangda Road, P.O. Box 111, Baoshan district, Shanghai 200444, People’s Republic of China
| | - Thanyada Rungrotmongkol
- Program
in Bioinformatics and Computational Biology, Graduated School, Chulalongkorn University, Bangkok 10330, Thailand
- Center
of Excellence in Structural and Computational Biology, Department
of Biochemistry, Faculty of Science, Chulalongkorn
University, Bangkok 10330, Thailand
| | - Warinthorn Chavasiri
- Center
of Excellence in Natural Products Chemistry, Department of Chemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand
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Taha M, Rahim F, Zaman K, Anouar EH, Uddin N, Nawaz F, Sajid M, Khan KM, Shah AA, Wadood A, Rehman AU, Alhibshi AH. Synthesis, in vitro biological screening and docking study of benzo[ d]oxazole bis Schiff base derivatives as a potent anti-Alzheimer agent. J Biomol Struct Dyn 2023; 41:1649-1664. [PMID: 34989316 DOI: 10.1080/07391102.2021.2023640] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
We have synthesized benzo[d]oxazole derivatives (1-21) through a multistep reaction. Alteration in the structure of derivatives was brought in the last step via using various substituted aromatic aldehydes. In search of an anti-Alzheimer agent, all derivatives were evaluated against acetylcholinesterase and butyrylcholinesterase enzyme under positive control of standard drug donepezil (IC50 = 0.016 ± 0.12 and 4.5 ± 0.11 µM) respectively. In case of acetylcholinesterase enzyme inhibition, derivatives 8, 9 and 18 (IC50 = 0.50 ± 0.01, 0.90 ± 0.05 and 0.3 ± 0.05 µM) showed very promising inhibitory potentials. While in case of butyrylcholinesterase enzyme inhibition, most of the derivatives like 6, 8, 9, 13, 15, 18 and 19 (IC50 = 2.70 ± 0.10, 2.60 ± 0.10, 2.20 ± 0.10, 4.25 ± 0.10, 3.30 ± 0.10, 0.96 ± 0.05 and 3.20 ± 0.10 µM) displayed better inhibitory potential than donepezil. Moreover, derivative 18 is the most potent one among the series in both inhibitions. The binding interaction of derivatives with the active gorge of the enzyme was confirmed via a docking study. Furthermore, the binding interaction between derivatives and the active site of enzymes was correlated through the SAR study. Structures of all derivatives were confirmed through spectroscopic techniques such as 1H-NMR, 13C-NMR and HREI-MS, respectively.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Muhammad Taha
- Department of Clinical Pharmacy, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Fazal Rahim
- Department of Chemistry, Hazara University, Mansehra, Khyber Pakhtunkhwa, Pakistan
| | - Khalid Zaman
- Department of Chemistry, Hazara University, Mansehra, Khyber Pakhtunkhwa, Pakistan
| | - El Hassane Anouar
- Department of Chemistry, College of Science and Humanities in Al-Kharj, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Nizam Uddin
- Department of Chemistry, University of Karachi, Karachi, Pakistan
| | - Faisal Nawaz
- Department of Chemistry, University of Wah, Wah Cantt, Pakistan
| | - Muhammad Sajid
- Department of Biochemistry, Hazara University, Mansehra, Khyber Pakhtunkhwa, Pakistan
| | - Khalid Mohammed Khan
- H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Adnan Ali Shah
- Atta-ur-Rahman Institute for Natural Product Discovery (AuRIns), Universiti Teknologi MARA Cawangan Selangor Kampus Puncak Alam, Bandar Puncak Alam, Selangor 42300, Malaysia.,Faculty of Pharmacy, Universiti Teknologi MARA Cawangan Selangor Kampus Puncak Alam, Bandar Puncak Alam, Selangor 42300, Malaysia
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Ashfaq Ur Rehman
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Amani H Alhibshi
- Department of Neuroscience Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
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5
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Taha M, Imran S, Rahim F, Uddin N, Iqbal N, Khan KM, Farooq RK, Alomari M, Islam I, Algheribe S. Discovering biological efficacy of new thiadiazole as effective inhibitors of urease, glycation, and (DPPH) scavengers: Biochemical and in silico study. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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6
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Irshad S, Ahmad S, Khan MA, Aziz M, Ejaz SA, Elhadi M. 2‐Chloro‐5‐(1‐hydroxy‐3‐oxoisoindolin‐1‐yl)benzenesulfonamides as potential inhibitors of urease: Synthesis, in‐vitro and molecular modeling approach. J CHIN CHEM SOC-TAIP 2022. [DOI: 10.1002/jccs.202200295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Sajid Irshad
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Alternative Medicine The Islamia University of Bahawalpur Bahawalpur Pakistan
| | - Saeed Ahmad
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Alternative Medicine The Islamia University of Bahawalpur Bahawalpur Pakistan
| | - Mohsin Abbas Khan
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Alternative Medicine The Islamia University of Bahawalpur Bahawalpur Pakistan
| | - Mubashir Aziz
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Alternative Medicine The Islamia University of Bahawalpur Bahawalpur Pakistan
| | - Syeda Abida Ejaz
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Alternative Medicine The Islamia University of Bahawalpur Bahawalpur Pakistan
| | - Muawya Elhadi
- Department of Physics, College of Science and Humanities Shaqra University Ad‐Dawadmi Saudi Arabia
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7
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H J Al-Qaisi Z, Al-Garawi ZS, M Al-Karawi AJ, Jasim Hammood A, Mosaad Abdallah A, Clegg W, Mohamed GG. Antiureolytic activity of new water-soluble thiadiazole derivatives: Spectroscopic, DFT, and molecular docking studies. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 272:120971. [PMID: 35152095 DOI: 10.1016/j.saa.2022.120971] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 12/29/2021] [Accepted: 01/27/2022] [Indexed: 06/14/2023]
Abstract
Two new water-soluble thiadiazole compounds are prepared and characterized with various techniques. These compounds, 5-amino-1,3,4-thiadiazole hydrochloride (1) and 5-amino-3-(N-propane-2-imine)-1,3,4-thiadiazole chloride salt (2) were synthesized via Mannich reaction, and characterized by microelemental analysis, and some spectroscopic means (FTIR, UV-Vis, 1H NMR, 13C NMR and mass), in addition to single-crystal X-ray diffraction for compound 2. DFT calculations were conducted to study their geometry optimization, vibrational spectra, MEP maps, and NBO analysis. In addition, TD-DFT calculations were performed to study their absorption spectra. The prepared compounds were tested against Jack beans urease enzyme (in vitro) to indicate their antiureolytic activity potency. The activity of the enzyme was measured under optimal conditions, before and after mixing with the prepared organic compounds. The results showed that both compounds have potentially inhibited the enzyme activity with respect to their IC50 values: 13.76 µM ± 0.15 for 1, and 18.81 µM ± 0.18 for 2. These values are even lower than that of thiourea (21.40 ± 0.21 µM) as a standard inhibitor. The inhibition activity of urease enzyme was confirmed by a Lineweaver-Burk plot. According to the kinetic parameters obtained from the Lineweaver-Burk plot, the inhibition of urease enzyme by compounds 1 and 2 seems to be non-competitive. Molecular docking studies of the prepared compounds 1 and 2 were performed in order to interpret the obtained biological results and to investigate their interactions with the urease enzyme active site. These studies reveal that compounds 1 and 2 are good candidates as inhibitors for urease enzyme. Moreover, compound 1 exhibits a higher promising inhibition activity.
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Affiliation(s)
- Zyad H J Al-Qaisi
- Department of Chemistry, College of Science, Mustansiriyah University, P.O. Box 46010, Baghdad, Iraq
| | - Zahraa S Al-Garawi
- Department of Chemistry, College of Science, Mustansiriyah University, P.O. Box 46010, Baghdad, Iraq
| | - Ahmed Jasim M Al-Karawi
- Department of Chemistry, College of Science, Mustansiriyah University, P.O. Box 46010, Baghdad, Iraq.
| | - Ali Jasim Hammood
- Department of Chemistry, College of Science, Mustansiriyah University, P.O. Box 46010, Baghdad, Iraq; Ministry of Education, Karkh-2, Baghdad, Iraq
| | - Abanoub Mosaad Abdallah
- Narcotic Research Department, National Center for Social and Criminological Research (NCSCR), Giza 11561, Egypt
| | - William Clegg
- Chemistry, School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE17RU, UK
| | - Gehad G Mohamed
- Chemistry Department, Faculty of Science, Cairo University, Giza 12613, Egypt
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8
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Aleaba G, Asadi SK, Daneshvar N, Shirini F. [2,2'-Bipyridine]-1,1'-diium perchlorate as a new and efficient dicationic organic salt for the promotion of the synthesis of bis(4-hydroxycoumarin), 5-arylidene barbituric acid and pyrano[2,3-d]pyrimidinone derivatives in water. RESEARCH ON CHEMICAL INTERMEDIATES 2022. [DOI: 10.1007/s11164-022-04692-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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9
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Synthesis, Molecular Docking and Biological Evaluation of Diaryl Pyrimidine Derivatives as Urease Inhibitors. Pharm Chem J 2022. [DOI: 10.1007/s11094-022-02582-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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10
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Yang XC, Zhang PL, Kumar KV, Li S, Geng RX, Zhou CH. Discovery of unique thiazolidinone-conjugated coumarins as novel broad spectrum antibacterial agents. Eur J Med Chem 2022; 232:114192. [DOI: 10.1016/j.ejmech.2022.114192] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/28/2022] [Accepted: 02/07/2022] [Indexed: 01/06/2023]
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11
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Song WQ, Liu ML, Li SY, Xiao ZP. Recent Efforts in the Discovery of Urease Inhibitor Identifications. Curr Top Med Chem 2021; 22:95-107. [PMID: 34844543 DOI: 10.2174/1568026621666211129095441] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 11/16/2021] [Accepted: 11/19/2021] [Indexed: 11/22/2022]
Abstract
Urease is an attractive drug target for designing anti-infective agents against pathogens such as Helicobacter pylori, Proteus mirabilis, and Ureaplasma urealyticum. In the past century, hundreds of medicinal chemists focused their efforts on explorations of urease inhibitors. Despite the FDA's approval of acetohydroxamic acid as a urease inhibitor for the treatment of struvite nephrolithiasis and the widespread use of N-(n-butyl)thiophosphoric triamide as a soil urease inhibitor as nitrogen fertilizer synergists in agriculture, urease inhibitors with high potency and safety are urgently needed. Exploration of novel urease inhibitors has therefore become a hot research topic recently. Herein, inhibitors identified worldwide from 2016 to 2021 have been reviewed. They structurally belong to more than 20 classes of compounds such as urea/thioure analogues, hydroxamic acids, sulfonamides, metal complexes, and triazoles. Some inhibitors showed excellent potency with IC50 values lower than 10 nM, having 10000-fold higher potency than the positive control thiourea.
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Affiliation(s)
- Wan-Qin Song
- Hunan Provincial Key Laboratory of Research, Resource Mining and High-valued Utilization on Edible & Medicinal Plant, Hunan Engineering Laboratory for Analyse and Drugs Development of Ethnomedicine in Wuling Mountains, National Demonstration Center for Experimental Chemistry Education, Jishou University, Jishou 416000. China
| | - Mei-Ling Liu
- Hunan Provincial Key Laboratory of Research, Resource Mining and High-valued Utilization on Edible & Medicinal Plant, Hunan Engineering Laboratory for Analyse and Drugs Development of Ethnomedicine in Wuling Mountains, National Demonstration Center for Experimental Chemistry Education, Jishou University, Jishou 416000. China
| | - Su-Ya Li
- Hunan Provincial Key Laboratory of Research, Resource Mining and High-valued Utilization on Edible & Medicinal Plant, Hunan Engineering Laboratory for Analyse and Drugs Development of Ethnomedicine in Wuling Mountains, National Demonstration Center for Experimental Chemistry Education, Jishou University, Jishou 416000. China
| | - Zhu-Ping Xiao
- Hunan Provincial Key Laboratory of Research, Resource Mining and High-valued Utilization on Edible & Medicinal Plant, Hunan Engineering Laboratory for Analyse and Drugs Development of Ethnomedicine in Wuling Mountains, National Demonstration Center for Experimental Chemistry Education, Jishou University, Jishou 416000. China
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12
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Taha M, Rahim F, Uddin N, Khan IU, Iqbal N, Anouar EH, Salahuddin M, Farooq RK, Gollapalli M, Khan KM, Zafar A. Exploring indole-based-thiadiazole derivatives as potent acetylcholinesterase and butyrylcholinesterase enzyme inhibitors. Int J Biol Macromol 2021; 188:1025-1036. [PMID: 34390751 DOI: 10.1016/j.ijbiomac.2021.08.065] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 07/26/2021] [Accepted: 08/08/2021] [Indexed: 11/27/2022]
Abstract
Indole based thiadiazole derivatives (1-18) were synthesized and evaluated for their acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) inhibition. The IC50 values of the synthesized analogues ranging between 0.17 ± 0.05 to 33.10 ± 0.6 μM against (AChE) and 0.30 ± 0.1 to 37.60 ± 0.6 μM against (BChE) enzymes. Among the series compounds 8 (IC50 = 0.17 ± 0.05 μM) (IC50 = 0.30 ± 0.1 μM), 9 (IC50 = 0.30 ± 0.05 μM) (IC50 = 0.60 ± 0.05 μM) and 10 (IC50 = 1.30 ± 0.1 μM) (IC50 = 2.60 ± 0.1) were found to be the most potent analogues bearing para, ortho, and meta-fluoro substitutions on phenyl ring attached to thiadiazole. In addition, all the synthesized scaffolds were characterized by using 1H NMR, 13C NMR spectroscopy, and high-resolution Mass Spectrometry (HR-MS). To apprehend the binding mode of interaction of the most potent synthesized derivatives, a molecular docking study was performed.
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Affiliation(s)
- Muhammad Taha
- Department of Clinical Pharmacy, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P. O. Box 1982, Dammam 31441, Saudi Arabia.
| | - Fazal Rahim
- Department of Chemistry, Hazara University, Mansehra 21120, Pakistan
| | - Nizam Uddin
- Department of Chemistry, University of Karachi, Karachi 75270, Pakistan
| | - Ihsan Ullah Khan
- Department of Chemistry, Hazara University, Mansehra 21120, Pakistan
| | - Naveed Iqbal
- Department of Chemistry, University of Poonch, Rawalakot, AJK, Pakistan
| | - El Hassane Anouar
- Department of Chemistry, College of Science and Humanities in Al-Kharj, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Mohammed Salahuddin
- Department of Clinical Pharmacy, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P. O. Box 1982, Dammam 31441, Saudi Arabia
| | - Rai Khalid Farooq
- Department of Neuroscience Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P. O. Box 1982, Dammam 31441, Saudi Arabia
| | - Mohammed Gollapalli
- College of Computer Science & Information Technology (CCSIT), Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 31441, Saudi Arabia
| | - Khalid Mohammed Khan
- H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Ameeduzzafar Zafar
- Department of Pharmaceutics, College of Pharmacy, Jouf University, Sakaka, Aljouf, Saudi Arabia
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Taha M, Ismail S, Imran S, Almandil NB, Alomari M, Rahim F, Uddin N, Hayat S, Zaman K, Ibrahim M, Alghanem B, Islam I, Farooq RK, Boudjelal M, Khan KM. Synthesis of new urease enzyme inhibitors as antiulcer drug and computational study. J Biomol Struct Dyn 2021; 40:8232-8247. [PMID: 33860726 DOI: 10.1080/07391102.2021.1910072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
In search of potent urease inhibitor indole analogues (1-22) were synthesized and evaluated for their urease inhibitory potential. All analogues (1-22) showed a variable degree of inhibitory interaction potential having IC50 value ranging between 0.60 ± 0.05 to 30.90 ± 0.90 µM when compared with standard thiourea having IC50 value 21.86 ± 0.90 µM. Among the synthesized analogues, the compounds 1, 2, 3, 5, 6, 8, 12, 14, 18, 20 and 22 having IC50 value 3.10 ± 0.10, 1.20 ± 0.10, 4.60 ± 0.10, 0.60 ± 0.05, 5.30 ± 0.20, 2.50 ± 0.10, 7.50 ± 0.20, 3.90 ± 0.10, 3.90 ± 0.10, 2.30 ± 0.05 and 0.90 ± 0.05 µM respectively were found many fold better than the standard thiourea. All other analogues showed better urease interaction inhibition. Structure activity relationship (SAR) has been established for all analogues containing different substituents on the phenyl ring. To understand the binding interaction of most active analogues with enzyme active site docking study were performed.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Muhammad Taha
- Department of clinical pharmacy, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Sukinah Ismail
- Department of clinical pharmacy, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia.,College of clinical pharmacy, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Syahrul Imran
- Atta-ur-Rahman Institute for Natural Product Discovery, Universiti Teknologi MARA (UiTM), Bandar Puncak Alam, Selangor, Malaysia.,Faculty of Applied Science, UiTM Shah Alam, Shah Alam, Selangor, Malaysia
| | - Noor Barak Almandil
- Department of clinical pharmacy, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Munther Alomari
- Department of Stem Cell Biology, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Fazal Rahim
- Department of Chemistry, Hazara University, Mansehra, Khyber Pakhtunkhwa, Pakistan
| | - Nizam Uddin
- Department of Chemistry, University of Karachi, Karachi, Pakistan
| | - Shawkat Hayat
- Department of Chemistry, Hazara University, Mansehra, Khyber Pakhtunkhwa, Pakistan
| | - Khalid Zaman
- Department of Chemistry, Hazara University, Mansehra, Khyber Pakhtunkhwa, Pakistan
| | - Mohamad Ibrahim
- Department of clinical pharmacy, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Bandar Alghanem
- Medical Research Core Facility and Platforms (MRCFP, King Abdullah International Medical Research Center/King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), King Abdulaziz Medical City (KAMC), NGHA, Riyadh, Saudi Arabia
| | - Imadul Islam
- Medical Research Core Facility and Platforms (MRCFP, King Abdullah International Medical Research Center/King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), King Abdulaziz Medical City (KAMC), NGHA, Riyadh, Saudi Arabia
| | - Rai Khalid Farooq
- Department of Neuroscience Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Mohamed Boudjelal
- Medical Research Core Facility and Platforms (MRCFP, King Abdullah International Medical Research Center/King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), King Abdulaziz Medical City (KAMC), NGHA, Riyadh, Saudi Arabia
| | - Khalid Mohammed Khan
- H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
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Nazari Montazer M, Asadi M, Bahadorikhalili S, Hosseini FS, Amanlou A, Biglar M, Amanlou M. Design, synthesis, docking study and urease inhibitory activity evaluation of novel 2-((5-amino-1,3,4-thiadiazol-2-yl)thio)-N-arylacetamide derivatives. Med Chem Res 2021. [DOI: 10.1007/s00044-020-02683-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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15
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4-Oxycoumarinyl linked acetohydrazide Schiff bases as potent urease inhibitors. Bioorg Chem 2020; 105:104365. [DOI: 10.1016/j.bioorg.2020.104365] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 09/07/2020] [Accepted: 10/08/2020] [Indexed: 01/10/2023]
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16
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Asgari MS, Azizian H, Nazari Montazer M, Mohammadi-Khanaposhtani M, Asadi M, Sepehri S, Ranjbar PR, Rahimi R, Biglar M, Larijani B, Amanlou M, Mahdavi M. New 1,2,3-triazole-(thio)barbituric acid hybrids as urease inhibitors: Design, synthesis, in vitro urease inhibition, docking study, and molecular dynamic simulation. Arch Pharm (Weinheim) 2020; 353:e2000023. [PMID: 32596826 DOI: 10.1002/ardp.202000023] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 05/26/2020] [Accepted: 05/30/2020] [Indexed: 12/23/2022]
Abstract
A new series of 1,2,3-triazole-(thio)barbituric acid hybrids 8a-n was designed and synthesized on the basis of potent pharmacophores with urease inhibitory activity. Therefore, these compounds were evaluated against Helicobacter pylori urease. The obtained result demonstrated that all the synthesized compounds, 8a-n, were more potent than the standard urease inhibitor, hydroxyurea. Moreover, among them, compounds 8a, 8c-e, 8g,h, and 8k,l exhibited higher urease inhibitory activities than the other standard inhibitor used: thiourea. Docking studies were performed with the synthesized compounds. Furthermore, molecular dynamic simulation of the most potent compounds, 8e and 8l, showed that these compounds interacted with the conserved residues Cys592 and His593, which belong to the active site flap and are essential for enzymatic activity. These interactions have two consequences: (a) blocking the movement of a flap at the entrance of the active site channel and (b) stabilizing the closed active site flap conformation, which significantly reduces the catalytic activity of urease. Calculation of the physicochemical and topological properties of the synthesized compounds 8a-n predicted that all these compounds can be orally active. The ADME prediction of compounds 8a-n was also performed.
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Affiliation(s)
- Mohammad S Asgari
- School of Chemistry, College of Science, University of Tehran, Tehran, Iran
| | - Homa Azizian
- Department of Medicinal Chemistry, School of Pharmacy-International Campus, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Nazari Montazer
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutical Sciences Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Mohammadi-Khanaposhtani
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Mehdi Asadi
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutical Sciences Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Saghi Sepehri
- Department of Medicinal Chemistry, School of Pharmacy, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Parviz R Ranjbar
- School of Chemistry, College of Science, University of Tehran, Tehran, Iran
| | - Rahmatollah Rahimi
- Department of Chemistry, Iran University of Science and Technology, Tehran, Iran
| | - Mahmood Biglar
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Bagher Larijani
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Massoud Amanlou
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutical Sciences Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Mahdavi
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
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17
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Overview on developed synthesis procedures of coumarin heterocycles. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2020. [DOI: 10.1007/s13738-020-01984-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
AbstractConsidering highly valuable biological and pharmaceutical properties of coumarins, the synthesis of these heterocycles has been considered for many organic and pharmaceutical chemists. This review includes the recent research in synthesis methods of coumarin systems, investigating their biological properties and describing the literature reports for the period of 2016 to the middle of 2020. In this review, we have classified the contents based on co-groups of coumarin ring. These reported methods are carried out in the classical and non-classical conditions particularly under green condition such as using green solvent, catalyst and other procedures.
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Synthesis and Structure-Activity Relationship of Palmatine Derivatives as a Novel Class of Antibacterial Agents against Helicobacter pylori. Molecules 2020; 25:molecules25061352. [PMID: 32188132 PMCID: PMC7146163 DOI: 10.3390/molecules25061352] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 03/10/2020] [Accepted: 03/12/2020] [Indexed: 12/15/2022] Open
Abstract
Taking palmatine (PMT) as the lead, 20 new PMT derivatives were synthesized and examined for their antibacterial activities against six tested metronidazole (MTZ)-resistant Helicobacter pylori (H. pylori) strains. The structure–activity relationship (SAR) indicated that the introduction of a suitable secondary amine substituent at the 9-position might be beneficial for potency. Among them, compound 1c exhibited the most potent activities against MTZ-resistant strains, with minimum inhibitory concentration (MIC) values of 4–16 μg/mL, better than that of the lead. It also exhibited a good safety profile with a half-lethal dose (LD50) of over 1000 mg/kg. Meanwhile, 1c might exert its antimicrobial activity through targeting H. pylori urease. These results suggested that PMT derivatives might be a new family of anti-H. pylori components.
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Biglar M, Mirzazadeh R, Asadi M, Sepehri S, Valizadeh Y, Sarrafi Y, Amanlou M, Larijani B, Mohammadi-Khanaposhtani M, Mahdavi M. Novel N,N-dimethylbarbituric-pyridinium derivatives as potent urease inhibitors: Synthesis, in vitro, and in silico studies. Bioorg Chem 2019; 95:103529. [PMID: 31884139 DOI: 10.1016/j.bioorg.2019.103529] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 12/16/2019] [Accepted: 12/19/2019] [Indexed: 01/19/2023]
Abstract
A new series of N,N-dimethylbarbituric-pyridinium derivatives 7a-n was synthesized and evaluated as Helicobacter pylori urease inhibitors. All the synthesized compounds (IC50 = 10.37 ± 1.0-77.52 ± 2.7 μM) were more potent than standard inhibitor hydroxyurea against urease (IC50 = 100.00 ± 0.2 μM). Furthermore, comparison of IC50 values of the synthesized compounds with the second standard inhibitor thiourea (IC50 = 22.0 ± 0.03 µM) revealed that compounds 7a-b and 7f-h were more potent than thiourea. Molecular modeling study of the most potent compounds 7a, 7b, 7f, and 7g was also conducted. Additionally, the drug-likeness properties of the synthesized compounds, based on Lipinski rule and other filters, were evaluated.
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Affiliation(s)
- Mahmood Biglar
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Mehdi Asadi
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutical Sciences, Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Saghi Sepehri
- Department of Medicinal Chemistry, School of Pharmacy, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Yousef Valizadeh
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Yaghoub Sarrafi
- Faculty of Chemistry, University of Mazandaran, Babolsar, Iran
| | - Massoud Amanlou
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutical Sciences, Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Bagher Larijani
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Mohammadi-Khanaposhtani
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran.
| | - Mohammad Mahdavi
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran.
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