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Haque Z, Taleuzzaman M, Jamal R, Al-Qahtani NH, Haque A. Targeting protein receptors and enzymes for precision management of urolithiasis: A comprehensive review. Eur J Pharmacol 2024; 981:176904. [PMID: 39153649 DOI: 10.1016/j.ejphar.2024.176904] [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: 05/27/2024] [Revised: 08/09/2024] [Accepted: 08/14/2024] [Indexed: 08/19/2024]
Abstract
Urolithiasis, characterized by the formation of solid crystalline structures within the urinary tract, presents a significant global health burden with high recurrence rates and limited treatment efficacy. Recent research has identified various protein receptors and enzymes implicated in the pathogenesis of urolithiasis, offering potential targets for therapeutic intervention. Protein receptors such as the calcium-sensing receptor and vasopressin V2 receptor play crucial roles in regulating urinary calcium excretion and water reabsorption, respectively, influencing stone formation. Additionally, modulation of receptors like the angiotensin II receptor and aldosterone receptor can impact renal function and electrolyte balance, contributing to stone prevention. Furthermore, enzymes such as urease inhibitors and xanthine oxidase inhibitors offer targeted approaches to prevent the formation of specific stone types. This review discusses the potential of targeting these receptors and enzymes for the treatment of urolithiasis, exploring associated drugs and their mechanisms of action. Despite promising avenues for personalized and precision medicine approaches, challenges such as the need for robust clinical evidence and ensuring cost-effectiveness must be addressed for the translation of these interventions into clinical practice. By overcoming these challenges, receptor-targeted therapies and enzyme inhibitors hold promise for revolutionizing the management of urolithiasis and reducing its global burden.
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Affiliation(s)
- Ziyaul Haque
- Anjumane-I-Islam Kalsekar Technical Campus (AIKTC), School of Pharmacy, Plot No: 2&3, Sector:16, Near Thana Naka, Khandagaon, New Panvel, Mumbai, Maharashtra 410206, India; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Maulana Azad University, Village Bujhawar, Tehsil Luni, Jodhpur, Rajasthan, 342802, India
| | - Mohamad Taleuzzaman
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Maulana Azad University, Village Bujhawar, Tehsil Luni, Jodhpur, Rajasthan, 342802, India.
| | - Ruqaiya Jamal
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Maulana Azad University, Village Bujhawar, Tehsil Luni, Jodhpur, Rajasthan, 342802, India
| | - Noora H Al-Qahtani
- Central Laboratories Unit (CLU), Qatar University, Doha P.O. Box 2713, Qatar; Center for Advanced Materials, Qatar University, Doha P.O. Box 2713, Qatar
| | - Anzarul Haque
- Central Laboratories Unit (CLU), Qatar University, Doha P.O. Box 2713, Qatar
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2
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Contini L, Paul A, Mazzei L, Ciurli S, Roncarati D, Braga D, Grepioni F. Is bismuth(III) able to inhibit the activity of urease? Puzzling results in the quest for soluble urease complexes for agrochemical and medicinal applications. Dalton Trans 2024; 53:10553-10562. [PMID: 38847020 DOI: 10.1039/d4dt00778f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Bismuth(III) complexes have been reported to act as inhibitors of the enzyme urease, ubiquitously present in soils and implicated in the pathogenesis of several microorganisms. The general insolubility of Bi(III) complexes in water at neutral pH, however, is an obstacle to their utilization. In our quest to improve the solubility of Bi(III) complexes, we selected a compound reported to inhibit urease, namely [Bi(HEDTA)]·2H2O, and co-crystallized it with (i) racemic DL-histidine to obtain the conglomerate [Bi2(HEDTA)2(μ-D-His)2]·6H2O + [Bi2(HEDTA)2(μ-L-His)2]·6H2O, (ii) enantiopure L-histidine to yield [Bi2(HEDTA)2(μ-L-His)2]·6H2O, and (iii) cytosine to obtain [Bi(HEDTA)]·Cyt·2H2O. All compounds, synthesised by mechanochemical methods and by slurry, were characterized in the solid state by calorimetric (DSC and TGA) and spectroscopic (IR) methods, and their structures were determined using powder X-ray diffraction (PXRD) data. All compounds show an appreciable solubility in water, with values ranging from 6.8 mg mL-1 for the starting compound [Bi(HEDTA)]·2H2O to 36 mg mL-1 for [Bi2(HEDTA)2(μ-L-His)2]·6H2O. The three synthesized compounds as well as [Bi(HEDTA)]·2H2O were then tested for inhibition activity against urease. Surprisingly, no enzymatic inhibition was observed during in vitro assays using Canavalia ensiformis urease and in vivo assays using cultures of Helicobacter pylori, raising questions on the efficacy of Bi(III) compounds to counteract the negative effects of urease activity in the agro-environment and in human health.
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Affiliation(s)
- Laura Contini
- Department of Chemistry "G. Ciamician", University of Bologna, Via Selmi 2, 40126 Bologna, Italy.
| | - Arundhati Paul
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Viale Giuseppe Fanin 40, Bologna I-40127, Italy.
| | - Luca Mazzei
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Viale Giuseppe Fanin 40, Bologna I-40127, Italy.
| | - Stefano Ciurli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Viale Giuseppe Fanin 40, Bologna I-40127, Italy.
| | - Davide Roncarati
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Via Selmi 3, 40126 Bologna, Italy.
| | - Dario Braga
- Department of Chemistry "G. Ciamician", University of Bologna, Via Selmi 2, 40126 Bologna, Italy.
| | - Fabrizia Grepioni
- Department of Chemistry "G. Ciamician", University of Bologna, Via Selmi 2, 40126 Bologna, Italy.
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3
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Liu H, Huang J, Zhang H, Xi S, Luo T, Jiang X. Effect and mechanism of Mn 2+ on urease activity during anaerobic biological treatment of landfill leachate. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:41290-41300. [PMID: 38849617 DOI: 10.1007/s11356-024-33907-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 06/01/2024] [Indexed: 06/09/2024]
Abstract
As a crucial hydrolytic enzyme, urease plays a vital role in anaerobic biological treatment. It is well-known that manganese ions are abundant in landfill leachate, but their concentration fluctuates significantly. However, few studies have investigated the effect and mechanism of different concentrations of Mn2+ on urease activity during anaerobic biological treatment of landfill leachate. This paper aimed to investigate the effects and mechanisms of different concentrations of Mn2+ on urease activity. The results showed that an appropriate amount of Mn2+ could significantly enhance urease activity, while a high concentration of Mn2+ could inhibit it. Insight into the mechanisms behind this phenomenon, various methods such as Zeta potential, particle size, ultraviolet spectroscopy, fluorescence spectroscopy, Fourier transform infrared spectroscopy, and statistical analysis were employed in our study. Research suggested that, on one hand, Mn2+ may form hydrogen bonds with the side chain amino or carboxyl groups of urease amino acid residues, affecting the structure of urease through hydrogen bonding. Additionally, Mn2+ also binds to urease through hydrophobic interactions. On the other hand, the C-OH and C-N functional groups in urease have a strong affinity for Mn2+, and changes in these functional groups can greatly enhance the activity of urease. Furthermore, under the action of high concentrations of Mn2+, while the structure of urease becomes more stable, there is also a steric hindrance phenomenon that affects the substrate from entering the catalytic center. Therefore, studying the mechanism of Mn2+ affecting urease activity has significant biological significance and provides a new perspective for exploring the impact of metals on anaerobic bioprocessing of landfill leachate.
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Affiliation(s)
- Hao Liu
- School of Environmental and Energy Engineering, Anhui Jianzhu University, 292, Ziyun Rd., Shushan District, Hefei, 230601, Anhui Province, China
- Anhui Provincial Key Laboratory of Environment Pollution Control and Resource Reuse, Hefei, 230601, China
- Anhui Research Academy of Ecological Civilization, Hefei, 230601, China
| | - Jian Huang
- School of Environmental and Energy Engineering, Anhui Jianzhu University, 292, Ziyun Rd., Shushan District, Hefei, 230601, Anhui Province, China
- Anhui Provincial Key Laboratory of Environment Pollution Control and Resource Reuse, Hefei, 230601, China
- Anhui Research Academy of Ecological Civilization, Hefei, 230601, China
| | - Hua Zhang
- School of Environmental and Energy Engineering, Anhui Jianzhu University, 292, Ziyun Rd., Shushan District, Hefei, 230601, Anhui Province, China
- Anhui Provincial Key Laboratory of Environment Pollution Control and Resource Reuse, Hefei, 230601, China
- Anhui Research Academy of Ecological Civilization, Hefei, 230601, China
| | - Shanshan Xi
- School of Environmental and Energy Engineering, Anhui Jianzhu University, 292, Ziyun Rd., Shushan District, Hefei, 230601, Anhui Province, China.
- Anhui Provincial Key Laboratory of Environment Pollution Control and Resource Reuse, Hefei, 230601, China.
- Anhui Research Academy of Ecological Civilization, Hefei, 230601, China.
| | - Tao Luo
- School of Environmental and Energy Engineering, Anhui Jianzhu University, 292, Ziyun Rd., Shushan District, Hefei, 230601, Anhui Province, China
- Anhui Provincial Key Laboratory of Environment Pollution Control and Resource Reuse, Hefei, 230601, China
- Anhui Research Academy of Ecological Civilization, Hefei, 230601, China
| | - Xinqin Jiang
- School of Environmental and Energy Engineering, Anhui Jianzhu University, 292, Ziyun Rd., Shushan District, Hefei, 230601, Anhui Province, China
- Anhui Provincial Key Laboratory of Environment Pollution Control and Resource Reuse, Hefei, 230601, China
- Anhui Research Academy of Ecological Civilization, Hefei, 230601, China
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4
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Svane S, Lyngsie MC, Klitgaard JK, Karring H. Synergistic inhibition of ureolytic activity and growth of Klebsiella pneumoniae in vitro suggests cobinding of fluoride and acetohydroxamic acid at the urease active site and provides a novel strategy to combat ureolytic bacteria. Heliyon 2024; 10:e31209. [PMID: 38826744 PMCID: PMC11141357 DOI: 10.1016/j.heliyon.2024.e31209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/18/2024] [Accepted: 05/13/2024] [Indexed: 06/04/2024] Open
Abstract
The ability of ureolytic bacteria to break down stable urea to alkaline ammonia leads to several environmental and health challenges. Ureolytic bacteria such as Helicobacter pylori, Klebsiella pneumoniae, and Proteus mirabilis can become pathogenic and cause persistent infections that can be difficult to treat. Inhibiting urease activity can reduce the growth and pathogenicity of ureolytic bacteria. In the present in vitro study, we investigated the synergistic effects of tannic acid (TA) and the urease inhibitors fluoride (F-) and acetohydroxamic acid (AHA). The concentration of AHA needed for efficient inhibition of the ureolytic activity of K. pneumoniae can be significantly reduced if AHA is coapplied with tannic acid and sodium fluoride (NaF). Thus, only 1.20 μmol l-1 AHA in combination with 0.30 mmol l-1 tannic acid and 0.60 mmol l-1 NaF delayed the onset of ureolytic pH increase by 95.8 % and increased the growth lag phase by 124.3 % relative to untreated K. pneumoniae. At these concentrations, without AHA, TA and NaF increased the onset of the ureolytic pH change by only 37.0 % and the growth lag phase by 52.5 %. The strong inhibition obtained with low concentrations of AHA in triple-compound treatments suggests cobinding of F- and AHA at the urease active site and could reduce the side effects of AHA when it is employed as a drug against e.g. urinary tract infections (UTIs) and blocked catheters. This study reports the basis for a promising novel therapeutic strategy to combat infections caused by ureolytic bacteria and the formation of urinary tract stones and crystalline biofilms on catheters.
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Affiliation(s)
- Simon Svane
- Department of Green Technology, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Mie C. Lyngsie
- Department of Biochemistry and Molecular Biology, Research Unit of Molecular Microbiology, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Janne K. Klitgaard
- Department of Biochemistry and Molecular Biology, Research Unit of Molecular Microbiology, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
- Institute of Clinical Research, Research Unit of Clinical Microbiology, University of Southern Denmark, J. B. Winsløws Vej 21, 2. sal, 5000, Odense C, Denmark
| | - Henrik Karring
- Department of Green Technology, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
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5
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Aslam M, Rahman J, Iqbal A, Mujtaba S, Ashok AK, Kaouche FC, Hayat MM, Nisa MU, Ashraf M. Antiurease Activity of Antibiotics: In Vitro, In Silico, Structure Activity Relationship, and MD Simulations of Cephalosporins and Fluoroquinolones. ACS OMEGA 2024; 9:14005-14016. [PMID: 38559955 PMCID: PMC10975586 DOI: 10.1021/acsomega.3c09355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 02/22/2024] [Accepted: 03/01/2024] [Indexed: 04/04/2024]
Abstract
Helicobacter pylori infection is widespread in 50% of the world's population and is associated with gastric ulcers and related disorders that ultimately culminate in gastric cancer. Levofloxacin-based, or clarithromycin-based, triple therapy is frequently used to inhibit the bacterial urease enzyme for the eradication of H. pylori. A comprehensive investigation based on the urease inhibitory profiles of antibiotics and their computational implications is lacking in the scientific literature. The present study was aimed specifically to determine the antiurease activities within the realms of cephalosporins and fluoroquinolones by in vitro methods supported with in silico investigations. The results demonstrate the jack bean urease inhibitory activity of cephalosporins, wherein cefadroxil, cefpodoxime, cefotaxime, and cefaclor displayed inhibitions (IC50 21.35 ± 0.64 to 62.86 ± 0.78 μM) compared with the standard thiourea (IC50 21.25 ± 0.15 μM). Among fluoroquinolones, levofloxacin, ofloxacin, and gemifloxacin (IC50 7.24 ± 0.29 to 16.53 ± 0.85 μM) unveiled remarkable inhibitory profiles. Levofloxacin and ofloxacin exhibited competitive inhibition against the said enzyme. Ciprofloxacin and moxifloxacin displayed weak urease inhibitions. During molecular docking studies, Asp362, Gly279, Arg338, Asn168, Asp223, Gln364, and Met366 were involved in hydrogen bonding in fluoroquinolones, and hydrogen bonding was established with Arg338, His248, Asn168 residues, and metal Ni601 and Ni602 of the enzyme. MD simulations and MMPBSA results demonstrated the existence of significant protein-ligand binding. Overall, these results warrant further investigations into the significance of these active molecules in relation to their inhibitory potential against the targeted urease enzyme.
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Affiliation(s)
- Misbah Aslam
- Institute
of Chemistry, B.J. Campus, The Islamia University
of Bahawalpur, Bahawalpur 36000, Pakistan
| | - Jameel Rahman
- Institute
of Chemistry, B.J. Campus, The Islamia University
of Bahawalpur, Bahawalpur 36000, Pakistan
| | - Ambar Iqbal
- Institute
of Chemistry, B.J. Campus, The Islamia University
of Bahawalpur, Bahawalpur 36000, Pakistan
- Department
of Biochemistry and Molecular Biology, Institute of Biochemistry,
Biotechnology, Bioinformatics (IBBB), B.J. Campus, The Islamia University of Bahawalpur, Bahawalpur 36000, Pakistan
| | - Sara Mujtaba
- Institute
of Chemistry, B.J. Campus, The Islamia University
of Bahawalpur, Bahawalpur 36000, Pakistan
| | - Avinash Karkada Ashok
- Department
of Biotechnology, Siddaganga Institute of
Technology, Tumakuru 572103, Karnataka, India
| | - Farah Chafika Kaouche
- Department
of Chemistry, Faculty of Sciences of Mater, Ibn Khaldoun University, BP 78 zaaoura, 14000 Tiaret, Algeria
| | - Muhammad Munawar Hayat
- P
& SH Department, Punjab Drug Testing
Laboratory, 1-Bird Wood
Road, Lahore 631000, Pakistan
| | - Mouqadus-Un Nisa
- Multan Drug
Testing Laboratory, near Multan Institute
of Kidney Disease, Muzaffargarh
Road, Multan 261000, Pakistan
| | - Muhammad Ashraf
- Institute
of Chemistry, B.J. Campus, The Islamia University
of Bahawalpur, Bahawalpur 36000, Pakistan
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6
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Le TH, Ho DNP, Nguyen HX, Van Do TN, Nguyen MTT, Huynh LK, Nguyen NT. In vitro biological evaluation and in silico studies of linear diarylheptanoids from Curcuma aromatica Salisb. as urease inhibitors. RSC Med Chem 2024; 15:1046-1054. [PMID: 38516598 PMCID: PMC10953472 DOI: 10.1039/d3md00645j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 01/31/2024] [Indexed: 03/23/2024] Open
Abstract
Plants of the Zingiberaceae family, specifically those belonging to the Curcuma species, are commonly under consideration as potential therapeutic agents for the management of gastrointestinal diseases. In this study, we carried out a phytochemical study on Curcuma aromatica Salisb. (or so-called "Nghe trang" in Vietnamese) grown in Vietnam, which yields three newly discovered 3,5-diacetoxy diarylheptanoids (1-3) and six known 3,5-dihydroxyl diarylheptanoids (4-9). The bioactivity assessment shows that all isolated compounds, except compounds 3, 7, and 8, could inhibit urease. Compounds 4 and 9 significantly inhibit urease, with an IC50 value of 9.6 and 21.4 μM, respectively, more substantial than the positive control, hydroxyurea (IC50 = 77.4 μM). The structure-activity relationship (SAR) of linear diarylheptanoids was also established, suggesting that the hydroxyl groups at any position of skeleton diarylheptanoids are essential for exerting anti-urease action. Through a comparative analysis of the binding sites of hydroxyurea and diarylheptanoid compounds via our constructed in silico model, the mechanism of action of diarylheptanoid compounds is predicted to bind to the dynamic region close to the dinickel active center, resulting in a loss of catalytic activity. Such insights certainly help design and/or find diarylheptanoid-based compounds for treating gastric ulcers through inhibiting urease.
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Affiliation(s)
- Tho Huu Le
- Faculty of Chemistry, University of Science Ho Chi Minh City Vietnam
- Research Lab for Drug Discovery and Development, University of Science Ho Chi Minh City Vietnam
- Vietnam National University of Ho Chi Minh City Ho Chi Minh City Vietnam
| | - Dung Ngoc Phuong Ho
- School of Chemical and Environmental Engineering, International University Ho Chi Minh City Vietnam
- Vietnam National University of Ho Chi Minh City Ho Chi Minh City Vietnam
| | - Hai Xuan Nguyen
- Faculty of Chemistry, University of Science Ho Chi Minh City Vietnam
- Research Lab for Drug Discovery and Development, University of Science Ho Chi Minh City Vietnam
- Vietnam National University of Ho Chi Minh City Ho Chi Minh City Vietnam
| | - Truong Nhat Van Do
- Faculty of Chemistry, University of Science Ho Chi Minh City Vietnam
- Research Lab for Drug Discovery and Development, University of Science Ho Chi Minh City Vietnam
- Vietnam National University of Ho Chi Minh City Ho Chi Minh City Vietnam
| | - Mai Thanh Thi Nguyen
- Faculty of Chemistry, University of Science Ho Chi Minh City Vietnam
- Research Lab for Drug Discovery and Development, University of Science Ho Chi Minh City Vietnam
- Vietnam National University of Ho Chi Minh City Ho Chi Minh City Vietnam
| | - Lam K Huynh
- School of Chemical and Environmental Engineering, International University Ho Chi Minh City Vietnam
- Vietnam National University of Ho Chi Minh City Ho Chi Minh City Vietnam
| | - Nhan Trung Nguyen
- Faculty of Chemistry, University of Science Ho Chi Minh City Vietnam
- Research Lab for Drug Discovery and Development, University of Science Ho Chi Minh City Vietnam
- Vietnam National University of Ho Chi Minh City Ho Chi Minh City Vietnam
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7
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Evstafeva D, Ilievski F, Bao Y, Luo Z, Abramovic B, Kang S, Steuer C, Montanari E, Casalini T, Simicic D, Sessa D, Mitrea SO, Pierzchala K, Cudalbu C, Armbruster CE, Leroux JC. Inhibition of urease-mediated ammonia production by 2-octynohydroxamic acid in hepatic encephalopathy. Nat Commun 2024; 15:2226. [PMID: 38472276 DOI: 10.1038/s41467-024-46481-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 02/28/2024] [Indexed: 03/14/2024] Open
Abstract
Hepatic encephalopathy is a neuropsychiatric complication of liver disease which is partly associated with elevated ammonemia. Urea hydrolysis by urease-producing bacteria in the colon is often mentioned as one of the main routes of ammonia production in the body, yet research on treatments targeting bacterial ureases in hepatic encephalopathy is limited. Herein we report a hydroxamate-based urease inhibitor, 2-octynohydroxamic acid, exhibiting improved in vitro potency compared to hydroxamic acids that were previously investigated for hepatic encephalopathy. 2-octynohydroxamic acid shows low cytotoxic and mutagenic potential within a micromolar concentration range as well as reduces ammonemia in rodent models of liver disease. Furthermore, 2-octynohydroxamic acid treatment decreases cerebellar glutamine, a product of ammonia metabolism, in male bile duct ligated rats. A prototype colonic formulation enables reduced systemic exposure to 2-octynohydroxamic acid in male dogs. Overall, this work suggests that urease inhibitors delivered to the colon by means of colonic formulations represent a prospective approach for the treatment of hepatic encephalopathy.
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Affiliation(s)
- Diana Evstafeva
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Filip Ilievski
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Yinyin Bao
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Zhi Luo
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Boris Abramovic
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Sunghyun Kang
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Christian Steuer
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Elita Montanari
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Tommaso Casalini
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Dunja Simicic
- CIBM Center for Biomedical Imaging, Lausanne, Switzerland
- Animal Imaging and Technology, EPFL, Lausanne, Switzerland
| | - Dario Sessa
- Swiss Pediatric Liver Center, Department of Pediatrics, Gynecology and Obstetrics, University Hospitals Geneva and University of Geneva, Geneva, Switzerland
| | - Stefanita-Octavian Mitrea
- CIBM Center for Biomedical Imaging, Lausanne, Switzerland
- Animal Imaging and Technology, EPFL, Lausanne, Switzerland
| | - Katarzyna Pierzchala
- CIBM Center for Biomedical Imaging, Lausanne, Switzerland
- Animal Imaging and Technology, EPFL, Lausanne, Switzerland
| | - Cristina Cudalbu
- CIBM Center for Biomedical Imaging, Lausanne, Switzerland
- Animal Imaging and Technology, EPFL, Lausanne, Switzerland
| | - Chelsie E Armbruster
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - Jean-Christophe Leroux
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland.
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8
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Ni J, Wood JL, White MY, Lihi N, Markham TE, Wang J, Chivers PT, Codd R. Reduction-cleavable desferrioxamine B pulldown system enriches Ni(ii)-superoxide dismutase from a Streptomyces proteome. RSC Chem Biol 2023; 4:1064-1072. [PMID: 38033724 PMCID: PMC10685849 DOI: 10.1039/d3cb00097d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 10/02/2023] [Indexed: 12/02/2023] Open
Abstract
Two resins with the hydroxamic acid siderophore desferrioxamine B (DFOB) immobilised as a free ligand or its Fe(iii) complex were prepared to screen the Streptomyces pilosus proteome for proteins involved in siderophore-mediated Fe(iii) uptake. The resin design included a disulfide bond to enable the release of bound proteins under mild reducing conditions. Proteomics analysis of the bound fractions did not identify proteins associated with siderophore-mediated Fe(iii) uptake, but identified nickel superoxide dismutase (NiSOD), which was enriched on the apo-DFOB-resin but not the Fe(iii)-DFOB-resin or the control resin. While DFOB is unable to sequester Fe(iii) from sites deeply buried in metalloproteins, the coordinatively unsaturated Ni(ii) ion in NiSOD is present in a surface-exposed loop region at the N-terminus, which might enable partial chelation. The results were consistent with the notion that the apo-DFOB-resin formed a ternary complex with NiSOD, which was not possible for either the coordinatively saturated Fe(iii)-DFOB-resin or the non-coordinating control resin systems. In support, ESI-TOF-MS measurements from a solution of a model Ni(ii)-SOD peptide and DFOB showed signals that correlated with a ternary Ni(ii)-SOD peptide-DFOB complex. Although any biological implications of a DFOB-NiSOD complex are unclear, the work shows that the metal coordination properties of siderophores might influence an array of metal-dependent biological processes beyond those established in iron uptake.
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Affiliation(s)
- Jenny Ni
- School of Medical Sciences, The University of Sydney New South Wales 2006 Australia
| | - James L Wood
- School of Medical Sciences, The University of Sydney New South Wales 2006 Australia
| | - Melanie Y White
- School of Medical Sciences, The University of Sydney New South Wales 2006 Australia
- Charles Perkins Centre, The University of Sydney New South Wales 2006 Australia
| | - Norbert Lihi
- ELKH-DE Mechanisms of Complex Homogeneous and Heterogeneous Chemical Reactions Research Group, Department of Inorganic and Analytical Chemistry, University of Debrecen Debrecen H-4032 Hungary
| | - Todd E Markham
- School of Medical Sciences, The University of Sydney New South Wales 2006 Australia
| | - Joseph Wang
- School of Medical Sciences, The University of Sydney New South Wales 2006 Australia
| | - Peter T Chivers
- Department of Chemistry, Durham University Durham DH1 3LE UK
- Department of Biosciences, Durham University Durham DH1 3LE UK
| | - Rachel Codd
- School of Medical Sciences, The University of Sydney New South Wales 2006 Australia
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9
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Ersoy E, Süvari G, Ercan S, Eroğlu Özkan E, Karahan S, Aygün Tuncay E, Yeşil Cantürk Y, Mataracı Kara E, Zengin G, Boğa M. Towards a better understanding of commonly used medicinal plants from Turkiye: Detailed phytochemical screening and biological activity studies of two Teucrium L. species with in vitro and in silico approach. JOURNAL OF ETHNOPHARMACOLOGY 2023; 312:116482. [PMID: 37059244 DOI: 10.1016/j.jep.2023.116482] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/31/2023] [Accepted: 04/08/2023] [Indexed: 05/08/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Since ancient times, Teucrium L. species have been among the most commonly used traditional medicinal plants mainly in the Mediterranean region. From tackling gastrointestinal problems to maintaining the healthy functioning of endocrine glands, and from treating malaria to severe dermatological disorders, Teucrium species are known to have extensive therapeutic applications. Teucrium polium L. and Teucrium parviflorum Schreb. are the two members of the genus that have been used in Turkish folk medicine for various medicinal purposes. AIM OF THE STUDY To determine the phytochemical compositions of the essential oils and ethanol extracts of Teucrium polium and Teucrium parviflorum collected from different locations in Turkiye along with the investigation of in vitro antioxidant, anticancer, antimicrobial activities, and both in vitro and in silico enzyme inhibitory activities of the extracts. MATERIALS AND METHODS Ethanol extracts of Teucrium polium aerial parts and roots, and aerial parts of Teucrium parviflorum were prepared. Volatile profiling of the essential oils by GC-MS, phytochemical profiling of the ethanol extracts by LC-HRMS, antioxidant activity by DPPH radical scavenging, ABTS cation radical scavenging, CUPRAC, and metal chelating activity assays, anticholinesterase, antityrosinase, antiurease, activities by different enzyme inhibitory activity assays, anticancer activity by SRB cell viability assay, and antimicrobial activity against a standard panel of bacteria and fungi by the microbroth dilution technique. Molecular docking studies were performed by Autodock Vina (Ver. 1.1.2). RESULTS The studied extracts were found to be quite rich in various biologically important volatile and phenolic compounds. (-)-Epigallocatechin gallate, which is a molecule renowned for having great therapeutic potential, was the major compound of all extracts. Teucrium polium aerial parts extract was revealed as a great source for naringenin with 16327 ± 685.23 μg/g extract. All extracts exerted significant antioxidant activity by different methods. All extracts demonstrated antibutrylcholinesterase, antityrosinase, and antiurease activities by in vitro and in silico assays. Teucrium polium roots extract stood out with remarkable tyrosinase and urease inhibitory and cytotoxic activities. CONCLUSION The obtained results from this multi-disciplinary study proves that the traditional use of these two Teucrium species is justified, and the mechanisms behind are enlightened.
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Affiliation(s)
- Ezgi Ersoy
- Department of Pharmacognosy, Faculty of Pharmacy, Biruni University, 34010, Topkapı, Istanbul, Turkiye.
| | - Goncagül Süvari
- Department of Analytical Chemistry, Faculty of Pharmacy, Dicle University, 21280, Sur, Diyarbakır, Turkiye
| | - Selami Ercan
- Department of Chemistry, Faculty of Sciences, Batman University, 72060, Batman, Turkiye
| | - Esra Eroğlu Özkan
- Department of Pharmacognosy, Faculty of Pharmacy, Istanbul University, 34116, Beyazit, Istanbul, Turkiye
| | - Selim Karahan
- Department of Medical Pharmacology, Faculty of Medicine, Mardin Artuklu University, 47100, Mardin, Turkiye; Dicle University Health Sciences Application and Research Center (DÜSAM), 21280, Sur, Diyarbakır, Turkiye
| | - Evin Aygün Tuncay
- Department of Analytical Chemistry, Faculty of Pharmacy, Dicle University, 21280, Sur, Diyarbakır, Turkiye
| | - Yeter Yeşil Cantürk
- Department of Pharmaceutical Botany, Faculty of Pharmacy, Istanbul University, 34116, Beyazıt, Istanbul, Turkiye
| | - Emel Mataracı Kara
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Istanbul University, 34116, Beyazıt, Istanbul, Turkiye
| | - Gökhan Zengin
- Department of Biology, Faculty of Science, Selçuk University, 42250, Konya, Turkiye
| | - Mehmet Boğa
- Department of Analytical Chemistry, Faculty of Pharmacy, Dicle University, 21280, Sur, Diyarbakır, Turkiye; Dicle University Health Sciences Application and Research Center (DÜSAM), 21280, Sur, Diyarbakır, Turkiye.
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10
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Islam M, Khan A, Khan M, Halim SA, Ullah S, Hussain J, Al-Harrasi A, Shafiq Z, Tasleem M, El-Gokha A. Synthesis and biological evaluation of 2-nitrocinnamaldehyde derived thiosemicarbazones as urease inhibitors. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
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11
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Temel H, Atlan M, Türkmenoğlu B, Ertaş A, Erdönmez D, Çalışkan UK. In silico and biological activity evaluation of quercetin-boron hybrid compounds, anti-quorum sensing effect as alternative potential against microbial resistance. J Trace Elem Med Biol 2023; 77:127139. [PMID: 36791625 DOI: 10.1016/j.jtemb.2023.127139] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 02/01/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023]
Abstract
Boronic acid compounds and the natural flavonoid compound quercetin were handled to synthesize two novel ligands encoded as B1(2,2'-(1,4-phenylenebis (benzo [1,3,2] dioxaborole-2,5-diyl)) bis (3,5,7-trihydroxy-4H- chromen-4-one) and B2(3.3.6. 3,5,7-trihydroxy-2-(2-(6-methoxypyridin-3-yl)benzo[d][1,3,2]dioxaborol-5-yl)- 4 H-chromene-4). Antioxidant activities of ligands were investigated by DPPH, ABTS and CUPRAC methods. Cholinesterase inhibition effects of ligands were determined by acetylcholinesterase and butyrylcholinesterase enzyme inhibition methods, cytotoxic effects of ligands were applied to healthy breast and colon cancer cell lines by MTT method, and urease and tyrosinase enzyme activities were determined. Antimicrobial properties of the compounds were analyzed by detecting their anti-QS potentials on Chromobacterium violaceum biosensor strain. Both compounds were found to have significant antioxidant effects compared to controls. It was determined that the compound B1 at 1-10 µg/mL was more active than the reference compounds (α-TOC and BHT). Moreover, the enzyme activity studies on ligands demonstrated that acetylchoinesterase and butyrylcholinesterase enzyme inhibitions were higher than the reference compounds. As expected, boron derivatives exhibited respectable activity against the biofilms of Escherichia coli (E. coli) and P. aeruginosa (P. aeruginosa). These results demonstrate the potential applicability of boron derivatives in the treatment of biofilm-associated infections and provide a practical strategy for the design of new boron-based antimicrobial materials. In silico molecular docking studies were performed on ligands to identify newly synthesized compounds. The binding parameter values and binding sites of the compounds were also determined. In conclusion, our studies showed that newly synthesized hybrid compounds could be solutions for antimicrobial resistance and enzyme-related disorders.
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Affiliation(s)
- Hamdi Temel
- Department of Chemistry, Institute of Science, Dicle University, 21280 Diyarbakir, Turkey; Department of Medical Pharmacology, Faculty of Medicine, Yozgat Bozok University, 66000 Yozgat, Turkey.
| | - Metin Atlan
- Department of Chemistry, Institute of Science, Dicle University, 21280 Diyarbakir, Turkey
| | - Burçin Türkmenoğlu
- Department of Analytical Chemistry, Faculty of Pharmacy, Erzincan Binali Yıldırım University, 24002, Erzincan, Turkey
| | - Abdulselam Ertaş
- Department of Analytical Chemistry, Faculty of Pharmacy, Dicle University, 21280 Diyarbakir, Turkey
| | - Demet Erdönmez
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Düzce University, 81620 Düzce, Turkey
| | - Ufuk Koca Çalışkan
- Department of Pharmacognosy, Faculty of Pharmacy, Gazi University, 06570 Ankara, Turkey
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Singh R, Kumar P, Devi M, Sindhu J, Kumar A, Lal S, Singh D, Kumar H, Kumar S. Urease Inhibition and Structure‐Activity Relationship Study of Thiazolidinone‐, Triazole‐, and Benzothiazole‐Based Heterocyclic Derivatives: A Focus Review. ChemistrySelect 2023. [DOI: 10.1002/slct.202300244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Affiliation(s)
- Rahul Singh
- Department of Chemistry Kurukshetra University Kurukshetra 136119 India
| | - Parvin Kumar
- Department of Chemistry Kurukshetra University Kurukshetra 136119 India
| | - Meena Devi
- Department of Chemistry Kurukshetra University Kurukshetra 136119 India
| | - Jayant Sindhu
- Department of Chemistry COBS&H, CCS Haryana gricultural University Hisar 125004 India
| | - Ashwani Kumar
- Department of Pharmaceutical Sciences GJUS&T Hisar 125001 India
| | - Sohan Lal
- Department of Chemistry Kurukshetra University Kurukshetra 136119 India
| | - Devender Singh
- Department of Chemistry Maharshi Dayanand University Rohtak 124001 India
| | - Harish Kumar
- Department of Chemistry, School of Basic Sciences Central university Haryana Mahendergarh India
| | - Sumit Kumar
- Department of Chemistry DCR University of Science & Technology, Murthal Haryana 131039 India
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13
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Suenaga S, Takano Y, Saito T. Unraveling Binding Mechanism and Stability of Urease Inhibitors: A QM/MM MD Study. Molecules 2023; 28:molecules28062697. [PMID: 36985670 PMCID: PMC10051795 DOI: 10.3390/molecules28062697] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/06/2023] [Accepted: 03/13/2023] [Indexed: 03/19/2023] Open
Abstract
Soil bacteria can produce urease, which catalyzes the hydrolysis of urea to ammonia (NH3) and carbamate. A variety of urease inhibitors have been proposed to reduce NH3 volatilization by interfering with the urease activity. We report a quantum mechanics/molecular mechanics molecular dynamics (QM/MM MD) study on the mechanism employed for the inhibition of urease by three representative competitive inhibitors; namely, acetohydroxamic acid (AHA), hydroxyurea (HU), and N-(n-butyl)phosphorictriamide (NBPTO). The possible connections between the structural and thermodynamical properties and the experimentally observed inhibition efficiency were evaluated and characterized. We demonstrate that the binding affinity decreases in the order NBPTO >> AHA > HU in terms of the computed activation and reaction free energies. This trend also indicates that NBPTO shows the highest inhibitory activity and the lowest IC50 value of 2.1 nM, followed by AHA (42 μM) and HU (100 μM). It was also found that the X=O moiety (X = carbon or phosphorous) plays a crucial role in the inhibitor binding process. These findings not only elucidate why the potent urease inhibitors are effective but also have implications for the design of new inhibitors.
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Affiliation(s)
- Shunya Suenaga
- Faculty of Information Sciences, Hiroshima City University, 3-4-1 Ozuka-Higashi, Asa-Minami-Ku, Hiroshima 731-3194, Japan
| | - Yu Takano
- Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozuka-Higashi, Asa-Minami-Ku, Hiroshima 731-3194, Japan
| | - Toru Saito
- Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozuka-Higashi, Asa-Minami-Ku, Hiroshima 731-3194, Japan
- Correspondence: ; Tel.: +81-82-830-1617
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Ata A, Salar U, Saleem F, Lateef M, Khan SA, Khan KM, Taha M, Haider SM, Ul-Haq Z. Identification of potential urease inhibitors and antioxidants based on saccharin derived analogs: Synthesis, in vitro, and in silico studies. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134376] [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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15
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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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Sharma S, Sharma N, Kumari M, Thakur M. Synthesis, characterization and evaluation of antimicrobial potential of zinc(II) complexes of nitro-substituted hydroxamic acid chelators. J COORD CHEM 2022. [DOI: 10.1080/00958972.2022.2111259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Shubham Sharma
- Department of Chemistry, Himachal Pradesh University, Shimla, India
| | - Neeraj Sharma
- Department of Chemistry, Himachal Pradesh University, Shimla, India
| | - Meena Kumari
- Department of Chemistry, Himachal Pradesh University, Shimla, India
| | - Mridula Thakur
- Department of Chemistry, Himachal Pradesh University, Shimla, India
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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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Loharch S, Berlicki Ł. Rational Development of Bacterial Ureases Inhibitors. CHEM REC 2022; 22:e202200026. [PMID: 35502852 DOI: 10.1002/tcr.202200026] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/28/2022] [Indexed: 12/23/2022]
Abstract
Urease, an enzyme that catalyzes the hydrolysis of urea, is a virulence factor of various pathogenic bacteria. In particular, Helicobacter pylori, that colonizes the digestive tract and Proteus spp., that can infect the urinary tract, are related to urease activity. Therefore, urease inhibitors are considered as potential therapeutics against these infections. This review describes current knowledge of the structures, activity, and biological importance of bacterial ureases. Moreover, the structure-based design of several classes of bacterial urease inhibitors is presented and discussed. Phosphinic and phosphonic acids were applied as transition-state analogues, while Michael acceptors and ebselen derivatives were applied as covalent binders of cysteine residue. This review incorporates bacterial urease inhibitors from literature published between 2008 and 2021.
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Affiliation(s)
- Saurabh Loharch
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland
| | - Łukasz Berlicki
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland
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Abstract
![]()
Urease
catalyzes the hydrolysis of urea to form ammonia and carbamate,
inducing an overall pH increase that affects both human health and
agriculture. Inhibition, mutagenesis, and kinetic studies have provided
insights into its enzymatic role, but there have been debates on the
substrate binding mode as well as the reaction mechanism. In the present
study, we report quatum mechanics-only (QM-only) and quantum mechanics/molecular
mechanics molecular dynamics (QM/MM MD) calculations on urease that
mainly investigate the binding mode of urea and the mechanism of the
urease-catalyzed hydrolysis reaction. Comparison between the experimental
data and our QM(GFN2-xTB)/MM metadynamics results demonstrates that
urea hydrolysis via a complex with bidentate-bound urea is much more
favorable than via that with monodentate-bound urea for both nucleophilic
attack and the subsequent proton transfer steps. We also indicate
that the bidentate coordination of urea fits the active site with
a closed conformation of the mobile flap and can facilitate the stabilization
of transition states and intermediates by forming multiple hydrogen
bonds with certain active site residues.
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Affiliation(s)
- Toru Saito
- Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozuka-Higashi, Asa-Minami-Ku, Hiroshima 731-3194 Japan
| | - Yu Takano
- Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozuka-Higashi, Asa-Minami-Ku, Hiroshima 731-3194 Japan
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Expression, Purification, and Comparative Inhibition of Helicobacter pylori Urease by Regio-Selectively Alkylated Benzimidazole 2-Thione Derivatives. Molecules 2022; 27:molecules27030865. [PMID: 35164122 PMCID: PMC8838460 DOI: 10.3390/molecules27030865] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/22/2022] [Accepted: 01/24/2022] [Indexed: 11/17/2022] Open
Abstract
The urease enzyme has been an important target for the discovery of effective pharmacological and agricultural products. Thirteen regio-selectively alkylated benzimidazole-2-thione derivatives have been designed to carry the essential features of urease inhibitors. The urease enzyme was isolated from Helicobacter pylori as a recombinant urease utilizing the His-tag method. The isolated enzyme was purified and characterized using chromatographic and FPLC techniques showing a maximal activity of 200 mg/mL. Additionally, the commercial Jack bean urease was purchased and included in this study for comparative and mechanistic investigations. The designed compounds were synthesized and screened for their inhibitory activity against the two ureases. Compound 2 inhibited H. pylori and Jack bean ureases with IC50 values of 0.11; and 0.26 mM; respectively. While compound 5 showed IC50 values of 0.01; and 0.29 mM; respectively. Compounds 2 and 5 were docked against Helicobacter pylori urease (PDB ID: 1E9Y; resolution: 3.00 Å) and exhibited correct binding modes with free energy (ΔG) values of −9.74 and −13.82 kcal mol−1; respectively. Further; the in silico ADMET and toxicity properties of 2 and 5 indicated their general safeties and likeness to be used as drugs. Finally, the compounds’ safety was authenticated by an in vitro cytotoxicity assay against fibroblast cells.
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22
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Elbastawesy MA, Aly AA, El-Shaier YA, Brown AB, Abuo-Rahma GEDA, Ramadan M. New 4-thiazolidinone/quinoline-2-ones scaffold: Design, synthesis, docking studies and biological evaluation as potential urease inhibitors. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130845] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Naheed N, Maher S, Saleem F, Khan A, Wadood A, Rasheed S, Choudhary MI, Froeyen M, Abdullah I, Mirza MU, Trant JF, Ahmad S. New isolate from Salvinia molesta with antioxidant and urease inhibitory activity. Drug Dev Res 2021; 82:1169-1181. [PMID: 33983647 DOI: 10.1002/ddr.21831] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/16/2021] [Accepted: 04/23/2021] [Indexed: 11/10/2022]
Abstract
Urease plays a significant role in the pathogenesis of urolithiasis pyelonephritis, urinary catheter encrustation, hepatic coma, hepatic encephalopathy, and peptic acid duodenal ulcers. Salvinia molesta was explored to identify new bioactive compounds with particular emphasis on urease inhibitors. The aqueous methanol extract was fractionated using solvents of increasing polarity. A series of column chromatography and later HPLC were performed on butanol extract. The structures of the resulting pure compounds were resolved using NMR (1D and 2D), infrared, and mass spectroscopy. The novel isolate was evaluated for antioxidant activity (using DPPH, superoxide anion radical scavenging, oxidative burst, and Fe+2 chelation assays), anti-glycation behavior, anticancer activity, carbonic anhydrase inhibition, phosphodiesterase inhibition, and urease inhibition. One new glucopyranose derivative 6'-O-(3,4-dihydroxybenzoyl)-4'-O-(4-hydroxybenzoyl)-α/β-D-glucopyranoside (1) and four known glycosides were identified. Glycoside 1 demonstrated promising antioxidant potential with IC50 values of 48.2 ± 0.3, 60.3 ± 0.6, and 42.1 ± 1.8 μM against DPPH, superoxide radical, and oxidative burst, respectively. Its IC50 in the Jack bean urease inhibition assay was 99.1 ± 0.8 μM. The mechanism-based kinetic studies presented that compound 1 is a mixed-type inhibitor of urease with a Ki value of 91.8 ± 0.1 μM. Finally, molecular dynamic simulations exploring the binding mode of compound 1 with urease provided quantitative agreement between estimated binding free energies and the experimental results. The studies corroborate the use of compound 1 as a lead for QSAR studies as an antioxidant and urease inhibitor. Moreover, it needs to be further evaluated through the animal model, that is, in vivo or tissue culture-based ex-vivo studies, to establish their therapeutic potential against oxidative stress phosphodiesterase-II and urease-induced pathologies.
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Affiliation(s)
- Nadra Naheed
- H.E.J. Research Institute of Chemistry, International Centre for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Saima Maher
- Department of Chemistry, Sardar Bahadur Khan Women University, Quetta, Pakistan
| | - Farooq Saleem
- Faculty of Pharmacy, The University of Lahore, Lahore, Pakistan
| | - Ajmal Khan
- H.E.J. Research Institute of Chemistry, International Centre for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan.,Department of Chemistry, COMSATS Institute of Information Technology, Abbottabad, Pakistan
| | - Abdul Wadood
- Department of Biochemistry, Shankar Campus, Abdul Wali Khan University, Mardan, Pakistan
| | - Saima Rasheed
- Department of Chemistry, Sardar Bahadur Khan Women University, Quetta, Pakistan
| | - M Iqbal Choudhary
- H.E.J. Research Institute of Chemistry, International Centre for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan.,Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Matheus Froeyen
- Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Medicinal Chemistry, University of Leuven, Leuven, Belgium
| | - Iskandar Abdullah
- Drug Design Development Research Group, Department of Chemistry, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Muhammad Usman Mirza
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, Canada
| | - John F Trant
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, Canada
| | - Sarfraz Ahmad
- Drug Design Development Research Group, Department of Chemistry, Universiti Malaya, Kuala Lumpur, Malaysia
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Naseem S, Ashraf M, Khan S, Rafiq M, Kashif M, Rahman J, Rauf MK, Halim SA, Uddin J, Khan A, Al-Harrasi A, Shafiq Z. Exploring biologically active hybrid pharmacophore N-substituted hydrazine-carbothioamides for urease inhibition: In vitro and in silico approach. Int J Biol Macromol 2021; 182:534-544. [PMID: 33839183 DOI: 10.1016/j.ijbiomac.2021.04.036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/05/2021] [Accepted: 04/06/2021] [Indexed: 11/26/2022]
Abstract
Urease is potential target for various human's health complications, such as peptic ulcer, gastric cancer and kidney stone formation. The present study was based on synthesis of new hybrid pharmacophore N-substituted hydrazine-carbothioamides as potential urease inhibitors. Presented method gave excellent yield in range of 85-95% for hydrazine-carbothioamides derivatives (3a-s) after reaction of mono- and disubstituted hydrazides (1a-k) and substituted isothiocyanates (2a-d). All newly derivatives were characterized by advanced spectroscopic techniques (FTIR, 1HNMR, 13CNMR, EMS) and were assessed for their urease inhibition potential. All analogs except for 3k, 3l and 3m demonstrated strong inhibitory potential for urease with IC50 values of 8.45 ± 0.14 to 25.72 ± 0.23 μM as compared to standard thiourea (IC50 21.26 ± 0.35 μM). The structure-activity relationship and mode of interaction was established by molecular docking studies. It was revealed that the N-substituted hydrazine-carbothioamides interacted with nickel atoms present in the active site of urease and supported the correlations with the experimental findings. Therefore, the afforded hydrazine-carbothioamides derivatives are interesting hits for urease inhibition studies with future prospects of modification and optimization.
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Affiliation(s)
- Saira Naseem
- Institute of Chemical Sciences, Bahauddin Zakariya University, Multan 60800, Pakistan
| | - Muhammad Ashraf
- Institute of Chemistry, The Islamia University Bahawalpur, Bahawalpur 63100, Pakistan
| | - Samra Khan
- Institute of Chemical Sciences, Bahauddin Zakariya University, Multan 60800, Pakistan; Department of Chemistry, The Women University, Multan 60000, Pakistan
| | - Muhammad Rafiq
- School of Chemistry and Chemical Engineering, South China University of Technology, Guanzhou 510640, China
| | - Muhammad Kashif
- Department of Chemistry, Emerson University Multan, Bosan Road, Multan, Pakistan
| | - Jameel Rahman
- Institute of Chemistry, The Islamia University Bahawalpur, Bahawalpur 63100, Pakistan
| | - Muhammad Khawar Rauf
- Department of Chemistry, Govt. Post-Graduate Gordon College Rawalpindi, Pakistan
| | - Sobia Ahsan Halim
- Natural and Medical Sciences Research Center, University of Nizwa, PO Box 33, 616 Birkat Al Mauz, Nizwa, Oman
| | - Jalal Uddin
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Khalid University, Abha 62529, Saudi Arabia
| | - Ajmal Khan
- Natural and Medical Sciences Research Center, University of Nizwa, PO Box 33, 616 Birkat Al Mauz, Nizwa, Oman.
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, PO Box 33, 616 Birkat Al Mauz, Nizwa, Oman.
| | - Zahid Shafiq
- Institute of Chemical Sciences, Bahauddin Zakariya University, Multan 60800, Pakistan.
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Mazzei L, Contaldo U, Musiani F, Cianci M, Bagnolini G, Roberti M, Ciurli S. Inhibition of Urease, a Ni-Enzyme: The Reactivity of a Key Thiol With Mono- and Di-Substituted Catechols Elucidated by Kinetic, Structural, and Theoretical Studies. Angew Chem Int Ed Engl 2021; 60:6029-6035. [PMID: 33245574 DOI: 10.1002/anie.202014706] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Indexed: 12/30/2022]
Abstract
The inhibition of urease from Sporosarcina pasteurii (SPU) and Canavalia ensiformis (jack bean, JBU) by a class of six aromatic poly-hydroxylated molecules, namely mono- and dimethyl-substituted catechols, was investigated on the basis of the inhibitory efficiency of the catechol scaffold. The aim was to probe the key step of a mechanism proposed for the inhibition of SPU by catechol, namely the sulfanyl radical attack on the aromatic ring, as well as to obtain critical information on the effect of substituents of the catechol aromatic ring on the inhibition efficacy of its derivatives. The crystal structures of all six SPU-inhibitors complexes, determined at high resolution, as well as kinetic data obtained on JBU and theoretical studies of the reaction mechanism using quantum mechanical calculations, revealed the occurrence of an irreversible inactivation of urease by means of a radical-based autocatalytic multistep mechanism, and indicate that, among all tested catechols, the mono-substituted 3-methyl-catechol is the most efficient inhibitor for urease.
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Affiliation(s)
- Luca Mazzei
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Via Belmeloro 6, 40126, Bologna, Italy.,Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Via Giuseppe Fanin 40, 40127, Bologna, Italy
| | - Umberto Contaldo
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Via Belmeloro 6, 40126, Bologna, Italy.,Laboratory of Chemistry and Biology of Metals, Université Grenoble Alpes, CEA, CNRS, 17 Avenue des Martyrs, 38000, Grenoble, France
| | - Francesco Musiani
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Via Belmeloro 6, 40126, Bologna, Italy.,Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Via Giuseppe Fanin 40, 40127, Bologna, Italy
| | - Michele Cianci
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Greta Bagnolini
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Via Belmeloro 6, 40126, Bologna, Italy
| | - Marinella Roberti
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Via Belmeloro 6, 40126, Bologna, Italy
| | - Stefano Ciurli
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Via Belmeloro 6, 40126, Bologna, Italy.,Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Via Giuseppe Fanin 40, 40127, Bologna, Italy
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26
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Milo S, Heylen RA, Glancy J, Williams GT, Patenall BL, Hathaway HJ, Thet NT, Allinson SL, Laabei M, Jenkins ATA. A small-molecular inhibitor against Proteus mirabilis urease to treat catheter-associated urinary tract infections. Sci Rep 2021; 11:3726. [PMID: 33580163 PMCID: PMC7881204 DOI: 10.1038/s41598-021-83257-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 01/26/2021] [Indexed: 01/30/2023] Open
Abstract
Infection and blockage of indwelling urinary catheters is significant owing to its high incidence rate and severe medical consequences. Bacterial enzymes are employed as targets for small molecular intervention in human bacterial infections. Urease is a metalloenzyme known to play a crucial role in the pathogenesis and virulence of catheter-associated Proteus mirabilis infection. Targeting urease as a therapeutic candidate facilitates the disarming of bacterial virulence without affecting bacterial fitness, thereby limiting the selective pressure placed on the invading population and lowering the rate at which it will acquire resistance. We describe the design, synthesis, and in vitro evaluation of the small molecular enzyme inhibitor 2-mercaptoacetamide (2-MA), which can prevent encrustation and blockage of urinary catheters in a physiologically representative in vitro model of the catheterized urinary tract. 2-MA is a structural analogue of urea, showing promising competitive activity against urease. In silico docking experiments demonstrated 2-MA's competitive inhibition, whilst further quantum level modelling suggests two possible binding mechanisms.
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Affiliation(s)
- Scarlet Milo
- grid.7340.00000 0001 2162 1699Department of Chemistry, University of Bath, Bath, BA2 7AY UK
| | - Rachel A. Heylen
- grid.7340.00000 0001 2162 1699Department of Chemistry, University of Bath, Bath, BA2 7AY UK
| | - John Glancy
- grid.7340.00000 0001 2162 1699Department of Chemistry, University of Bath, Bath, BA2 7AY UK
| | - George T. Williams
- grid.9759.20000 0001 2232 2818School of Physical Sciences, University of Kent, Canterbury, CT2 7NH UK
| | - Bethany L. Patenall
- grid.7340.00000 0001 2162 1699Department of Chemistry, University of Bath, Bath, BA2 7AY UK
| | - Hollie J. Hathaway
- grid.9835.70000 0000 8190 6402Department of Chemistry, Lancaster University, Bailrigg, Lancaster, LA1 4YB UK
| | - Naing T. Thet
- grid.7340.00000 0001 2162 1699Department of Chemistry, University of Bath, Bath, BA2 7AY UK
| | - Sarah L. Allinson
- grid.9835.70000 0000 8190 6402Biomedical and Life Sciences Division, Lancaster University, Bailrigg, Lancaster, LA1 4YB UK
| | - Maisem Laabei
- grid.7340.00000 0001 2162 1699Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY UK
| | - A. Toby A. Jenkins
- grid.7340.00000 0001 2162 1699Department of Chemistry, University of Bath, Bath, BA2 7AY UK
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27
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Mazzei L, Contaldo U, Musiani F, Cianci M, Bagnolini G, Roberti M, Ciurli S. Inhibition of Urease, a Ni‐Enzyme: The Reactivity of a Key Thiol With Mono‐ and Di‐Substituted Catechols Elucidated by Kinetic, Structural, and Theoretical Studies. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202014706] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Luca Mazzei
- Department of Pharmacy and Biotechnology (FaBiT) University of Bologna Via Belmeloro 6 40126 Bologna Italy
- Laboratory of Bioinorganic Chemistry Department of Pharmacy and Biotechnology (FaBiT) University of Bologna Via Giuseppe Fanin 40 40127 Bologna Italy
| | - Umberto Contaldo
- Department of Pharmacy and Biotechnology (FaBiT) University of Bologna Via Belmeloro 6 40126 Bologna Italy
- Laboratory of Chemistry and Biology of Metals Université Grenoble Alpes, CEA CNRS 17 Avenue des Martyrs 38000 Grenoble France
| | - Francesco Musiani
- Department of Pharmacy and Biotechnology (FaBiT) University of Bologna Via Belmeloro 6 40126 Bologna Italy
- Laboratory of Bioinorganic Chemistry Department of Pharmacy and Biotechnology (FaBiT) University of Bologna Via Giuseppe Fanin 40 40127 Bologna Italy
| | - Michele Cianci
- Department of Agricultural, Food and Environmental Sciences Polytechnic University of Marche Via Brecce Bianche 60131 Ancona Italy
| | - Greta Bagnolini
- Department of Pharmacy and Biotechnology (FaBiT) University of Bologna Via Belmeloro 6 40126 Bologna Italy
| | - Marinella Roberti
- Department of Pharmacy and Biotechnology (FaBiT) University of Bologna Via Belmeloro 6 40126 Bologna Italy
| | - Stefano Ciurli
- Department of Pharmacy and Biotechnology (FaBiT) University of Bologna Via Belmeloro 6 40126 Bologna Italy
- Laboratory of Bioinorganic Chemistry Department of Pharmacy and Biotechnology (FaBiT) University of Bologna Via Giuseppe Fanin 40 40127 Bologna Italy
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28
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Mazzei L, Cirri D, Cianci M, Messori L, Ciurli S. Kinetic and structural analysis of the inactivation of urease by mixed-ligand phosphine halide Ag(I) complexes. J Inorg Biochem 2021; 218:111375. [PMID: 33711632 DOI: 10.1016/j.jinorgbio.2021.111375] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/14/2021] [Accepted: 01/22/2021] [Indexed: 01/22/2023]
Abstract
Soft metal ions can inactivate urease, a Ni(II)-dependent enzyme whose hydrolytic activity has significant implications in agro-environmental science and human health. Kinetic and structural studies of the reaction of Canavalia ensiformis urease (JBU) and Sporosarcina pasteurii urease (SPU) with Ag(I) compounds of general formula [Ag(PEt3)X]4 (X = Cl, Br, I), and with the ionic species [Ag(PEt3)2]NO3, revealed the role of the Ag(I) ion and its ligands in modulating the metal-enzyme interaction. The activity of JBU is obliterated by the [Ag(PEt3)X]4 complexes, with IC50 values in the nanomolar range; the efficiency of the inhibition increases in the Cl- < Br- < I- order. The activity of JBU upon [Ag(PEt3)2]NO3 addition decreases to a plateau corresponding to ca. 60% of the original activity and decreases with time at a reduced rate. Synchrotron X-ray crystallography on single crystals obtained after the incubation of SPU with the Ag(I) complexes yielded high-resolution (1.63-1.97 Å) structures. The metal-protein adducts entail a dinuclear Ag(I) cluster bound to the conserved residues αCys322, αHis323, and αMet367, with a bridging cysteine thiolate atom, a weak Ag…Ag bond, and a quasi-linear Ag(I) coordination geometry. These observations suggest a mechanism that involves the initial substitution of the phosphine ligand, followed by a structural rearrangement to yield the dinuclear Ag(I) cluster. These findings indicate that urease, in addition to the active site dinuclear Ni(II) cluster, possesses a secondary metal binding site, located on the mobile flap domain, capable of recognizing pairs of soft metal ions and controlling catalysis.
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Affiliation(s)
- Luca Mazzei
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Via Giuseppe Fanin 40, I-40127 Bologna, Italy.
| | - Damiano Cirri
- Department of Chemistry and Industrial Chemistry (DCCI), University of Pisa, Via Moruzzi 13, I-56124 Pisa, Italy
| | - Michele Cianci
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, I-60131 Ancona, Italy
| | - Luigi Messori
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino, Italy
| | - Stefano Ciurli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Via Giuseppe Fanin 40, I-40127 Bologna, Italy.
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29
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Arshad M, Ahmed K, Iqbal Z, Rashid U, Arshad MN, Asiri AM, Mahmood T. Synthesis, structural properties, enzyme inhibition and molecular docking studies of (Z)-N'-(1-allyl-2-oxoindolin-3-ylidene) methanesulfono-hydrazide and (Z)-N'-(1-allyl-2-oxoindolin-3-ylidene)-3-nitrobenzenesulfono-hydrazide. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128880] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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30
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Khan FA, Shamim S, Ullah N, Lodhi MA, Khan KM, Kanwal, Ali F, Afridi SG, Perveen S, Khan A. Dihydropyrimidones: A ligands urease recognition study and mechanistic insight through in vitro and in silico approach. Med Chem Res 2020. [DOI: 10.1007/s00044-020-02643-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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31
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Anti-urease and cytotoxic activity of 1-Nitro-2-phenylethane and Nerolidol; two major compounds isolated from the seeds of Dennettia tripetala. Med Chem Res 2020. [DOI: 10.1007/s00044-020-02607-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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32
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The structure-based reaction mechanism of urease, a nickel dependent enzyme: tale of a long debate. J Biol Inorg Chem 2020; 25:829-845. [PMID: 32809087 PMCID: PMC7433671 DOI: 10.1007/s00775-020-01808-w] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 06/29/2020] [Indexed: 01/22/2023]
Abstract
This review is an attempt to retrace the chronicle that starts from the discovery of the role of nickel as the essential metal ion in urease for the enzymatic catalysis of urea, a key step in the biogeochemical cycle of nitrogen on Earth, to the most recent progress in understanding the chemistry of this historical enzyme. Data and facts are presented through the magnifying lenses of the authors, using their best judgment to filter and elaborate on the many facets of the research carried out on this metalloenzyme over the years. The tale is divided in chapters that discuss and describe the results obtained in the subsequent leaps in the knowledge that led from the discovery of a biological role for Ni to the most recent advancements in the comprehension of the relationship between the structure and function of urease. This review is intended not only to focus on the bioinorganic chemistry of this beautiful metal-based catalysis, but also, and maybe primarily, to evoke inspiration and motivation to further explore the realm of bio-based coordination chemistry.
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33
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Loubet P, Ranfaing J, Dinh A, Dunyach-Remy C, Bernard L, Bruyère F, Lavigne JP, Sotto A. Alternative Therapeutic Options to Antibiotics for the Treatment of Urinary Tract Infections. Front Microbiol 2020; 11:1509. [PMID: 32719668 PMCID: PMC7350282 DOI: 10.3389/fmicb.2020.01509] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 06/10/2020] [Indexed: 12/29/2022] Open
Abstract
Urinary tract infections (UTIs) mainly caused by Uropathogenic Escherichia coli (UPEC), are common bacterial infections. Many individuals suffer from chronically recurring UTIs, sometimes requiring long-term prophylactic antibiotic regimens. The global emergence of multi-drug resistant uropathogens in the last decade underlines the need for alternative non-antibiotic therapeutic and preventative strategies against UTIs. The research on non-antibiotic therapeutic options in UTIs has focused on the following phases of the pathogenesis: colonization, adherence of pathogens to uroepithelial cell receptors and invasion. In this review, we discuss vaccines, small compounds, nutraceuticals, immunomodulating agents, probiotics and bacteriophages, highlighting the challenges each of these approaches face. Most of these treatments show interesting but only preliminary results. Lactobacillus-containing products and cranberry products in conjunction with propolis have shown the most robust results to date and appear to be the most promising new alternative to currently used antibiotics. Larger efficacy clinical trials as well as studies on the interplay between non-antibiotic therapies, uropathogens and the host immune system are warranted.
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Affiliation(s)
- Paul Loubet
- VBMI, INSERM U1047, Université de Montpellier, Service des Maladies Infectieuses et Tropicales, CHU Nîmes, Nîmes, France
| | - Jérémy Ranfaing
- VBMI, INSERM U1047, Université de Montpellier, Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, Nîmes, France
| | - Aurélien Dinh
- Service des Maladies Infectieuses, AP-HP Raymond-Poincaré, Garches, France
| | - Catherine Dunyach-Remy
- VBMI, INSERM U1047, Université de Montpellier, Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, Nîmes, France
| | - Louis Bernard
- PRES Centre Val de Loire, Université François Rabelais de Tours, Tours, France.,Service des Maladies Infectieuses, CHU Tours, Tours, France
| | - Franck Bruyère
- PRES Centre Val de Loire, Université François Rabelais de Tours, Tours, France.,Service d'Urologie, CHU Tours, Tours, France
| | - Jean-Philippe Lavigne
- VBMI, INSERM U1047, Université de Montpellier, Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, Nîmes, France
| | - Albert Sotto
- VBMI, INSERM U1047, Université de Montpellier, Service des Maladies Infectieuses et Tropicales, CHU Nîmes, Nîmes, France
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34
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Karaali N, Aydin S, Baltas N, Mentese E. Synthesis of novel tetra‐substituted benzimidazole compounds containing certain heterostructures with antioxidant and anti‐urease activities. J Heterocycl Chem 2020. [DOI: 10.1002/jhet.3905] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Nesrin Karaali
- Department of Chemistry, Faculty of Arts and SciencesRecep Tayyip Erdogan University Rize Turkey
| | - Serdar Aydin
- Department of Chemistry, Faculty of Arts and SciencesRecep Tayyip Erdogan University Rize Turkey
| | - Nimet Baltas
- Department of Chemistry, Faculty of Arts and SciencesRecep Tayyip Erdogan University Rize Turkey
| | - Emre Mentese
- Department of Chemistry, Faculty of Arts and SciencesRecep Tayyip Erdogan University Rize Turkey
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35
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Elbastawesy MAI, El-Shaier YAMM, Ramadan M, Brown AB, Aly AA, Abuo-Rahma GEDA. Identification and molecular modeling of new quinolin-2-one thiosemicarbazide scaffold with antimicrobial urease inhibitory activity. Mol Divers 2020; 25:13-27. [PMID: 31916112 DOI: 10.1007/s11030-019-10021-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 11/29/2019] [Indexed: 01/03/2023]
Abstract
A new series of 6-substituted quinolin-2-one thiosemicarbazides 6a-j has been synthesized. The structure of the target compounds was proved by different spectroscopic and elemental analyses. All the designed final compounds were evaluated for their in vitro activity against the urease-producing R. mucilaginosa and Proteus mirabilis bacteria as fungal and bacterial pathogens, respectively. Moreover, all compounds were in vitro tested as potential urease inhibitors using the cup-plate diffusion method. Compounds 6a and 6b were the most active with (IC50 = 0.58 ± 0.15 and 0.43 ± 0.09 µM), respectively, in comparison with lead compound I (IC50 = 1.13 ± 0.00 µM). Also, the designed compounds were docked into urease proteins (ID: 3LA4 and ID: 4UBP) using Open Eye® software to understand correctly about ligand-receptor interactions. The docking results revealed that the designed compounds can interact with the active site of the enzyme through multiple strong hydrogen bonds. Moreover, rapid overlay of chemical structures' analysis was described to understand the 3D QSAR of synthesized compounds as urease inhibitors. The results emphasize the importance of polar thiosemicarbazide directly linked to 6-substituted quinolone moieties as promising antimicrobial urease inhibitors.
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Affiliation(s)
- Mohammed A I Elbastawesy
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Al-Azhar University, Assiut, 71524, Egypt
| | - Yaseen A M M El-Shaier
- Department of Organic and Medicinal Chemistry, Faculty of Pharmacy, University of Sadat City, Sadat-City, Menufia, Egypt
| | - Mohamed Ramadan
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Al-Azhar University, Assiut, 71524, Egypt
| | - Alan B Brown
- Chemistry Department, Florida Institute of Technology, Melbourne, FL, 32901, USA
| | - Ashraf A Aly
- Department of Chemistry, Faculty of Science, Minia University, El-Minia, 61519, Egypt.
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36
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Zambelli B, Mazzei L, Ciurli S. Intrinsic disorder in the nickel-dependent urease network. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 174:307-330. [DOI: 10.1016/bs.pmbts.2020.05.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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37
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Three Multi-Components Reaction: Synthesis and X-Ray Single-Crystal of Hydroacridinone-Based Hydrazino-S-Triazine Derivative as a New Class of Urease Inhibitor. CRYSTALS 2019. [DOI: 10.3390/cryst10010014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The one-pot fashion of three multi-component reaction provides the desired hydroacridinone-based hydrazino-s-triazine scaffold 4. Compound 4 was crystallized in an orthorhombic crystal system and Pbca space group with a = 11.6271(2) Å, b = 18.2018(4) Å, c = 32.4721(6) Å, and α = β = γ = 90° with one formula unit per asymmetric unit and eight molecules per unit cell. Additionally, structural features, Hirshfeld surfaces, and DFT studies were also investigated. Its packing in the crystal is controlled by H…H (63.4%), O…H (12.7%), Cl…H (7.2%), N…H (4.7%), and C…H (10.2%) contacts, where the O…H and Cl…H contacts were found the strongest. In vitro urease inhibition evaluation showed that the hydroacridinone-based hydrazino-s-triazine is more active (IC50 = 17.9 ± 0.47 µM) than the standard acetohydroxamic acid (IC50 = 20.3 ± 0.43 µM).
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38
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Mazzei L, Cianci M, Benini S, Ciurli S. The Impact of pH on Catalytically Critical Protein Conformational Changes: The Case of the Urease, a Nickel Enzyme. Chemistry 2019; 25:12145-12158. [DOI: 10.1002/chem.201902320] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 07/01/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Luca Mazzei
- Laboratory of Bioinorganic ChemistryDepartment of Pharmacy and BiotechnologyUniversity of Bologna Bologna Italy
| | - Michele Cianci
- Department of Agricultural, Food and Environmental SciencesPolytechnic University of Marche Ancona Italy
| | - Stefano Benini
- Bioorganic Chemistry and Bio-Crystallography LaboratoryFaculty of Science and TechnologyFree University of Bolzano Bolzano Italy
| | - Stefano Ciurli
- Laboratory of Bioinorganic ChemistryDepartment of Pharmacy and BiotechnologyUniversity of Bologna Bologna Italy
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39
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Arqué X, Romero-Rivera A, Feixas F, Patiño T, Osuna S, Sánchez S. Intrinsic enzymatic properties modulate the self-propulsion of micromotors. Nat Commun 2019; 10:2826. [PMID: 31249381 PMCID: PMC6597730 DOI: 10.1038/s41467-019-10726-8] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 05/24/2019] [Indexed: 11/17/2022] Open
Abstract
Bio-catalytic micro- and nanomotors self-propel by the enzymatic conversion of substrates into products. Despite the advances in the field, the fundamental aspects underlying enzyme-powered self-propulsion have rarely been studied. In this work, we select four enzymes (urease, acetylcholinesterase, glucose oxidase, and aldolase) to be attached on silica microcapsules and study how their turnover number and conformational dynamics affect the self-propulsion, combining both an experimental and molecular dynamics simulations approach. Urease and acetylcholinesterase, the enzymes with higher catalytic rates, are the only enzymes capable of producing active motion. Molecular dynamics simulations reveal that urease and acetylcholinesterase display the highest degree of flexibility near the active site, which could play a role on the catalytic process. We experimentally assess this hypothesis for urease micromotors through competitive inhibition (acetohydroxamic acid) and increasing enzyme rigidity (β-mercaptoethanol). We conclude that the conformational changes are a precondition of urease catalysis, which is essential to generate self-propulsion. Self-propulsion of biocatalytic micro- and nanomotors is facilitated by enzymes converting substrates into products. Here, the authors show that intrinsic enzymatic properties such as conformational changes are crucial for the self-propulsion of silica microcapsules modified with urease.
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Affiliation(s)
- Xavier Arqué
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 10-12, 08028, Barcelona, Spain
| | - Adrian Romero-Rivera
- CompBioLab Group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 69, 17003, Girona, Spain
| | - Ferran Feixas
- CompBioLab Group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 69, 17003, Girona, Spain
| | - Tania Patiño
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 10-12, 08028, Barcelona, Spain.
| | - Sílvia Osuna
- CompBioLab Group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 69, 17003, Girona, Spain. .,Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010, Barcelona, Spain.
| | - Samuel Sánchez
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 10-12, 08028, Barcelona, Spain. .,Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010, Barcelona, Spain.
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Islam M, Khan A, Shehzad MT, Hameed A, Ahmed N, Halim SA, Khiat M, Anwar MU, Hussain J, Csuk R, Shafiq Z, Al-Harrasi A. Synthesis and characterization of new thiosemicarbazones, as potent urease inhibitors: In vitro and in silico studies. Bioorg Chem 2019; 87:155-162. [DOI: 10.1016/j.bioorg.2019.03.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 02/23/2019] [Accepted: 03/04/2019] [Indexed: 01/25/2023]
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Mazzei L, Cianci M, Benini S, Ciurli S. The Structure of the Elusive Urease–Urea Complex Unveils the Mechanism of a Paradigmatic Nickel‐Dependent Enzyme. Angew Chem Int Ed Engl 2019; 58:7415-7419. [DOI: 10.1002/anie.201903565] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Indexed: 01/14/2023]
Affiliation(s)
- Luca Mazzei
- Laboratory of Bioinorganic ChemistryDepartement of Pharmacy and BiotechnologyUniversity of Bologna Via Giuseppe Fanin 40 40138 Bologna Italy
| | - Michele Cianci
- Department of Agricultural, Food and Environmental SciencesPolytechnic University of Marche Ancona Italy
| | - Stefano Benini
- Bioorganic Chemistry and Bio-Crystallography Laboratory (B2Cl)Faculty of Science and TechnologyFree University of Bolzano Bolzano Italy
| | - Stefano Ciurli
- Laboratory of Bioinorganic ChemistryDepartement of Pharmacy and BiotechnologyUniversity of Bologna Via Giuseppe Fanin 40 40138 Bologna Italy
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Mazzei L, Cianci M, Benini S, Ciurli S. The Structure of the Elusive Urease–Urea Complex Unveils the Mechanism of a Paradigmatic Nickel‐Dependent Enzyme. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201903565] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Luca Mazzei
- Laboratory of Bioinorganic ChemistryDepartement of Pharmacy and BiotechnologyUniversity of Bologna Via Giuseppe Fanin 40 40138 Bologna Italy
| | - Michele Cianci
- Department of Agricultural, Food and Environmental SciencesPolytechnic University of Marche Ancona Italy
| | - Stefano Benini
- Bioorganic Chemistry and Bio-Crystallography Laboratory (B2Cl)Faculty of Science and TechnologyFree University of Bolzano Bolzano Italy
| | - Stefano Ciurli
- Laboratory of Bioinorganic ChemistryDepartement of Pharmacy and BiotechnologyUniversity of Bologna Via Giuseppe Fanin 40 40138 Bologna Italy
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Natural urease inhibitors from Aloe vera resin and Lycium shawii and their structural-activity relationship and molecular docking study. Bioorg Chem 2019; 88:102955. [PMID: 31054431 DOI: 10.1016/j.bioorg.2019.102955] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 03/10/2019] [Accepted: 04/26/2019] [Indexed: 02/01/2023]
Abstract
Bio-assay guided fractionation of the methanolic extract of Aloe vera resin and Lycium shawii stem successively afforded twenty three compounds; fourteen (1-14) from A. vera and nine (15-23) from L. shawii. All these compounds were characterized by 1D and 2D NMR spectroscopic techniques viz., 1H, 13C, DEPT, HSQC, HMBC, and COSY, and NEOSY, ESI-MS and compared with the reported literature. These compounds were assessed for their potential as urease inhibitors targeted in peptic ulcer. Among crude extracts and fractions of A. vera resin, n-butanol fraction (23.5 ± 1.7 μg·mL-1) showed the most potent urease inhibition followed by methanol (30.9 ± 0.3 μg/mL) and ethyl acetate (31.7 ± 0.5 μg·mL-1). In case of L. shawii, ethyl acetate fraction exhibited the highest urease activity (41.0 ± 1.4 μg/mL) trailed by dichloromethane (55.2 ± 1.5 μg/mL) fraction. Among the isolates, compounds 7, 11 and 23 were found to be excellent urease inhibitors with IC50 values of 14.5 ± 0.90 µM, (16.7 ± 0.16 µM) and 14.0 ± 0.8 µM, respectively. To the best of our knowledge, this is the first report on the urease enzyme inhibitory activity of the said compounds excluding compound 18. In addition, the urease activity of different fractions of L. shawii stem was also reported for the first time. The molecular docking studies showed that all the active compounds well accommodate in the active site of the urease enzyme by interacting with key amino acids.
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Abstract
Covering: up to the end of 2017 The human body is composed of an equal number of human and microbial cells. While the microbial community inhabiting the human gastrointestinal tract plays an essential role in host health, these organisms have also been connected to various diseases. Yet, the gut microbial functions that modulate host biology are not well established. In this review, we describe metabolic functions of the human gut microbiota that involve metalloenzymes. These activities enable gut microbial colonization, mediate interactions with the host, and impact human health and disease. We highlight cases in which enzyme characterization has advanced our understanding of the gut microbiota and examples that illustrate the diverse ways in which metalloenzymes facilitate both essential and unique functions of this community. Finally, we analyze Human Microbiome Project sequencing datasets to assess the distribution of a prominent family of metalloenzymes in human-associated microbial communities, guiding future enzyme characterization efforts.
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Mazzei L, Wenzel MN, Cianci M, Palombo M, Casini A, Ciurli S. Inhibition Mechanism of Urease by Au(III) Compounds Unveiled by X-ray Diffraction Analysis. ACS Med Chem Lett 2019; 10:564-570. [PMID: 30996797 DOI: 10.1021/acsmedchemlett.8b00585] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 01/04/2019] [Indexed: 11/29/2022] Open
Abstract
The nickel-dependent enzyme urease is a virulence factor for a large number of critical human pathogens, making this enzyme a potential target of therapeutics for the treatment of resistant bacterial infections. In the search for novel urease inhibitors, five selected coordination and organometallic Au(III) compounds containing N∧N or C∧N and C∧N∧N ligands were tested for their inhibitory effects against Canavalia ensiformis (jack bean) urease. The results showed potent inhibition effects with IC50 values in the nanomolar range. The 2.14 Å resolution crystal structure of Sporosarcina pasteurii urease inhibited by the most effective Au(III) compound [Au(PbImMe)Cl2]PF6 (PbImMe = 1-methyl-2-(pyridin-2-yl)-benzimidazole) reveals the presence of two Au ions bound to the conserved triad αCys322/αHis323/αMet367. The binding of the Au ions to these residues blocks the movement of a flap, located at the edge of the active site channel and essential for enzyme catalysis, completely obliterating the catalytic activity of urease. Overall, the obtained results constitute the basis for the design of new gold complexes as selective urease inhibitors with future antibacterial applications.
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Affiliation(s)
- Luca Mazzei
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale Giuseppe Fanin 40, I-40127 Bologna, Italy
| | - Margot N. Wenzel
- School of Chemistry, Cardiff University, Main Building, Park Place, CF10 3AT Cardiff, United Kingdom
| | - Michele Cianci
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Via Brecce Bianche, I-60131 Ancona, Italy
| | - Marta Palombo
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale Giuseppe Fanin 40, I-40127 Bologna, Italy
| | - Angela Casini
- School of Chemistry, Cardiff University, Main Building, Park Place, CF10 3AT Cardiff, United Kingdom
| | - Stefano Ciurli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale Giuseppe Fanin 40, I-40127 Bologna, Italy
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Arshia, Begum F, Almandil NB, Lodhi MA, Khan KM, Hameed A, Perveen S. Synthesis and urease inhibitory potential of benzophenone sulfonamide hybrid in vitro and in silico. Bioorg Med Chem 2019; 27:1009-1022. [DOI: 10.1016/j.bmc.2019.01.043] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 01/29/2019] [Accepted: 01/31/2019] [Indexed: 10/27/2022]
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Mazzei L, Cianci M, Contaldo U, Ciurli S. Insights into Urease Inhibition by N-( n-Butyl) Phosphoric Triamide through an Integrated Structural and Kinetic Approach. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:2127-2138. [PMID: 30735374 DOI: 10.1021/acs.jafc.8b04791] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The nickel-dependent enzyme urease represents a negative element for the efficiency of soil nitrogen fertilization as well as a virulence factor for a large number of pathogenic and antibiotic-resistant bacteria. The development of ever more efficient urease inhibitors demands knowledge of their modes of action at the molecular level. N-( n-Butyl)-phosphoric triamide (NBPTO) is the oxo-derivative of N-( n-butyl)-thiophosphoric triamide (NBPT), which is extensively employed in agriculture to increase the efficiency of urea-based fertilizers. The 1.45 Å resolution structure of the enzyme-inhibitor complex obtained upon incubation of Sporosarcina pasteurii urease (SPU) with NBPTO shows the presence of diamido phosphoric acid (DAP), generated upon enzymatic hydrolysis of NBPTO with the release of n-butyl amine. DAP is bound in a tridentate binding mode to the two Ni(II) ions in the active site of urease via two O atoms and an amide NH2 group, whereas the second amide group of DAP points away from the metal center into the active-site channel. The mobile flap modulating the size of the active-site cavity is found in a disordered closed-open conformation. A kinetic characterization of the NBPTO-based inhibition of both bacterial (SPU) and plant ( Canavalia ensiformis or jack bean, JBU) ureases, carried out by calorimetric measurements, indicates the occurrence of a reversible slow-inhibition mode of action. The latter is characterized by a very small value of the equilibrium dissociation constant of the urease-DAP complex caused, in turn, by the large rate constant for the formation of the enzyme-inhibitor complex. The much greater capability of NBPTO to inhibit urease, as compared with that of NBPT, is thus not caused by the presence of a P═O moiety versus a P═S moiety, as previously suggested, but rather by the readiness of NBPTO to react with urease without the need to convert one of the P-NH2 amide moieties to its P-OH acid derivative, as in the case of NBPT. The latter process is indeed characterized by a very small equilibrium constant that reduces drastically the concentration of the active form of the inhibitor in the case of NBPT. This indicates that high-efficiency phosphoramide-based urease inhibitors must have at least one O atom bound to the central P atom in order for the molecule to efficiently and rapidly bind to the dinickel center of the enzyme.
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Affiliation(s)
- Luca Mazzei
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology , University of Bologna , 40126 Bologna , Italy
| | - Michele Cianci
- Department of Agricultural, Food and Environmental Sciences , Polytechnic University of Marche , 60121 Ancona , Italy
| | - Umberto Contaldo
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology , University of Bologna , 40126 Bologna , Italy
| | - Stefano Ciurli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology , University of Bologna , 40126 Bologna , Italy
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Li C, Huang P, Wong K, Xu Y, Tan L, Chen H, Lu Q, Luo C, Tam C, Zhu L, Su Z, Xie J. Coptisine-induced inhibition of Helicobacter pylori: elucidation of specific mechanisms by probing urease active site and its maturation process. J Enzyme Inhib Med Chem 2018; 33:1362-1375. [PMID: 30191728 PMCID: PMC6136390 DOI: 10.1080/14756366.2018.1501044] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
In this study, we examined the anti-Helicobactor pylori effects of the main protoberberine-type alkaloids in Rhizoma Coptidis. Coptisine exerted varying antibacterial and bactericidal effects against three standard H. pylori strains and eleven clinical isolates, including four drug-resistant strains, with minimum inhibitory concentrations ranging from 25 to 50 μg/mL and minimal bactericidal concentrations ranging from 37.5 to 125 μg/mL. Coptisine’s anti-H. pylori effects derived from specific inhibition of urease in vivo. In vitro, coptisine inactivated urease in a concentration-dependent manner through slow-binding inhibition and involved binding to the urease active site sulfhydryl group. Coptisine inhibition of H. pylori urease (HPU) was mixed type, while inhibition of jack bean urease was non-competitive. Importantly, coptisine also inhibited HPU by binding to its nickel metallocentre. Besides, coptisine interfered with urease maturation by inhibiting activity of prototypical urease accessory protein UreG and formation of UreG dimers and by promoting dissociation of nickel from UreG dimers. These findings demonstrate that coptisine inhibits urease activity by targeting its active site and inhibiting its maturation, thereby effectively inhibiting H. pylori. Coptisine may thus be an effective anti-H. pylori agent.
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Affiliation(s)
- Cailan Li
- a Guangdong Provincial Key Laboratory of New Drug Development and Research of Chinese Medicine, Mathematical Engineering Academy of Chinese Medicine , Guangzhou University of Chinese Medicine , Guangzhou , P. R. China
| | - Ping Huang
- b School of Pharmaceutical Sciences , Guangzhou University of Chinese Medicine , Guangzhou , P. R. China
| | - Kambo Wong
- c School of Life Sciences , Center for Protein Science and Crystallography, The Chinese University of Hong Kong , P. R. China
| | - Yifei Xu
- b School of Pharmaceutical Sciences , Guangzhou University of Chinese Medicine , Guangzhou , P. R. China
| | - Lihua Tan
- a Guangdong Provincial Key Laboratory of New Drug Development and Research of Chinese Medicine, Mathematical Engineering Academy of Chinese Medicine , Guangzhou University of Chinese Medicine , Guangzhou , P. R. China
| | - Hanbin Chen
- d The First Affiliated Hospital of Chinese Medicine, Guangzhou University of Chinese Medicine , Guangzhou , P. R. China
| | - Qiang Lu
- e Key Laboratory of Chinese Medicinal Resource from Lingnan, Ministry of Education and Research Center of Chinese Herbal Resource Science and Engineering , Guangzhou University of Chinese Medicine , Guangzhou , P. R. China
| | - Chaodan Luo
- a Guangdong Provincial Key Laboratory of New Drug Development and Research of Chinese Medicine, Mathematical Engineering Academy of Chinese Medicine , Guangzhou University of Chinese Medicine , Guangzhou , P. R. China
| | - Chunlai Tam
- c School of Life Sciences , Center for Protein Science and Crystallography, The Chinese University of Hong Kong , P. R. China
| | - Lixiang Zhu
- b School of Pharmaceutical Sciences , Guangzhou University of Chinese Medicine , Guangzhou , P. R. China
| | - Ziren Su
- a Guangdong Provincial Key Laboratory of New Drug Development and Research of Chinese Medicine, Mathematical Engineering Academy of Chinese Medicine , Guangzhou University of Chinese Medicine , Guangzhou , P. R. China
| | - Jianhui Xie
- f Guangdong Provincial Key Laboratory of Clinical Research on Traditional Chinese Medicine Syndrome , The Second Affiliated Hospital, Guangzhou University of Chinese Medicine , Guangzhou , P. R. China
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Rego YF, Queiroz MP, Brito TO, Carvalho PG, de Queiroz VT, de Fátima Â, Macedo Jr. F. A review on the development of urease inhibitors as antimicrobial agents against pathogenic bacteria. J Adv Res 2018; 13:69-100. [PMID: 30094084 PMCID: PMC6077150 DOI: 10.1016/j.jare.2018.05.003] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 04/30/2018] [Accepted: 05/01/2018] [Indexed: 01/24/2023] Open
Abstract
Ureases are enzymes that hydrolyze urea into ammonium and carbon dioxide. They have received considerable attention due to their impacts on living organism health, since the urease activity in microorganisms, particularly in bacteria, are potential causes and/or factors contributing to the persistence of some pathogen infections. This review compiles examples of the most potent antiurease organic substances. Emphasis was given to systematic screening studies on the inhibitory activity of rationally designed series of compounds with the corresponding SAR considerations. Ureases of Canavalia ensiformis, the usual model in antiureolytic studies, are emphasized. Although the active site of this class of hydrolases is conserved among bacteria and vegetal ureases, the same is not observerd for allosteric site. Therefore, inhibitors acting by participating in interactions with the allosteric site are more susceptible to a potential lack of association among their inhibitory profile for different ureases. The information about the inhibitory activity of different classes of compounds can be usefull to guide the development of new urease inhibitors that may be used in future in small molecular therapy against pathogenic bacteria.
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Affiliation(s)
- Yuri F. Rego
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Marcelo P. Queiroz
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Tiago O. Brito
- Departamento de Química, Centro de Ciências Exatas, Universidade Estadual de Londrina, Londrina, PR, Brazil
| | - Priscila G. Carvalho
- Departamento de Química, Centro de Ciências Exatas, Universidade Estadual de Londrina, Londrina, PR, Brazil
| | - Vagner T. de Queiroz
- Departamento de Química e Física, Centro de Ciências Exatas, Naturais e da Saúde, Universidade Federal do Espírito Santo, Alegre, ES, Brazil
| | - Ângelo de Fátima
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Fernando Macedo Jr.
- Departamento de Química, Centro de Ciências Exatas, Universidade Estadual de Londrina, Londrina, PR, Brazil
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Kafarski P, Talma M. Recent advances in design of new urease inhibitors: A review. J Adv Res 2018; 13:101-112. [PMID: 30094085 PMCID: PMC6077125 DOI: 10.1016/j.jare.2018.01.007] [Citation(s) in RCA: 115] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 01/09/2018] [Accepted: 01/16/2018] [Indexed: 12/22/2022] Open
Abstract
Urease is a nickel-dependent metalloenzyme found in plants, some bacteria, and fungi. Bacterial enzyme is of special importance since it has been demonstrated as a potent virulence factor for some species. Especially it is central to Helicobacter pylori metabolism and virulence being necessary for its colonization of the gastric mucosa, and is a potent immunogen that elicits a vigorous immune response. Therefore, it is not surprising that efforts to design, synthesize and evaluate of new inhibitors of urease are and active field of medicinal chemistry. In this paper recent advances on this field are reviewed.
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Affiliation(s)
- Paweł Kafarski
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
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