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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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Khalili Ghomi M, Noori M, Nazari Montazer M, Zomorodian K, Dastyafteh N, Yazdanpanah S, Sayahi MH, Javanshir S, Nouri A, Asadi M, Badali H, Larijani B, Irajie C, Iraji A, Mahdavi M. [1,2,4]triazolo[3,4-b][1,3,4]thiadiazole derivatives as new therapeutic candidates against urease positive microorganisms: design, synthesis, pharmacological evaluations, and in silico studies. Sci Rep 2023; 13:10136. [PMID: 37349372 PMCID: PMC10287669 DOI: 10.1038/s41598-023-37203-z] [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: 02/17/2023] [Accepted: 06/17/2023] [Indexed: 06/24/2023] Open
Abstract
Regarding the important role of the urease enzyme as a virulence factor in urease-positive microorganisms in this study, new series of [1,2,4]triazolo[3,4-b][1,3,4]thiadiazole derivatives were designed and synthesized. All compounds evaluated against urease enzyme exhibiting IC50 values of 0.87 ± 0.09 to 8.32 ± 1.21 µM as compared with thiourea as the positive control (IC50 = 22.54 ± 2.34 µM). The kinetic evaluations of 6a as the most potent derivative recorded a competitive type of inhibition. Molecular dynamic simulations of the 6a derivative were also conducted, showing that 6a occupied the active site with closed state. Antimicrobial activities of all derivatives were performed, and 6f (R = 3-Cl), 6g (R = 4-Cl), and 6h (R = 3,4-diCl) analogs demonstrated significant antifungal activities with MIC values of 1, 2, and 0.5 µg/mL compared with fluconazole with MIC = 2 µg/mL. Synthesized analogs also exhibited potent urease inhibitory activities against C. neoformans (IC50 = 83.7-118.7 µg/mL) and P. mirabilis (IC50 = 74.5-113.7 µg/mL), confirming their urease inhibitory potential. The results demonstrated that the designed scaffold could be considered a suitable pharmacophore to develop potent urease inhibitors.
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Affiliation(s)
- Minoo Khalili Ghomi
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
- Stem Cells Technology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Milad Noori
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Nazari Montazer
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Kamiar Zomorodian
- Department of Medical Mycology and Parasitology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Navid Dastyafteh
- Pharmaceutical and Heterocyclic Chemistry Research Laboratory, Department of Chemistry, Iran University of Science and Technology, Tehran, 16846-13114, Iran
| | - Somayeh Yazdanpanah
- Department of Medical Mycology and Parasitology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Hosein Sayahi
- Department of Chemistry, Payame Noor University (PNU), P.O. Box 19395-3697, Tehran, Iran
| | - Shahrzad Javanshir
- Pharmaceutical and Heterocyclic Chemistry Research Laboratory, Department of Chemistry, Iran University of Science and Technology, Tehran, 16846-13114, Iran
| | - Abbas Nouri
- Department of Medical Mycology and Parasitology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mehdi Asadi
- Department of Medicinal Chemistry, School of Pharmacy-International Campus, Iran University of Medical Science, Tehran, Iran
| | - Hamid Badali
- Department of Molecular Microbiology & Immunology, and South Texas Center for Emerging Infectious Diseases, The University of Texas at San Antonio, San Antonio, TX, USA
| | - Bagher Larijani
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Cambyz Irajie
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Aida Iraji
- Stem Cells Technology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
- Central Research Laboratory, Shiraz University of Medical Sciences, Shiraz, 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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Yang Z, Fu X, Zhao Y, Li X, Long J, Zhang L. Molecular insights into the inhibition mechanism of harringtonine against essential proteins associated with SARS-CoV-2 entry. Int J Biol Macromol 2023; 240:124352. [PMID: 37054859 PMCID: PMC10085973 DOI: 10.1016/j.ijbiomac.2023.124352] [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] [Received: 02/06/2023] [Revised: 03/11/2023] [Accepted: 04/03/2023] [Indexed: 04/15/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has recently posed a serious threat to global public health. Harringtonine (HT), as a small-molecule antagonist, has antiviral activity against a variety of viruses. There is evidence that HT can inhibit the SARS-CoV-2 entry into host cells by blocking the Spike protein and transmembrane protease serine 2 (TMPRSS2). However, the molecular mechanism underlying the inhibition effect of HT is largely elusive. Here, docking and all-atom molecular dynamic simulations were used to investigate the mechanism of HT against the receptor binding domain (RBD) of Spike, TMPRSS2, as well as the complex of RBD and angiotensin-converting enzyme 2 complex (RBD-ACE2). The results reveal that HT binds to all proteins primarily through hydrogen bond and hydrophobic interactions. Binding with HT influences the structural stability and dynamic motility processes of each protein. The interactions of HT with residues N33, H34 and K353 of ACE2, and residue K417 and Y453 of RBD contribute to disrupting the binding affinity between RBD and ACE2, which may hinder the virus entry into host cells. Our research provides molecular insights into the inhibition mechanism of HT against SARS-CoV-2 associated proteins, which will help for the novel antiviral drugs development.
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Affiliation(s)
- Zhiwei Yang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China; School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China.
| | - Xinyue Fu
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Yizhen Zhao
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Xuhua Li
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China.
| | - Jiangang Long
- School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
| | - Lei Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
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Gültekin E, Bekircan O, Kara Y, Güler Hİ, Soylu MS, Kolaylı S. 1,3,4-Thiadiazole and 1,2,4-triazole-5-thione derivatives bearing 2-pentyl-5-phenyl-2,4-dihydro-3H-1,2,4-triazole-3-one ring: Synthesis, molecular docking, urease inhibition, and crystal structure. Arch Pharm (Weinheim) 2023; 356:e2200355. [PMID: 36316247 DOI: 10.1002/ardp.202200355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 10/06/2022] [Accepted: 10/07/2022] [Indexed: 01/03/2023]
Abstract
Two series of 1,3,4-thiadiazole (40a-o) and 1,2,4-triazole-5-thione (41a-l) derivatives bearing a 2-pentyl-5-phenyl-1,2,4-triazole-3-one ring were synthesized and then studied for their urease inhibitory activities using thiourea as a standard drug. Among the two groups, the first group (40a-o) did not show good activity while the second group (41a-l) showed excellent activity. Compound 41j (1091.24 ± 14.02 µM) of the second series of compounds showed lower activity than thiourea, while the remaining 11 compounds (41a-i, k, and l) showed better activity than thiourea (183.92 ± 13.14 µM). Among the 11 compounds, 41b (15.96 ± 2.28 µM) having the 3-F group on the phenyl ring showed the highest inhibitory activity. Urease kinetic studies of 41b, which is the most active compound, determined it to have an un-competitive inhibition potential. Moreover, in silico analysis against urease from jack bean with 27 new heterocyclic compounds and the reference molecule was carried out to see the necessary interactions responsible for urease activity. The docking calculations of all compounds supported stronger binding to the receptor than the reference molecule, with high inhibition constants. In addition, compound 40m was characterized by single-crystal X-ray diffraction analysis. X-ray analysis reveals that the structures of the compound 40m crystallize in the monoclinic P21/c space group with the cell parameters: a = 10.2155(9) Å, b = 22.1709(18) Å, c = 21.4858(17) Å, β = 99.677(8)°, V = 4797.0(7) Å3 . X-ray diffraction analyses were also performed to gain insights into the role of weak intermolecular interactions and C-H…X (halogen) interactions in compound 40m that influence the crystal packing.
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Affiliation(s)
- Ergün Gültekin
- Science Technology Research and Application Center, Artvin Coruh University, Artvin, Turkey
| | - Olcay Bekircan
- Department of Chemistry, Faculty of Science, Karadeniz Technical University, Trabzon, Turkey
| | - Yakup Kara
- Department of Chemistry, Faculty of Science, Karadeniz Technical University, Trabzon, Turkey
| | - Halil İbrahim Güler
- Department of Molecular Biology and Genetics, Faculty of Science, Karadeniz Technical University, Trabzon, Turkey
| | - Mustafa Serkan Soylu
- Department of Physics, Art and Science Faculty, Giresun University, Giresun, Turkey
| | - Sevgi Kolaylı
- Department of Chemistry, Faculty of Science, Karadeniz Technical University, Trabzon, Turkey
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X-ray Structures and Computational Studies of Two Bioactive 2-(Adamantane-1-carbonyl)- N-substituted Hydrazine-1-carbothioamides. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27238425. [PMID: 36500517 PMCID: PMC9741201 DOI: 10.3390/molecules27238425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/11/2022] [Accepted: 11/25/2022] [Indexed: 12/05/2022]
Abstract
Two biologically active adamantane-linked hydrazine-1-carbothioamide derivatives, namely 2-(adamantane-1-carbonyl)-N-(tert-butyl)hydrazine-1-carbothioamide) 1 and 2-(adamantane-1-carbonyl)-N-cyclohexylhydrazine-1-carbothioamide 2, have been synthesized. X-ray analysis was conducted to study the effect of the t-butyl and cyclohexyl moieties on the intermolecular interactions and conformation of the molecules in the solid state. X-ray analysis reveals that compound 1 exhibits folded conformation, whereas compound 2 adopts extended conformation. The Hirshfeld surface analysis indicates that the contributions of the major intercontacts involved in the stabilization of the crystal structures do not change much as a result of the t-butyl and cyclohexyl moieties. However, the presence and absence of these contacts is revealed by the 2D-fingerprint plots. The CLP-Pixel method was used to identify the energetically significant molecular dimers. These dimers are stabilized by different types of intermolecular interactions such as N-H···S, N-H···O, C-H···S, C-H···O, H-H bonding and C-H···π interactions. The strength of these interactions was quantified by using the QTAIM approach. The results suggest that N-H···O interaction is found to be stronger among other interactions. The in vitro assay suggests that both compounds 1 and 2 exhibit urease inhibition potential, and these compounds also display moderate antiproliferative activities. Molecular docking analysis shows the key interaction between urease enzyme and title compounds.
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6
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Synthesis and Identification of New N, N-Disubstituted Thiourea, and Thiazolidinone Scaffolds Based on Quinolone Moiety as Urease Inhibitor. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27207126. [PMID: 36296723 PMCID: PMC9608620 DOI: 10.3390/molecules27207126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/15/2022] [Accepted: 10/18/2022] [Indexed: 11/16/2022]
Abstract
Synthesis of thiazolidinone based on quinolone moiety was established starting from 4-hydroxyquinol-2-ones. The strategy started with the reaction of ethyl bromoacetate with 4-hydroxyquinoline to give the corresponding ethyl oxoquinolinyl acetates, which reacted with hydrazine hydrate to afford the hydrazide derivatives. Subsequently, hydrazides reacted with isothiocyanate derivatives to give the corresponding N,N-disubstituted thioureas. Finally, on subjecting the N,N-disubstituted thioureas with dialkyl acetylenedicarboxylates, cyclization occurred, and thiazolidinone derivatives were obtained in good yields. The two series based on quinolone moiety, one containing N,N-disubstituted thioureas and the other containing thiazolidinone functionalities, were screened for their in vitro urease inhibition properties using thiourea and acetohydroxamic acid as standard inhibitors. The inhibition values of the synthesized thioureas and thiazolidinones exhibited moderate to good inhibitory effects. The structure-activity relationship revealed that N-methyl quinolonyl moiety exhibited a superior effect, since it was proved to be the most potent inhibitor in the present series achieving (IC50 = 1.83 ± 0.79 µM). The previous compound exhibited relatively much greater activity, being approximately 12-fold more potent than thiourea and acetohydroxamic acid as references. Molecular docking analysis showed a good protein-ligand interaction profile against the urease target (PDBID: 4UBP), emphasizing the electronic and geometric effect of N,N-disubstituted thiourea.
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Baltaş N. Synthesis of quinazolinone derivatives containing an acyl hydrazone skeleton as potent anti-urease agents enzyme kinetic studies and anti-oxidant properties. JOURNAL OF CHEMICAL RESEARCH 2022. [DOI: 10.1177/17475198221096568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
This paper covers the synthesis, in vitro urease inhibition, enzyme kinetic parameters, and anti-oxidant studies of a novel series of quinazolinone derivatives containing an acyl hydrazone skeleton. Compounds 3a, 3b, 5a, and 5b, having IC50 values ranging from 1.86 ± 0.07 to 6.38 ± 0.11 µg mL−1, show greater inhibitory activity than the standard inhibitor, thiourea. Among the products, (2-[2-(3-methoxybenzyl)-4-oxoquinazolin-3(4 H)-yl]acetohydrazide) proves to be the most potent, exhibiting enzyme inhibition activity with an IC50 value of 1.86 ± 0.07 µg mL−1. Kinetic studies involving the Lineweaver–Burk plots reveal that the inhibition mechanism of the most active compounds (3a, 3b, 5a, and 5b) on urease activity are found to be in competitive mode. Also, the anti-oxidant activity and radical-scavenging properties of the synthesized compounds are evaluated using cupric reducing anti-oxidant activity, ferric reducing anti-oxidant capacity, 2,2′-azinobis-(3-ethylbenzothiazoline-6-sulfonic acid), and 2,2-diphenyl-1-picrylhydrazyl assays. Compounds 3a, b and 5a, b have good anti-oxidant properties and radical-scavenging activity at various final concentrations.
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Affiliation(s)
- Nimet Baltaş
- Department of Chemistry, Faculty of Arts and Sciences, Recep Tayyip Erdogan University, Rize, Turkey
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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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Yang W, Feng Q, Peng Z, Wang G. An overview on the synthetic urease inhibitors with structure-activity relationship and molecular docking. Eur J Med Chem 2022; 234:114273. [PMID: 35305460 DOI: 10.1016/j.ejmech.2022.114273] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 03/04/2022] [Accepted: 03/08/2022] [Indexed: 01/06/2023]
Abstract
Urease is a kind of enzyme which could be found in various bacteria, fungi, plants, and algae, which can quickly catalyze the hydrolysis of urea into ammonia and carbon dioxide. With the ammonia concentration increasing, the activity of Helicobacter pylori has got an obvious enhancement and leads to mucosal damage in the stomach, gastroduodenal infection, peptic ulcers, and gastric cancer. The infectious diseases caused by Helicobacter pylori can be controlled to a certain extent by inhibiting urease activity with urease inhibitors. Hence, studies of urease inhibitors have attracted great attention all over the world and a variety of effective urease inhibitors have been synthesized in recent years. In this review, we will draw summaries for these inhibitors including urease inhibitory activity, inhibition kinetics, structure-activity relationship, and molecular docking. The collected information is expected to provide rational guidance and effective strategy to develop novel, potent, and safe urease inhibitors for better practical applications in the future.
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Affiliation(s)
- Wei Yang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Key Laboratory of Pharmaceutics, Guizhou Medical University, Guiyang, China; Teaching and Research Section of Natural Medicinal Chemistry, School of Pharmacy, Guizhou Medical University, Guiyang, China
| | - Qianqian Feng
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Key Laboratory of Pharmaceutics, Guizhou Medical University, Guiyang, China; Teaching and Research Section of Natural Medicinal Chemistry, School of Pharmacy, Guizhou Medical University, Guiyang, China
| | - Zhiyun Peng
- Office of Drug Clinical Trial Institutions, The Affiliated Hospital of Guizhou Medical University, Guiyang, China.
| | - Guangcheng Wang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Key Laboratory of Pharmaceutics, Guizhou Medical University, Guiyang, China; Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Medical University, Guiyang, China.
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10
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Sohrabi M, Nazari Montazer M, Farid SM, Tanideh N, Dianatpour M, Moazzam A, Zomorodian K, Yazdanpanah S, Asadi M, Hosseini S, Biglar M, Larijani B, Amanlou M, Barazandeh Tehrani M, Iraji A, Mahdavi M. Design and synthesis of novel nitrothiazolacetamide conjugated to different thioquinazolinone derivatives as anti-urease agents. Sci Rep 2022; 12:2003. [PMID: 35132095 PMCID: PMC8821706 DOI: 10.1038/s41598-022-05736-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 01/11/2022] [Indexed: 01/07/2023] Open
Abstract
The present article describes the design, synthesis, in vitro urease inhibition, and in silico molecular docking studies of a novel series of nitrothiazolacetamide conjugated to different thioquinazolinones. Fourteen nitrothiazolacetamide bearing thioquinazolinones derivatives (8a-n) were synthesized through the reaction of isatoic anhydride with different amine, followed by reaction with carbon disulfide and KOH in ethanol. The intermediates were then converted into final products by treating them with 2-chloro-N-(5-nitrothiazol-2-yl)acetamide in DMF. All derivatives were then characterized through different spectroscopic techniques (1H, 13C-NMR, MS, and FTIR). In vitro screening of these molecules against urease demonstrated the potent urease inhibitory potential of derivatives with IC50 values ranging between 2.22 ± 0.09 and 8.43 ± 0.61 μM when compared with the standard thiourea (IC50 = 22.50 ± 0.44 μM). Compound 8h as the most potent derivative exhibited an uncompetitive inhibition pattern against urease in the kinetic study. The high anti-ureolytic activity of 8h was confirmed against two urease-positive microorganisms. According to molecular docking study, 8h exhibited several hydrophobic interactions with Lys10, Leu11, Met44, Ala47, Ala85, Phe87, and Pro88 residues plus two hydrogen bound interactions with Thr86. According to the in silico assessment, the ADME-Toxicity and drug-likeness profile of synthesized compounds were in the acceptable range.
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Affiliation(s)
- Marzieh Sohrabi
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran 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
| | - Sara Moghadam Farid
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Nader Tanideh
- Stem Cells Technology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mehdi Dianatpour
- Stem Cells Technology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ali Moazzam
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Kamiar Zomorodian
- Department of Medical Mycology and Parasitology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Somayeh Yazdanpanah
- Department of Medical Mycology and Parasitology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mehdi Asadi
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Samanesadat Hosseini
- Department of Pharmaceutical Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, 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
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Maliheh Barazandeh Tehrani
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutical Sciences Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Aida Iraji
- Stem Cells Technology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
- Central Research Laboratory, Shiraz University of Medical Sciences, Shiraz, Iran.
- Liosa Pharmed Parseh Company, Shiraz, 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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11
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Uprety B, Chandran R, Arderne C, Abrahamse H. Anticancer Activity of Urease Mimetic Cobalt (III) Complexes on A549-Lung Cancer Cells: Targeting the Acidic Microenvironment. Pharmaceutics 2022; 14:pharmaceutics14010211. [PMID: 35057107 PMCID: PMC8780642 DOI: 10.3390/pharmaceutics14010211] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/23/2021] [Accepted: 01/11/2022] [Indexed: 12/30/2022] Open
Abstract
Tumour cells maintain a local hypoxic and acidic microenvironment which plays a crucial role in cancer progression and drug resistance. Urease is a metallohydrolases that catalyses the hydrolysis of urea into ammonia and carbon dioxide, causing an abrupt increase of pH. This enzymatic activity can be employed to target the acidic tumour microenvironment. In this study, we present the anticancer activities of urease mimetic cobalt (III) complexes on A549 cells. The cells were treated with different doses of cobalt (III) complexes to observe the cytotoxicity. The change in cellular morphology was observed using an inverted microscope. The cell death induced by these complexes was analysed through ATP proliferation, LDH release and caspase 3/7 activity. The effect of extracellular alkalinization by the cobalt (III) complexes on the efficacy of the weakly basic drug, doxorubicin (dox) was also evaluated. This combination therapy of dox with cobalt (III) complexes resulted in enhanced apoptosis in A549 cells, as evidenced by elevated caspase 3/7 activity in treated groups. The study confirms the urease mimicking anticancer activity of cobalt (III) complexes by neutralizing the tumour microenvironment. This study will motivate the applications of transition metal-based enzyme mimics in targeting the tumour microenvironment for effective anticancer treatments.
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Affiliation(s)
- Bhawna Uprety
- Laser Research Centre, Faculty of Health Sciences, University of Johannesburg, P.O. Box 17011, Johannesburg 2028, South Africa;
- Correspondence: (B.U.); (R.C.); Tel.: +27-11-559-6926 (R.C.)
| | - Rahul Chandran
- Laser Research Centre, Faculty of Health Sciences, University of Johannesburg, P.O. Box 17011, Johannesburg 2028, South Africa;
- Correspondence: (B.U.); (R.C.); Tel.: +27-11-559-6926 (R.C.)
| | - Charmaine Arderne
- Research Centre for Synthesis and Catalysis, Department of Chemical Sciences, University of Johannesburg, P.O. Box 524, Johannesburg 2092, South Africa;
| | - Heidi Abrahamse
- Laser Research Centre, Faculty of Health Sciences, University of Johannesburg, P.O. Box 17011, Johannesburg 2028, South Africa;
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12
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Tok F, Baltaş N, Tatar G, Koçyiğit-Kaymakçıoğlu B. Synthesis, biological evaluation and in silico studies of new pyrazoline derivatives bearing benzo[d]thiazol-2(3H)-one moiety as potential urease inhibitors. Chem Biodivers 2022; 19:e202100826. [PMID: 35018718 DOI: 10.1002/cbdv.202100826] [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] [Received: 10/12/2021] [Accepted: 01/11/2022] [Indexed: 11/09/2022]
Abstract
Novel pyrazoline derivatives containing benzo[d]thiazol-2(3H)-one moiety were synthesized and screened for their inhibitory properties against to urease, a clinically important metabolic enzyme. In vitro enzyme inhibition studies revealed that all pyrazolines (7.21-87.77 µM) were more potent than the standard inhibitor acetohydroxamic acid (251.74 µM) against the urease enzyme. Most notably, compound 2m , which is more active than the other compounds in in vitro and molecular docking studies, showed a significant inhibition potential and efficient IC 50 values (7.21±0.09 µM) and in silico inhibition constant (0.11 µM). Furthermore, molecular dynamics (MD) simulation analysis suggests that the binding stability of urease enzyme and compound 2m were stably maintained during the 100 ns simulation time. Compound 2m also exhibited good physicochemical and pharmacokinetic parameters. The overall results of urease inhibition have indicated that these pyrazoline derivative compounds can be further optimized and developed for the discovery of novel urease inhibitors.
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Affiliation(s)
- Fatih Tok
- Marmara Universitesi Eczacilik Fakultesi, Pharmaceutical Chemistry, Marmara University, Faculty of Pharmacy, Department of Pharmaceutical Chemistry,, 34854 4/A, Istanbul, TURKEY
| | - Nimet Baltaş
- Recep Tayyip Erdogan University Faculty of Arts and Sciences: Recep Tayyip Erdogan Universitesi Fen Edebiyat Fakultesi, Chemistry, Department of Chemistry, Faculty of Arts and Sciences, Rize, TURKEY
| | - Gizem Tatar
- Karadeniz Technical University: Karadeniz Teknik Universitesi, Bioistatistics and Medical Informatics, Department of Biostatistics and Medical Informatics, Faculty of Medicine, Trabzon, TURKEY
| | - Bedia Koçyiğit-Kaymakçıoğlu
- Marmara University: Marmara Universitesi, Pharmaceutical Chemistry, Marmara University, Faculty of Pharmacy, Department of Pharmaceutical Chemistry,, Türkiye, 34854 4/A, Istanbul, TURKEY
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13
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Jafari E, Rezaeinasab R, Khodarahmi G. Quinazolinone-based hybrids with diverse biological activities: A mini-review. JOURNAL OF RESEARCH IN MEDICAL SCIENCES 2022; 27:68. [PMID: 36353342 PMCID: PMC9639715 DOI: 10.4103/jrms.jrms_1025_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 02/12/2022] [Accepted: 04/04/2022] [Indexed: 11/16/2022]
Abstract
Quinazolinone and quinazoline have been shown different pharmacological activities, namely anticancer, anti-inflammatory, anti-hyperlipidemia, analgesic, antihypertensive, and antibacterial. On the other hand, molecular hybridization is a structural modification technique in the design of new ligands which consist of two or more pharmacologically active molecules in one structure. Therefore, due to the importance of the biological activities of quinazolinones for the development of new therapeutic agents, this review emphasizes current findings on various quinazolinone-based hybrids in medicinal chemistry. Moreover, it highlights the biological activities and structure-activity relationship of these hybrids.
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14
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Sharma S, Basu B. Biomaterials assisted reconstructive urology: The pursuit of an implantable bioengineered neo-urinary bladder. Biomaterials 2021; 281:121331. [PMID: 35016066 DOI: 10.1016/j.biomaterials.2021.121331] [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: 05/24/2021] [Revised: 12/14/2021] [Accepted: 12/24/2021] [Indexed: 12/27/2022]
Abstract
Urinary bladder is a dynamic organ performing complex physiological activities. Together with ureters and urethra, it forms the lower urinary tract that facilitates urine collection, low-pressure storage, and volitional voiding. However, pathological disorders are often liable to cause irreversible damage and compromise the normal functionality of the bladder, necessitating surgical intervention for a reconstructive procedure. Non-urinary autologous grafts, primarily derived from gastrointestinal tract, have long been the gold standard in clinics to augment or to replace the diseased bladder tissue. Unfortunately, such treatment strategy is commonly associated with several clinical complications. In absence of an optimal autologous therapy, a biomaterial based bioengineered platform is an attractive prospect revolutionizing the modern urology. Predictably, extensive investigative research has been carried out in pursuit of better urological biomaterials, that overcome the limitations of conventional gastrointestinal graft. Against the above backdrop, this review aims to provide a comprehensive and one-stop update on different biomaterial-based strategies that have been proposed and explored over the past 60 years to restore the dynamic function of the otherwise dysfunctional bladder tissue. Broadly, two unique perspectives of bladder tissue engineering and total alloplastic bladder replacement are critically discussed in terms of their status and progress. While the former is pivoted on scaffold mediated regenerative medicine; in contrast, the latter is directed towards the development of a biostable bladder prosthesis. Together, these routes share a common aspiration of designing and creating a functional equivalent of the bladder wall, albeit, using fundamentally different aspects of biocompatibility and clinical needs. Therefore, an attempt has been made to systematically analyze and summarize the evolution of various classes as well as generations of polymeric biomaterials in urology. Considerable emphasis has been laid on explaining the bioengineering methodologies, pre-clinical and clinical outcomes. Some of the unaddressed challenges, including vascularization, innervation, hollow 3D prototype fabrication and urinary encrustation, have been highlighted that currently delay the successful commercial translation. More importantly, the rapidly evolving and expanding concepts of bioelectronic medicine are discussed to inspire future research efforts towards the further advancement of the field. At the closure, crucial insights are provided to forge the biomaterial assisted reconstruction as a long-term therapeutic strategy in urological practice for patients' care.
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Affiliation(s)
- Swati Sharma
- Laboratory for Biomaterials, Materials Research Centre, Indian Institute of Science, Bangalore, 560012, India
| | - Bikramjit Basu
- Laboratory for Biomaterials, Materials Research Centre, Indian Institute of Science, Bangalore, 560012, India; Centre for Biosystems Science and Engineering, Indian Institute of Science, Bangalore, 560012, India.
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15
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Mirgany TO, Abdalla AN, Arifuzzaman M, Motiur Rahman AFM, Al-Salem HS. Quinazolin-4(3 H)-one based potential multiple tyrosine kinase inhibitors with excellent cytotoxicity. J Enzyme Inhib Med Chem 2021; 36:2055-2067. [PMID: 34551654 PMCID: PMC8462848 DOI: 10.1080/14756366.2021.1972992] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
A series of quinazolin-4(3H)-one derivatives were synthesised and evaluated for their cytotoxicity against human Caucasian breast adenocarcinoma (MCF-7) and human ovarian carcinoma (A2780) cell lines. Cytotoxicity of the most tested compounds was 2- to 30-fold more than the positive control lapatinib (IC50 of 2j = 3.79 ± 0.96; 3j = 0.20 ± 0.02; and lapatinib = 5.9 ± 0.74) against MCF7 cell lines except two compounds (IC50 of 2 b = 15.72 ± 0.07 and 2e = 14.88 ± 0.99). On the other hand, cytotoxicity was 4 − 87 folds (IC50 of 3a = 3.00 ± 1.20; 3 g = 0.14 ± 0.03) more the positive control lapatinib (IC50 = 12.11 ± 1.03) against A2780 cell lines except compound 2e (IC50 = 16.43 ± 1.80). Among the synthesised quinazolin-4(3H)-one derivatives, potent cytotoxic 2f-j and 3f-j were investigated for molecular mechanism of action. Inhibitory activities of the compounds were tested against multiple tyrosine protein kinases (CDK2, HER2, EGFR and VEGFR2) enzymes. As expected, all the quinazolin-4(3H)-one derivatives were showed comparable inhibitory activity against those kinases tested, especially, compound 2i and 3i showed potent inhibitory activity against CDK2, HER2, EGFR tyrosine kinases. Therefore, molecular docking analysis for quinazolin-4(3H)-one derivatives 2i and 3i were performed, and it was revealed that compounds 2i and 3i act as ATP non-competitive type-II inhibitor against CDK2 kinase enzymes and ATP competitive type-I inhibitor against EGFR kinase enzymes. However, in case of HER2, compounds 2i act as ATP non-competitive type-II inhibitor and 3i act as ATP competitive type-I inhibitor. Docking results of known inhibitors were compared with synthesised compounds and found synthesised 2i and 3i are superior than the known inhibitors in case of interactions. In addition, in silico drug likeness properties of quinazolin-4(3H)-one derivatives showed better predicted ADME values than lapatinib.
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Affiliation(s)
- Tebyan O Mirgany
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Ashraf N Abdalla
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Md Arifuzzaman
- College of Pharmacy, Yeungnam University, Gyeongsan, Korea
| | - A F M Motiur Rahman
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Huda S Al-Salem
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
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16
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Ali F, Shamim S, Lateef M, Khan KM, Taha M, Salar U, Wadood A, Rehman AU, Nawaz NUA, Perveen S. N-Aryl-3,4-dihydroisoquinoline Carbothioamide Analogues as Potential Urease Inhibitors. ACS OMEGA 2021; 6:15794-15803. [PMID: 34179623 PMCID: PMC8223216 DOI: 10.1021/acsomega.1c01182] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 04/29/2021] [Indexed: 05/06/2023]
Abstract
N-Aryl-3,4-dihydroisoquinoline carbothioamide analogues 1-22 were synthesized by a simple one-step reaction protocol and subjected to in vitro urease inhibition studies for the first time. All compounds 1-22 were found active and showed significant to moderate urease inhibitory potential. Specifically, analogues 1, 2, 4, and 7 were identified to be more potent (IC50 = 11.2 ± 0.81-20.4 ± 0.22 μM) than the standard thiourea (IC50 = 21.7 ± 0.34 μM). The structure-activity relationship showed that compounds bearing electron-donating groups showed superior activity. Molecular docking study on the most active derivatives revealed a good protein-ligand interaction profile against the corresponding target with key interactions, including hydrogen bonding, hydrophobic, and π-anion interactions.
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Affiliation(s)
- Fayaz Ali
- H.
E. J. Research Institute of Chemistry, International Center for Chemical
and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Shahbaz Shamim
- H.
E. J. Research Institute of Chemistry, International Center for Chemical
and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Mehreen Lateef
- Department
of Biochemistry, Multi-Disciplinary Research Laboratory, Bahria University Medical and Dental College, Karachi 75270, Pakistan
| | - Khalid Mohammed Khan
- H.
E. J. Research Institute of Chemistry, International Center for Chemical
and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
- Pakistan
Academy of Sciences, 3-Constitution Avenue G-5/2, Islamabad 44000, Pakistan
- Department
of Clinical Pharmacy, Institute for Research
and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 31441, Saudi Arabia
- ; . Tel.: 00922134824910. Fax: 00922134819018
| | - 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
| | - Uzma Salar
- Dr.
Panjwani Center for Molecular Medicine and Drug Research, International
Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Abdul Wadood
- Department
of Biochemistry, Computational Medicinal Chemistry Laboratory, UCSS, Abdul Wali Khan University, Mardan 23200, Pakistan
| | - Ashfaq Ur Rehman
- Department
of Biochemistry, Computational Medicinal Chemistry Laboratory, UCSS, Abdul Wali Khan University, Mardan 23200, Pakistan
| | - Noor Ul Ain Nawaz
- Department
of Pharmacy, University of Peshawar, Peshawar 25120, Pakistan
| | - Shahnaz Perveen
- PCSIR
Laboratories Complex, Karachi, Shahrah-e-Dr. Salimuzzaman Siddiqui, Karachi 75280, Pakistan
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17
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Affiliation(s)
- Gülay Akyüz
- Department of Chemistry, Art and Science Faculty Recep Tayyip Erdoğan University Rize Turkey
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18
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Acharya PT, Bhavsar ZA, Jethava DJ, Patel DB, Patel HD. A review on development of bio-active thiosemicarbazide derivatives: Recent advances. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129268] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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19
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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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20
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Emirik M. Potential therapeutic effect of turmeric contents against SARS-CoV-2 compared with experimental COVID-19 therapies: in silico study. J Biomol Struct Dyn 2020; 40:2024-2037. [PMID: 33078675 DOI: 10.1080/07391102.2020.1835719] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Inspired by the 'There is no scientific evidence that turmeric prevents COVID-19' statement made by WHO, the protective or therapeutic potential of the compounds in turmeric contents was investigated against COVID-19 with in silico methodology. The drugs used for experimental COVID-19 therapies were included in this study using the same method for comparison with turmeric components. The 30 turmeric compounds and nine drugs were performed in the docking procedure for vital proteins of COVID-19. With evaluations based on docking scores, the Prime MMGBSA binding free energy and protein-ligand interactions were identified in detail. The 100 ns MD simulations were also performed to assess the stability of the ligands at the binding site of the target proteins. The Root Mean Square Deviation (RMSD) is used to obtain the average displacement for a particular frame concerning a reference frame. The results of this study are suggesting that turmeric spice have a potential to inhibit the SARS-CoV-2 vital proteins and can be use a therapeutic or protective agent against SARS-CoV-2 via inhibiting key protein of the SARS-CoV-2 virus. The compound 4, 23 and 6 are the most prominent inhibitor for the main protease, the spike glycoprotein and RNA polymerase of virus, respectively. The MD simulation validated the stability of ligand-protein interactions. The compactness of the complexes was shown using a radius of gyration. ADME properties of featured compounds are in range of 95% drug molecules. It is hoped that the outputs of this study will contribute to the struggle of humanity with COVID-19.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mustafa Emirik
- Department of Chemistry, Recep Tayyip Erdogan University, Rize, Turkey
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21
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Yilmaz F, Menteşe E, Sökmen BB. Synthesis and biological evaluation of some 1,
3‐benzoxazol
‐2(
3H
)‐one hybrid molecules as potential antioxidant and urease inhibitors. J Heterocycl Chem 2020. [DOI: 10.1002/jhet.4165] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Fatih Yilmaz
- Department of Chemistry and Chemical Process Technology, Vocational School of Technical Sciences Recep Tayyip Erdogan University Rize Turkey
| | - Emre Menteşe
- Department of Chemistry, Faculty of Art and Sciences Recep Tayyip Erdogan University Rize Turkey
| | - Bahar Bilgin Sökmen
- Department of Chemistry, Faculty of Art and Sciences Giresun University Giresun Turkey
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22
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Chaudhry F, Naureen S, Aslam M, Al‐Rashida M, Rahman J, Huma R, Fatima J, Khan M, Munawar MA, Ain Khan M. Identification of Imidazolylpyrazole Ligands as Potent Urease Inhibitors: Synthesis, Antiurease Activity and In Silico Docking Studies. ChemistrySelect 2020. [DOI: 10.1002/slct.202002482] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Faryal Chaudhry
- Department of Chemistry Kinnaird College for Women Lahore 93-Jail Road Lahore 54000 Pakistan
| | - Sadia Naureen
- Institute of the Chemistry, Quaid-e-Azam Campus University of the Punjab Lahore 54590 Pakistan
| | - Misbah Aslam
- Department of Chemistry the Islamia University of Bahawalpur Bahawalpur 63100 Pakistan
| | - Mariya Al‐Rashida
- Department of Chemistry, Forman Christian College A Chartered University) Ferozepur Road Lahore 54600 Pakistan
| | - Jameel Rahman
- Department of Chemistry the Islamia University of Bahawalpur Bahawalpur 63100 Pakistan
| | - Rahila Huma
- Department of Chemistry Kinnaird College for Women Lahore 93-Jail Road Lahore 54000 Pakistan
| | - Javeria Fatima
- Department of Chemistry Kinnaird College for Women Lahore 93-Jail Road Lahore 54000 Pakistan
| | - Mavra Khan
- Department of Chemistry Kinnaird College for Women Lahore 93-Jail Road Lahore 54000 Pakistan
| | - Munawar Ali Munawar
- Institute of the Chemistry, Quaid-e-Azam Campus University of the Punjab Lahore 54590 Pakistan
| | - Misbahul Ain Khan
- Institute of the Chemistry, Quaid-e-Azam Campus University of the Punjab Lahore 54590 Pakistan
- Department of Chemistry the Islamia University of Bahawalpur Bahawalpur 63100 Pakistan
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23
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Menteşe E, Baltaş N, Emirik M. Synthesis, α-glucosidase inhibition and in silico studies of some 4-(5-fluoro-2-substituted-1H-benzimidazol-6-yl)morpholine derivatives. Bioorg Chem 2020; 101:104002. [DOI: 10.1016/j.bioorg.2020.104002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/28/2020] [Accepted: 06/07/2020] [Indexed: 01/13/2023]
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24
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Taha M, Rahim F, Khan AA, Anouar EH, Ahmed N, Shah SAA, Ibrahim M, Zakari ZA. Synthesis of diindolylmethane (DIM) bearing thiadiazole derivatives as a potent urease inhibitor. Sci Rep 2020; 10:7969. [PMID: 32409737 PMCID: PMC7224224 DOI: 10.1038/s41598-020-64729-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 03/26/2020] [Indexed: 11/30/2022] Open
Abstract
The current study describes synthesis of diindolylmethane (DIM) derivatives based-thiadiazole as a new class of urease inhibitors. Diindolylmethane is natural product alkaloid reported to use in medicinal chemistry extensively. Diindolylmethane-based-thiadiazole analogs (1–18) were synthesized and characterized by various spectroscopic techniques 1HNMR, 13C-NMR, EI-MS and evaluated for urease (jack bean urease) inhibitory potential. All compounds showed excellent to moderate inhibitory potential having IC50 value within the range of 0.50 ± 0.01 to 33.20 ± 1.20 µM compared with the standard thiourea (21.60 ± 0.70 µM). Compound 8 (IC50 = 0.50 ± 0.01 µM) was the most potent inhibitor amongst all derivatives. Structure-activity relationships have been established for all compounds. The key binding interactions of most active compounds with enzyme were confirmed through molecular docking studies.
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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 31441, Dammam, Saudi Arabia.
| | - Fazal Rahim
- Department of Chemistry, Hazara University, Mansehra, 21300, Khyber Pakhtunkhwa, Pakistan
| | - Aftab Ahmad Khan
- Department of Chemistry, Hazara University, Mansehra, 21300, Khyber Pakhtunkhwa, 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
| | - Naveed Ahmed
- Department of Pharmacy, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Syed Adnan Ali Shah
- Atta-ur-Rahman Institute for Natural Product Discovery (AuRIns), Universiti Teknologi MARA Cawangan Selangor Kampus Puncak Alam, 42300 Bandar Puncak Alam, Selangor Darul Ehsan, Malaysia, 42300, D. E., Selangor, Malaysia.,Faculty of Pharmacy, Universiti Teknologi MARA Cawangan Selangor Kampus Puncak Alam, 42300 Bandar Puncak Alam, Selangor Darul Ehsan, Malaysia, 42300, Darul Ehsan, Selangor, Malaysia
| | - Mohamed Ibrahim
- Department of clinical pharmacy, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 31441, Dammam, Saudi Arabia
| | - Zainul Amiruddin Zakari
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia. .,Halal Institute Research Institute, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
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25
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Synthesis, pharmacological evaluation and structure-activity relationship of recently discovered enzyme antagonist azoles. Heliyon 2020; 6:e03656. [PMID: 32274429 PMCID: PMC7132078 DOI: 10.1016/j.heliyon.2020.e03656] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 03/06/2020] [Accepted: 03/20/2020] [Indexed: 12/18/2022] Open
Abstract
Global people are suffering from the legion of diseases. Cytotoxic property of the chemical compound would not solely influence effective drug properties and reduce unnecessary side effects. Proteins/enzymes responsible for microbe proliferation or survival are specifically targeted and inhibited successfully making the cells to undergo apoptosis. Furthermore, isoforms of essential enzymes have distinct physiological functions; thereby inhibition of essential enzyme isoforms is an apt way to the clinical approach of disease neutralization. Drugs are designed so as to play significant roles such as signaling pathways in the oncogenic process including cell proliferation, invasion, and angiogenesis. The present review comprises collective information of the recent synthesis of various organic drug compounds in brief, which could inhibit particular enzyme. The review also covers the correlation of the structure of a drug molecule designed and its inhibitory activity. Also, the most significant enzyme inhibitors are highlighted and structural moieties/core units responsible for remarkable inhibitory values are emphasized.
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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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Shehzad MT, Khan A, Islam M, Halim SA, Khiat M, Anwar MU, Hussain J, Hameed A, Pasha AR, Khan FA, Al-Harrasi A, Shafiq Z. Synthesis, characterization and molecular docking of some novel hydrazonothiazolines as urease inhibitors. Bioorg Chem 2020; 94:103404. [DOI: 10.1016/j.bioorg.2019.103404] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 09/16/2019] [Accepted: 10/25/2019] [Indexed: 10/25/2022]
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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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Demir A, Turumtay H, Emirik M, Sandalli C, Kanbolat Ş, Özgen U, Turumtay EA. Paeoniflorigenone purified from Paeonia daurica roots potently inhibits viral and bacterial DNA polymerases: investigation by experimental validation and docking simulation. Med Chem Res 2019. [DOI: 10.1007/s00044-019-02449-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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