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Wang N, Wu X, Liang J, Liu B, Wang B. Molecular design of hydroxamic acid-based derivatives as urease inhibitors of Helicobacter pylori. Mol Divers 2024:10.1007/s11030-024-10914-9. [PMID: 39020133 DOI: 10.1007/s11030-024-10914-9] [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: 04/27/2024] [Accepted: 06/08/2024] [Indexed: 07/19/2024]
Abstract
Helicobacter pylori is the main causative agent of gastric cancer, especially non-cardiac gastric cancers. This bacterium relies on urease producing much ammonia to colonize the host. Herein, the study provides valuable insights into structural patterns driving urease inhibition for high-activity molecules designed via exploring known inhibitors. Firstly, an ensemble model was devised to predict the inhibitory activity of novel compounds in an automated workflow (R2 = 0.761) that combines four machine learning approaches. The dataset was characterized in terms of chemical space, including molecular scaffolds, clustering analysis, distribution for physicochemical properties, and activity cliffs. Through these analyses, the hydroxamic acid group and the benzene ring responsible for distinct activity were highlighted. Activity cliff pairs uncovered substituents of the benzene ring on hydroxamic acid derivatives are key structures for substantial activity enhancement. Moreover, 11 hydroxamic acid derivatives were designed, named mol1-11. Results of molecular dynamic simulations showed that the mol9 exhibited stabilization of the active site flap's closed conformation and are expected to be promising drug candidates for Helicobacter pylori infection and further in vitro, in vivo, and clinical trials to demonstrate in future.
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Affiliation(s)
- Na Wang
- College of Materials and Energy, South China Agricultural University, Guangzhou, 510630, China
| | - Xiaoyan Wu
- College of Materials and Energy, South China Agricultural University, Guangzhou, 510630, China
| | - Jianhuai Liang
- College of Materials and Energy, South China Agricultural University, Guangzhou, 510630, China
| | - Boping Liu
- College of Materials and Energy, South China Agricultural University, Guangzhou, 510630, China.
| | - Bingfeng Wang
- College of Materials and Energy, South China Agricultural University, Guangzhou, 510630, China.
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2
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Haq MA, Nazir M, Jabeen G, Jabeen N, Naz S, Nawaz H, Xu J. Inhibitory effect of polyphenols from sumac, pomegranate and Indian almond on urease producing bacteria and jack bean urease activity. Int J Biol Macromol 2024; 276:133735. [PMID: 38986980 DOI: 10.1016/j.ijbiomac.2024.133735] [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: 12/15/2023] [Revised: 05/27/2024] [Accepted: 07/06/2024] [Indexed: 07/12/2024]
Abstract
Urinary tract infection caused by Klebsiella, Proteus and Streptococcus is a urease dependent process, hence treatment of these infections by antibacterial compounds lies in inhibition of their virulence factors. The crude methanolic extracts derived from sumac fruit, pomegranate peel and Indian almond leaves were separated into anthocyanin and non-anthocyanin fractions using solid phase cartridges. The inhibitory effect of these fractions was determined on the growth of urease producing species and jack bean urease activity. Known compounds in the fractions were also docked with ureases of different biological origins viz. K. pneumoniae (PDB ID: 8HCN), K. aerogenes (PDB ID: 2KAU), Helicobacter pylori (PDB ID:8HC1)and Canavalia ensiformis (jack bean) (PDB ID: 3LA4) to determine their binding affinities and interaction with the enzyme. All the fractions showed significant inhibition growth for P. mirabilis, S. epidermidis and K.pneumoniae. Among the samples, sumac showed greatest inhibition against all (MIC 6-25 mg.mL-1) while among the fractions, anthocyanin was found to be most active (MIC 6-12 mg/mL). Likewise, all fractions inhibited urease with lowest ICs50 shown by sumac fractions (21-116 μg.mL-1). Out of 39 compounds docked, 27 showed interaction with movable flaps and/or active site of ureases which explains their mode of inhibition.
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Affiliation(s)
- Muhammad Abdul Haq
- Department of Food Science & Technology, University of Karachi, 75270, Pakistan.
| | - Mudassir Nazir
- Department of Food Science & Technology, University of Karachi, 75270, Pakistan
| | - Gul Jabeen
- Department of Microbiology, University of Karachi, 75270, Pakistan
| | - Nusrat Jabeen
- Department of Microbiology, University of Karachi, 75270, Pakistan.
| | - Shahina Naz
- Department of Food Science & Technology, University of Karachi, 75270, Pakistan.
| | - Haq Nawaz
- Jiangsu Key Laboratory for Biomass-Based Energy and Enzyme Technology, School of Chemistry and Chemical Engineering, Huaiyin Normal University, Changjiangxi Road, Huaian 223300, Jiangsu, PR China.
| | - Jiaxing Xu
- Jiangsu Key Laboratory for Biomass-Based Energy and Enzyme Technology, School of Chemistry and Chemical Engineering, Huaiyin Normal University, Changjiangxi Road, Huaian 223300, Jiangsu, PR China.
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3
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Hashem O, Zaib S, Zaraei SO, Javed H, Kedia RA, Anbar HS, Khan I, Ravi A, El-Gamal MI, Khoder G. Design and discovery of urease and Helicobacter pylori inhibitors based on benzofuran/benzothiophene-sulfonate and sulfamate scaffolds for the treatment of ureolytic bacterial infections. Int J Biol Macromol 2024; 271:132502. [PMID: 38768915 DOI: 10.1016/j.ijbiomac.2024.132502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 05/14/2024] [Accepted: 05/17/2024] [Indexed: 05/22/2024]
Abstract
A series of sulfonate and sulfamate derivatives bearing benzofuran or benzothiophene scaffold exhibited potent inhibitory effect on urease enzyme. Most of the derivatives exhibited significantly higher potency than thiourea, the standard inhibitor. Compound 1s was identified as the most potent urease inhibitor with an IC50 value of 0.42 ± 0.08 μM, which is 53-fold more potent than thiourea, positive control (IC50 = 22.3 ± 0.031 μM). The docking results further revealed the binding interactions towards the urease active site. Phenotypic screening revealed that compounds 1c, 1d, 1e, 1f, 1j, 1n, and 1t exhibit high potency against H. pylori with MIC values ranging from 0.00625 to 0.05 mM and IC50 values ranging from 0.0031 to 0.0095 mM, much more potent than the positive control, acetohydroxamic acid (MIC and IC50 values were 12.5 and 7.38 mM, respectively). Additional studies were performed to investigate the toxicity of these compounds against the gastric epithelial cell line (AGS) and their selectivity profile against E. coli, and five Lactobacillus species representative of the gut microflora. Permeability characteristics of the most promising derivatives were investigated in Caco-2 cell line. The results indicate that the compounds could be targeted in the GIT only without systemic side effects.
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Affiliation(s)
- Omar Hashem
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Sumera Zaib
- Department of Basic and Applied Chemistry, Faculty of Science and Technology, University of Central Punjab, Lahore 54590, Pakistan.
| | - Seyed-Omar Zaraei
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Hira Javed
- Department of Basic and Applied Chemistry, Faculty of Science and Technology, University of Central Punjab, Lahore 54590, Pakistan
| | - Reena A Kedia
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Hanan S Anbar
- Department of Pharmaceutical Sciences, Dubai Pharmacy College for Girls, Dubai 19099, United Arab Emirates.
| | - Imtiaz Khan
- Department of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Anil Ravi
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Mohammed I El-Gamal
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates; Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates; Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt.
| | - Ghalia Khoder
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates; Department of Pharmaceutics and Pharmaceutical Technology, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates.
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4
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Jiang X, Long J, Song Y, Qi X, Li P, Pan K, Yan C, Xu H, Liu H. The effect of triclosan on intergeneric horizontal transmission of plasmid-mediated tigecycline resistance gene tet(X4) from Citrobacter freundii isolated from grass carp gut. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 346:123658. [PMID: 38432343 DOI: 10.1016/j.envpol.2024.123658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 01/26/2024] [Accepted: 02/24/2024] [Indexed: 03/05/2024]
Abstract
The transmission of antibiotic resistance genes (ARGs) in pathogenic bacteria affects culture animal health, endangers food safety, and thus gravely threatens public health. However, information about the effect of disinfectants - triclosan (TCS) on ARGs dissemination of bacterial pathogens in aquatic animals is still limited. One Citrobacter freundii (C. freundii) strain harboring tet(X4)-resistant plasmid was isolated from farmed grass carp guts, and subsequently conjugative transfer frequency from C. freundii to Escherichia coli C600 (E. coli C600) was analyzed under different mating time, temperature, and ratio. The effect of different concentrations of TCS (0.02, 0.2, 2, 20, 200 and 2000 μg/L) on the conjugative transfer was detected. The optimum conditions for conjugative transfer were at 37 °C for 8h with mating ratio of 2:1 or 1:1 (C. freundii: E. coli C600). The conjugative transfer frequency was significantly promoted under TCS treatment and reached the maximum value under 2.00 μg/L TCS with 18.39 times that of the control group. Reactive oxygen species (ROS), superoxide dismutase (SOD) and catalase (CAT) activities, cell membrane permeability of C. freundii and E. coli C600 were obviously increased under TCS stress. Scanning electron microscope showed that the cell membrane surface of the conjugative strains was wrinkled and pitted, even broken at 2.00 μg/L TCS, while lysed or even ruptured at 200.00 μg/L TCS. In addition, TCS up-regulated expression levels of oxidative stress genes (katE, hemF, bcp, hemA, katG, ahpF, and ahpC) and cell membrane-related genes (fimC, bamE and ompA) of donor and recipient bacteria. Gene Ontology (GO) enrichment demonstrated significant changes in categories relevant to pilus, porin activity, transmembrane transporter activity, transferase activity, hydrolase activity, material transport and metabolism. Taken together, a tet(X4)-resistant plasmid could horizontal transmission among different pathogens, while TCS can promote the propagation of the resistant plasmid.
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Affiliation(s)
- Xinxin Jiang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jingfei Long
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yanzhen Song
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xiaoyu Qi
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Ping Li
- Powerchina Northwest Engineering Corporation Limited, Xi'an, 710065, China
| | - Kuiquan Pan
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Chenyang Yan
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Hongzhou Xu
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Haixia Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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Al-Shuhaib MBS, Hashim HO, Al-Shuhaib JMB. D-Glucosamine is a Potential Urease Inhibitor from Middle Eastern Medicinal Plants for Combatting Helicobacter Pylori Infections; a Molecular Docking and Simulation Approach. Biochem Genet 2024:10.1007/s10528-024-10709-5. [PMID: 38430447 DOI: 10.1007/s10528-024-10709-5] [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: 09/03/2023] [Accepted: 01/19/2024] [Indexed: 03/03/2024]
Abstract
Helicobacter pylori stands as a significant risk factor for both peptic and stomach ulcers. Their resistance to the highly acidic host environment primarily stems from their capability to produce urease, an enzyme that rapidly converts urea into NH3 and CO2. These byproducts are crucial for the bacterium's survival under such harsh conditions. Given the pivotal role of medicinal plants in treating various ailments with minimal side effects, there is an urgent need for a natural drug that can effectively eliminate H. pylori by inhibiting urease. Hence, the current study aims to identify the most potent urease inhibitor among the natural compounds found in Middle Eastern medicinal plants, taking into consideration factors such as optimal affinity, drug-like properties, pharmacokinetic characteristics, and thermodynamic attributes. In total, 5599 ligand conformers from 151 medicinal plants were subjected to docking against the urease's active site. The top-ranking natural compounds, as determined by their high docking scores, were selected for further analysis. Among these compounds, D-glucosamine (PubChem code 439,213) exhibited the most interactions with the crucial amino acid residues in the urease's active site. Furthermore, D-glucosamine demonstrated superior absorption, distribution, metabolism, excretion, and toxicity properties compared to other top-ranked candidates. Molecular dynamics simulations conducted over 100 nanoseconds revealed stable root mean square deviations and fluctuations of the protein upon complexation with D-glucosamine. Additionally, the radius of gyration and solvent-accessible surface area values for the D-glucosamine-urease complex were notably lower than those observed in other typical urease-inhibitor complexes. In conclusion, this study provides valuable insights into the potential development of D-glucosamine as a novel urease inhibitor. This promising compound holds the potential to serve as an effective drug for combating H. pylori infections in the near future.
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Affiliation(s)
- Mohammed Baqur S Al-Shuhaib
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, 8, Al-Qasim, Babil, 51013, Iraq.
| | - Hayder O Hashim
- Department of Clinical Laboratory Sciences, College of Pharmacy, University of Babylon, Hillah, Babil, 51001, Iraq
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Huang M, Cui P, Zhou J, Liu C, Wang Y. Theoretical study on the inhibition mechanisms of heavy metal ions on urease activity. CHEMOSPHERE 2023; 345:140416. [PMID: 37827462 DOI: 10.1016/j.chemosphere.2023.140416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 10/08/2023] [Accepted: 10/09/2023] [Indexed: 10/14/2023]
Abstract
Soil urease is highly sensitive to soil heavy metal pollution, and thus its activity can be used as bio-indicator of soil health. However, little is known about the inhibition mechanisms of heavy metals on urease. The effects of dimetallic substitution (i.e., Cd, Co, Cu, Hg, and Zn) on the binding of urea in the urease and its subsequent decomposition were studied using quantum chemical methodologies with a urease mimic (phthalazine-dinickel complex). The dimetallic substitution altered the structural features of the dimetal complexes and the M-O bond length between the dimetals and the carbonyl-O of coordinated urea molecules, weakening the binding energies of urea in dimetal complexes, which further affected the transformation of urea. In the urea decomposition via intra-molecular proton transfer, all dimetal complexes have a high activation barrier due to the weak binding of urea in complexes and hydrogen bonding within urea molecules, which are therefore difficult to occur spontaneously. In the urea decomposition via water-assisted inter-molecular proton transfer, the addition of water molecules decreased the energy barrier of urea decomposition. Regardless of the urea decomposition pathway, the dimetallic substitution altered the M-O bond length and hydrogen bond pattern of intermediates and transition states, and also affected the leave of the resulting NH3 from the dimetal complexes by regulating the C-N bond length within the decomposed urea molecule. Overall, the theoretical study provided insight into the molecular mechanisms of the inhibitory effects of heavy metals on urease activity.
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Affiliation(s)
- Meiying Huang
- State Key Laboratory of Soil & Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Peixin Cui
- State Key Laboratory of Soil & Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Jing Zhou
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Cun Liu
- State Key Laboratory of Soil & Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.
| | - Yujun Wang
- State Key Laboratory of Soil & Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China
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7
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Sepehri S, Khedmati M. An overview of the privileged synthetic heterocycles as urease enzyme inhibitors: Structure-activity relationship. Arch Pharm (Weinheim) 2023; 356:e2300252. [PMID: 37401193 DOI: 10.1002/ardp.202300252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/10/2023] [Accepted: 06/12/2023] [Indexed: 07/05/2023]
Abstract
Urease is a metalloenzyme including two Ni2+ ions, found in some plants, bacteria, fungi, microorganisms, invertebrate animals, and animal tissues. Urease acts as a significant virulence factor, mainly in catheter blockage and infective urolithiasis as well as in the pathogenesis of gastric infection. Therefore, studies on urease lead to novel synthetic inhibitors. In this review, the synthesis and antiurease activities of a collection of privileged synthetic heterocycles such as (thio)barbiturate, (thio)urea, dihydropyrimidine, and triazol derivatives were described and discussed according to structure-activity relationship findings in search of the best moieties and substituents that are answerable for encouraging the desired activity even more potent than the standard. It was found that linking substituted phenyl and benzyl rings to the heterocycles led to potent urease inhibitors.
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Affiliation(s)
- Saghi Sepehri
- Pharmaceutical Sciences Research Center, Ardabil University of Medical Sciences, Ardabil, Iran
- Department of Medicinal Chemistry, School of Pharmacy, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Mina Khedmati
- Students Research Committee, School of Pharmacy, Ardabil University of Medical Sciences, Ardabil, Iran
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Oriakhi K, Ibeji CU, Essien EE, Eluehike N, Orumwensodia K, Uadia P, Choudhary IM. In vitro and computational studies on the antiglycation activity of compounds isolated from antidiabetic Tetracera alnifolia stem bark. J Biomol Struct Dyn 2022; 40:9742-9751. [PMID: 34096463 DOI: 10.1080/07391102.2021.1934542] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The continuous search for new compounds in natural-based plants is a promising strategy for the prevention of diseases. This work examined antiglycation activity compounds isolated from the antidiabetic extract of T. alnifolia stem bark via in vitro and computational [molecular dynamics (MD)] approach. Phytochemical investigation of ethyl acetate fraction and the application of spectroscopic methods led to the isolation and elucidation of 3 compounds: quercetin (1), kaempferol (2), and gallic acid (3). Compounds 1, 2 and 3 were then screened for antioxidant and antiglycation activities. Results show that the ethanol extract of T. alnifolia demonstrated good antioxidant activity compared to the standard gallic acid. There was a significant reduction in fasting blood glucose level progressively in diabetic rats, for 21 days compared to diabetic control. Consequently, the antiglycation activity of ethyl acetate fraction had the highest antiglycation activities, followed by dichloromethane (DCM) fraction. Compounds isolated from ethyl acetate fraction, exhibited the highest antiglycation effect for kaempferol followed by quercetin, while gallic acid had the least antiglycation effect. The root mean square of deviation (RMSD) and MM/GBSA energies obtained from molecular dynamics agree with the in vitro antiglycation activity with the sequence of structural stability in the order; kaempferol > quercetin > gallic acid. Therefore, findings from these results suggest that compounds isolated from T. alnifolia possess antiglycation activity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kelly Oriakhi
- Department of Medical Biochemistry, University of Benin, Benin, Nigeria
| | - Collins U Ibeji
- Department of Pure and Industrial Chemistry, Faculty of Physical Sciences, University of Nigeria, Nsukka, Enugu State, Nigeria.,Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | | | - Nkeiruka Eluehike
- Department of Medical Biochemistry, University of Benin, Benin, Nigeria
| | | | - Patrick Uadia
- Department of Biochemistry, University of Benin, Benin, Nigeria
| | - Iqbal M Choudhary
- International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
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Alarifi SA, Mustafa A, Omarov K, Baig AR, Tariq Z, Mahmoud M. A Review of Enzyme-Induced Calcium Carbonate Precipitation Applicability in the Oil and Gas Industry. Front Bioeng Biotechnol 2022; 10:900881. [PMID: 35795168 PMCID: PMC9251129 DOI: 10.3389/fbioe.2022.900881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 05/09/2022] [Indexed: 11/13/2022] Open
Abstract
Enzyme-induced calcium carbonate precipitation (EICP) techniques are used in several disciplines and for a wide range of applications. In the oil and gas industry, EICP is a relatively new technique and is actively used for enhanced oil recovery applications, removal of undesired chemicals and generating desired chemicals in situ, and plugging of fractures, lost circulation, and sand consolidation. Many oil- and gas-bearing formations encounter the problem of the flow of sand grains into the wellbore along with the reservoir fluids. This study offers a detailed review of sand consolidation using EICP to solve and prevent sand production issues in oil and gas wells. Interest in bio-cementation techniques has gained a sharp increase recently due to their sustainable and environmentally friendly nature. An overview of the factors affecting the EICP technique is discussed with an emphasis on the in situ reactions, leading to sand consolidation. Furthermore, this study provides a guideline to assess sand consolidation performance and the applicability of EICP to mitigate sand production issues in oil and gas wells.
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Affiliation(s)
- Sulaiman A. Alarifi
- Department of Petroleum Engineering, College of Petroleum Engineering and Geosciences, King Fahd University of Petroleum and Minerals (KFUPM), Dhahran, Saudi Arabia
- *Correspondence: Sulaiman A. Alarifi,
| | - Ayyaz Mustafa
- Center for Integrative Petroleum Research (CIPR), College of Petroleum Engineering and Geosciences, King Fahd University of Petroleum and Minerals, Dhahran, Saudi Arabia
| | - Kamal Omarov
- Department of Petroleum Engineering, College of Petroleum Engineering and Geosciences, King Fahd University of Petroleum and Minerals (KFUPM), Dhahran, Saudi Arabia
| | - Abdul Rehman Baig
- Department of Petroleum Engineering, College of Petroleum Engineering and Geosciences, King Fahd University of Petroleum and Minerals (KFUPM), Dhahran, Saudi Arabia
| | - Zeeshan Tariq
- Physical Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Mohamed Mahmoud
- Department of Petroleum Engineering, College of Petroleum Engineering and Geosciences, King Fahd University of Petroleum and Minerals (KFUPM), Dhahran, Saudi Arabia
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10
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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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11
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Marimuthu P, Gorle S, Karnati KR. Mechanistic Insights into SARS-CoV-2 Main Protease Inhibition Reveals Hotspot Residues. J Chem Inf Model 2021; 61:6053-6065. [PMID: 34842417 DOI: 10.1021/acs.jcim.1c00928] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The main protease (Mpro) is a key enzyme responsible for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication that causes the spread of the global pandemic novel coronavirus (nCOVID-19) infection. In the present study, multiple computational approaches such as docking, long-range molecular dynamics (MD) simulations, and binding free-energy (BFE) estimation techniques were employed to investigate the mechanistic basis of the high-affinity inhibitors─GC-376, Calpain XII, and Calpain II (hereafter Calpain as Cal) from the literature─binding to Mpro. Redocking GC-376 and docking Cal XII and Cal II inhibitors to Mpro were able to reproduce all crucial interactions like the X-ray conformation. Subsequently, the apo (ligand-free) and three holo (ligand-bound) complexes were subjected to extensive MD simulations, which revealed that the ligand binding did not alter the overall Mpro structural features, whereas the heatmap analysis showed that the residues located in subsites S1 and S2, the catalytic dyad, and the 45TSEDMLN51 loop in Mpro exhibit a conformational deviation. Moreover, the BFE estimation method was used to elucidate the crucial thermodynamic properties, which revealed that Coulomb, solvation surface accessibility (Solv_SA), and lipophilic components contributed significant energies for complex formation. The decomposition of the total BFE to per-residue showed that H41, H163, M165, Q166, and Q189 residues contributed maximum energies. The overall results from the current investigation might be valuable for designing novel anti-Mpro inhibitors.
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Affiliation(s)
- Parthiban Marimuthu
- Pharmaceutical Science Laboratory (PSL─Pharmacy) and Structural Bioinformatics Laboratory (SBL─Biochemistry), Faculty of Science and Engineering, Åbo Akademi University, FI-20520 Turku, Finland
| | - Suresh Gorle
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Konda Reddy Karnati
- Department of Natural Sciences, Bowie State University, 14000 Jericho Park Road, Bowie, Maryland 20715-9465, United States
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12
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Kalatuwawege IP, Gunaratna MJ, Udukala DN. Synthesis, In Silico Studies, and Evaluation of Syn and Anti Isomers of N-Substituted Indole-3-carbaldehyde Oxime Derivatives as Urease Inhibitors against Helicobacter pylori. Molecules 2021; 26:molecules26216658. [PMID: 34771067 PMCID: PMC8588131 DOI: 10.3390/molecules26216658] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/20/2021] [Accepted: 10/28/2021] [Indexed: 12/24/2022] Open
Abstract
Gastrointestinal tract infection caused by Helicobacter pylori is a common virulent disease found worldwide, and the infection rate is much higher in developing countries than in developed ones. In the pathogenesis of H. pylori in the gastrointestinal tract, the secretion of the urease enzyme plays a major role. Therefore, inhibition of urease is a better approach against H. pylori infection. In the present study, a series of syn and anti isomers of N-substituted indole-3-carbaldehyde oxime derivatives was synthesized via Schiff base reaction of appropriate carbaldehyde derivatives with hydroxylamine hydrochloride. The in vitro urease inhibitory activities of those derivatives were evaluated against that of Macrotyloma uniflorum urease using the modified Berthelot reaction. Out of the tested compounds, compound 8 (IC50 = 0.0516 ± 0.0035 mM) and compound 9 (IC50 = 0.0345 ± 0.0008 mM) were identified as the derivatives with potent urease inhibitory activity with compared to thiourea (IC50 = 0.2387 ± 0.0048 mM). Additionally, in silico studies for all oxime compounds were performed to investigate the binding interactions with the active site of the urease enzyme compared to thiourea. Furthermore, the drug-likeness of the synthesized oxime compounds was also predicted.
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Affiliation(s)
- Ishani P. Kalatuwawege
- College of Chemical Sciences, Institute of Chemistry Ceylon, Rajagiriya 10100, Sri Lanka; (I.P.K.); (D.N.U.)
| | - Medha J. Gunaratna
- Department of Chemistry, University of Kelaniya, Kelaniya 10300, Sri Lanka
- Correspondence:
| | - Dinusha N. Udukala
- College of Chemical Sciences, Institute of Chemistry Ceylon, Rajagiriya 10100, Sri Lanka; (I.P.K.); (D.N.U.)
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13
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Li Z, Song LF, Li P, Merz KM. Parametrization of Trivalent and Tetravalent Metal Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models. J Chem Theory Comput 2021; 17:2342-2354. [PMID: 33793233 DOI: 10.1021/acs.jctc.0c01320] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Commonly seen in rare-earth chemistry and materials science, highly charged metal ions play key roles in many chemical processes. Computer simulations have become an important tool for scientific research nowadays. Meaningful simulations require reliable parameters. In the present work, we parametrized 18 M(III) and 6 M(IV) metal ions for four new water models (OPC3, OPC, TIP3P-FB, TIP4P-FB) in conjunction with each of the 12-6 and 12-6-4 nonbonded models. Similar to what was observed previously, issues with the 12-6 model can be fixed by using the 12-6-4 model. Moreover, the four new water models showed comparable performance or considerable improvement over the previous water models (TIP3P, SPC/E, and TIP4PEW) in the same category (3-point or 4-point water models, respectively). Finally, we reported a study of a metalloprotein system demonstrating the capability of the 12-6-4 model to model metalloproteins. The reported parameters will facilitate accurate simulations of highly charged metal ions in aqueous solution.
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Affiliation(s)
- Zhen Li
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Lin Frank Song
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Pengfei Li
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States.,Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Kenneth M Merz
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States.,Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
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14
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Cunha ES, Chen X, Sanz-Gaitero M, Mills DJ, Luecke H. Cryo-EM structure of Helicobacter pylori urease with an inhibitor in the active site at 2.0 Å resolution. Nat Commun 2021; 12:230. [PMID: 33431861 PMCID: PMC7801526 DOI: 10.1038/s41467-020-20485-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 12/04/2020] [Indexed: 02/08/2023] Open
Abstract
Infection of the human stomach by Helicobacter pylori remains a worldwide problem and greatly contributes to peptic ulcer disease and gastric cancer. Without active intervention approximately 50% of the world population will continue to be infected with this gastric pathogen. Current eradication, called triple therapy, entails a proton-pump inhibitor and two broadband antibiotics, however resistance to either clarithromycin or metronidazole is greater than 25% and rising. Therefore, there is an urgent need for a targeted, high-specificity eradication drug. Gastric infection by H. pylori depends on the expression of a nickel-dependent urease in the cytoplasm of the bacteria. Here, we report the 2.0 Å resolution structure of the 1.1 MDa urease in complex with an inhibitor by cryo-electron microscopy and compare it to a β-mercaptoethanol-inhibited structure at 2.5 Å resolution. The structural information is of sufficient detail to aid in the development of inhibitors with high specificity and affinity.
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Affiliation(s)
- Eva S. Cunha
- grid.5510.10000 0004 1936 8921Structural Biology and Drug Discovery Group, Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, 0318 Oslo, Norway
| | - Xiaorui Chen
- grid.266093.80000 0001 0668 7243Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697 USA ,grid.506938.10000 0004 0633 8088Present Address: Genomics Research Center, Academia Sinica, 128 Academia Road, Sect. 2, Nankang District, Taipei, Taiwan
| | - Marta Sanz-Gaitero
- grid.5510.10000 0004 1936 8921Structural Biology and Drug Discovery Group, Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, 0318 Oslo, Norway
| | - Deryck J. Mills
- grid.419494.50000 0001 1018 9466Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Hartmut Luecke
- Structural Biology and Drug Discovery Group, Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, 0318, Oslo, Norway. .,Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, 92697, USA. .,Department of Medical Biochemistry, University of Oslo and Oslo University Hospital, 0372, Oslo, Norway. .,Department of Physiology and Biophysics, University of California, Irvine, CA, 92697, USA.
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15
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Effect of pH on the Supramolecular Structure of Helicobacter pylori Urease by Molecular Dynamics Simulations. Polymers (Basel) 2020; 12:polym12112713. [PMID: 33212749 PMCID: PMC7696613 DOI: 10.3390/polym12112713] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 11/09/2020] [Accepted: 11/11/2020] [Indexed: 12/24/2022] Open
Abstract
The effect of pH on the supramolecular structure of Helicobacter pylori urease was studied by means of molecular dynamics simulations at seven different pHs. Appropriate urease charge distributions were calculated using a semi-grand canonical Monte Carlo (SGCMC) procedure that assigns each residue’s charge state depending on the assigned individual pKa obtained by PROPKA. The effect of pH on protein stability has been analyzed through root-mean-square deviation (RMSD), radius of gyration (RG), solvent-accessible surface area (SASA), hydrogen bonds (HB) and salt bridges (SB). Urease catalyses the hydrolysis of urea in 12 active sites that are covered by mobile regions that act like flaps. The mobility of these flaps is increased at acidic pHs. However, extreme acidic conditions cause urease to have the least number of stabilizing interactions. This initiates the process of denaturalization, wherein the four (αβ)3 subunits of the global structure ((αβ)3)4 of urease start to separate.
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16
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Development of sulfonamide-based Schiff bases targeting urease inhibition: Synthesis, characterization, inhibitory activity assessment, molecular docking and ADME studies. Bioorg Chem 2020; 102:104057. [DOI: 10.1016/j.bioorg.2020.104057] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/04/2020] [Accepted: 06/26/2020] [Indexed: 01/24/2023]
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17
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Fiori-Duarte AT, Rodrigues RP, Kitagawa RR, Kawano DF. Insights into the Design of Inhibitors of the Urease Enzyme - A Major Target for the Treatment of Helicobacter pylori Infections. Curr Med Chem 2020; 27:3967-3982. [PMID: 30827224 DOI: 10.2174/0929867326666190301143549] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 02/01/2019] [Accepted: 02/19/2019] [Indexed: 12/12/2022]
Abstract
Expressed by a variety of plants, fungi and bacteria, the urease enzyme is directly associated with the virulence factor of many bacteria, including Helicobacter pylori, a gram-negative bacterium related to several gastrointestinal diseases and responsible for one of the most frequent bacterial infections throughout the world. The Helicobacter pylori Urease (HPU) is a nickel-dependent metalloenzyme expressed in response to the environmental stress caused by the acidic pH of the stomach. The enzyme promotes the increase of gastric pH through acid neutralization by the products of urea hydrolysis, then critically contributing to the colonization and pathogenesis of the microorganism. At the same time, standard treatments for Helicobacter pylori infections have limitations such as the increasing bacterial resistance to the antibiotics used in the clinical practice. As a strategy for the development of novel treatments, urease inhibitors have proved to be promising, with a wide range of chemical compounds, including natural, synthetic and semisynthetic products to be researched and potentially developed as new drugs. In this context, this review highlights the advances in the field of HPU inhibition, presenting and discussing the basis for the research of new molecules aiming at the identification of more efficient therapeutic entities.
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Affiliation(s)
- Ana Thereza Fiori-Duarte
- Faculty of Pharmaceutical Sciences, University of Campinas - UNICAMP, Rua Candido Portinari 200, 13083-871 Campinas, SP, Brazil
| | - Ricardo Pereira Rodrigues
- Department of Pharmaceutical Sciences, Health Sciences Center - CCS, Federal University of Espírito Santo - UFES, Av. Marechal Campos 1468, 29047-105 Vitoria, ES, Brazil
| | - Rodrigo Rezende Kitagawa
- Department of Pharmaceutical Sciences, Health Sciences Center - CCS, Federal University of Espírito Santo - UFES, Av. Marechal Campos 1468, 29047-105 Vitoria, ES, Brazil
| | - Daniel Fábio Kawano
- Faculty of Pharmaceutical Sciences, University of Campinas - UNICAMP, Rua Candido Portinari 200, 13083-871 Campinas, SP, Brazil.,Institute of Chemistry, University of Campinas - UNICAMP, Rua Josué de Castro s/n, 13083-970 Campinas, SP, Brazil
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18
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Imran M, Waqar S, Ogata K, Ahmed M, Noreen Z, Javed S, Bibi N, Bokhari H, Amjad A, Muddassar M. Identification of novel bacterial urease inhibitors through molecular shape and structure based virtual screening approaches. RSC Adv 2020; 10:16061-16070. [PMID: 35493653 PMCID: PMC9052855 DOI: 10.1039/d0ra02363a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 04/15/2020] [Indexed: 12/24/2022] Open
Abstract
The enzyme urease is an essential colonizing factor of the notorious carcinogenic pathogen Helicobacter pylori (H. pylori), conferring acid resistance to the bacterium. Recently, antibiotic resistant strains have emerged globally with little to no alternative treatment available. In this study we propose novel urease inhibitors capable of controlling infection by H. pylori and other pathogenic bacteria. We employed hierarchal computational approaches to screen new urease inhibitors from commercial chemical databases followed by in vitro anti-urease assays. Initially ROCS shape-based screening was performed using o-chloro-hippurohydroxamic acid followed by molecular docking studies. Out of 1.83 million compounds, 1700 compounds were retrieved based on having a ROCS Tanimoto combo score in the range of values from 1.216 to 1.679. These compounds were further screened using molecular docking simulations and the 100 top ranked compounds were selected based on their Glide score. After structural classification of the top ranked compounds, eight compounds were selected and purchased for biological assays. The plausible binding modes of the most active compounds were also confirmed using molecular dynamics (MD) simulations. Compounds 1, 2 and 3 demonstrated good urease inhibitory properties (IC50 = 0.32, 0.68 and 0.42 μM) compared to the other compounds. Enzyme kinetic studies revealed that compounds 1 and 3 are competitive inhibitors while 2 is a mixed type inhibitor of the urease enzyme. Cell based urease inhibition and MTT assay showed that these compounds blocked H. pylori urease activity, affecting bacterial growth and acid tolerance. The enzyme urease is an essential colonizing factor of the notorious carcinogenic pathogen Helicobacter pylori (H. pylori), conferring acid resistance to the bacterium.![]()
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Affiliation(s)
- Muhammad Imran
- School of Life Sciences, FC College University Lahore Pakistan
| | - Saba Waqar
- Department of Biosciences, COMSATS University Islamabad Park Road Islamabad Pakistan
| | - Koji Ogata
- Faculty of Pharmaceutical Sciences, Sanyo-Onoda City University 1-1-1 Daigaku-Dori, Sanyo-Onoda Yamaguchi 859-0884 Japan
| | | | - Zobia Noreen
- Department of Biosciences, COMSATS University Islamabad Park Road Islamabad Pakistan
| | - Sundus Javed
- Department of Biosciences, COMSATS University Islamabad Park Road Islamabad Pakistan
| | - Nazia Bibi
- Department of Biosciences, COMSATS University Islamabad Park Road Islamabad Pakistan
| | - Habib Bokhari
- Department of Biosciences, COMSATS University Islamabad Park Road Islamabad Pakistan
| | - Asma Amjad
- Department of Biosciences, COMSATS University Islamabad Park Road Islamabad Pakistan
| | - Muhammad Muddassar
- Department of Biosciences, COMSATS University Islamabad Park Road Islamabad Pakistan
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19
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Ibeji CU. Molecular dynamics and DFT study on the structure and dynamics of N-terminal domain HIV-1 capsid inhibitors. MOLECULAR SIMULATION 2019. [DOI: 10.1080/08927022.2019.1674850] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Collins U. Ibeji
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
- Department of Pure and Industrial Chemistry, University of Nigeria, Nsukka, Nigeria
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20
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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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21
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Costa CHS, Oliveira ARS, Dos Santos AM, da Costa KS, Lima AHLE, Alves CN, Lameira J. Computational study of conformational changes in human 3-hydroxy-3-methylglutaryl coenzyme reductase induced by substrate binding. J Biomol Struct Dyn 2019; 37:4374-4383. [PMID: 30470158 DOI: 10.1080/07391102.2018.1549508] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The enzyme 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR) is mainly involved in the regulation of cholesterol biosynthesis. HMGR catalyses the reduction of 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) to mevalonate at the expense of two NADPH molecules in a two-step reversible reaction. In the present study, we constructed a model of human HMGR (hHMGR) to explore the conformational changes of HMGR in complex with HMG-CoA and NADPH. In addition, we analysed the complete sequence of the Flap domain using molecular dynamics (MD) simulations and principal component analysis (PCA). The simulations revealed that the Flap domain plays an important role in catalytic site activation and substrate binding. The apo form of hHMGR remained in an open state, while a substrate-induced closure of the Flap domain was observed for holo hHMGR. Our study also demonstrated that the phosphorylation of Ser872 induces significant conformational changes in the Flap domain that lead to a complete closure of the active site, suggesting three principal conformations for the first stage of hHMGR catalysis. Our results were consistent with previous proposed models for the catalytic mechanism of hHMGR. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | - Alberto M Dos Santos
- Institute of Biological Sciences, Federal University of Pará , Belém , Pará , Brazil
| | - Kauê Santana da Costa
- Institute of Biodiversity, Federal University of West of Pará , Santarém , Pará , Brazil
| | | | - Cláudio N Alves
- Institute of Natural Sciences, Federal University of Pará , Belém , Pará , Brazil
| | - Jerônimo Lameira
- Institute of Biological Sciences, Federal University of Pará , Belém , Pará , Brazil
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22
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Sala D, Musiani F, Rosato A. Application of Molecular Dynamics to the Investigation of Metalloproteins Involved in Metal Homeostasis. Eur J Inorg Chem 2018. [DOI: 10.1002/ejic.201800602] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Davide Sala
- Magnetic Resonance Center (CERM); University of Florence; Via Luigi Sacconi 6 50019 Sesto Fiorentino Italy
| | - Francesco Musiani
- Laboratory of Bioinorganic Chemistry; Department of Pharmacy and Biotechnology; University of Bologna; Viale Giuseppe Fanin 40, I 40127 Bologna Italy
| | - Antonio Rosato
- Magnetic Resonance Center (CERM); University of Florence; Via Luigi Sacconi 6 50019 Sesto Fiorentino Italy
- Consorzio Interuniversitario di Risonanze Magnetiche di Metallo Proteine; Via Luigi Sacconi 6 50019 Sesto Fiorentino Italy
- Department of Chemistry; University of Florence; Via della Lastruccia 3 50019 Sesto Fiorentino Italy
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23
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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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24
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Abstract
Metal ions play significant roles in numerous fields including chemistry, geochemistry, biochemistry, and materials science. With computational tools increasingly becoming important in chemical research, methods have emerged to effectively face the challenge of modeling metal ions in the gas, aqueous, and solid phases. Herein, we review both quantum and classical modeling strategies for metal ion-containing systems that have been developed over the past few decades. This Review focuses on classical metal ion modeling based on unpolarized models (including the nonbonded, bonded, cationic dummy atom, and combined models), polarizable models (e.g., the fluctuating charge, Drude oscillator, and the induced dipole models), the angular overlap model, and valence bond-based models. Quantum mechanical studies of metal ion-containing systems at the semiempirical, ab initio, and density functional levels of theory are reviewed as well with a particular focus on how these methods inform classical modeling efforts. Finally, conclusions and future prospects and directions are offered that will further enhance the classical modeling of metal ion-containing systems.
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Affiliation(s)
| | - Kenneth M. Merz
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute of Cyber-Enabled Research, Michigan State University, East Lansing, Michigan 48824, United States
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25
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Inhibition of Urease by Disulfiram, an FDA-Approved Thiol Reagent Used in Humans. Molecules 2016; 21:molecules21121628. [PMID: 27898047 PMCID: PMC6274061 DOI: 10.3390/molecules21121628] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Revised: 11/18/2016] [Accepted: 11/21/2016] [Indexed: 12/22/2022] Open
Abstract
Urease is a nickel-dependent amidohydrolase that catalyses the decomposition of urea into carbamate and ammonia, a reaction that constitutes an important source of nitrogen for bacteria, fungi and plants. It is recognized as a potential antimicrobial target with an impact on medicine, agriculture, and the environment. The list of possible urease inhibitors is continuously increasing, with a special interest in those that interact with and block the flexible active site flap. We show that disulfiram inhibits urease in Citrullus vulgaris (CVU), following a non-competitive mechanism, and may be one of this kind of inhibitors. Disulfiram is a well-known thiol reagent that has been approved by the FDA for treatment of chronic alcoholism. We also found that other thiol reactive compounds (l-captopril and Bithionol) and quercetin inhibits CVU. These inhibitors protect the enzyme against its full inactivation by the thiol-specific reagent Aldrithiol (2,2'-dipyridyl disulphide, DPS), suggesting that the three drugs bind to the same subsite. Enzyme kinetics, competing inhibition experiments, auto-fluorescence binding experiments, and docking suggest that the disulfiram reactive site is Cys592, which has been proposed as a "hinge" located in the flexible active site flap. This study presents the basis for the use of disulfiram as one potential inhibitor to control urease activity.
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26
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Minkara MS, Weaver MN, Gorske J, Bowers CR, Merz KM. Implementation of Protocols To Enable Doctoral Training in Physical and Computational Chemistry of a Blind Graduate Student. JOURNAL OF CHEMICAL EDUCATION 2015; 92:1280-1283. [PMID: 26300560 PMCID: PMC4535363 DOI: 10.1021/ed5009552] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
There exists a sparse representation of blind and low-vision students in science, technology, engineering and mathematics (STEM) fields. This is due in part to these individuals being discouraged from pursuing STEM degrees as well as a lack of appropriate adaptive resources in upper level STEM courses and research. Mona Minkara is a rising fifth year graduate student in computational chemistry at the University of Florida. She is also blind. This account presents efforts conducted by an expansive team of university and student personnel in conjunction with Mona to adapt different portions of the graduate student curriculum to meet Mona's needs. The most important consideration is prior preparation of materials to assist with coursework and cumulative exams. Herein we present an account of the first four years of Mona's graduate experience hoping this will assist in the development of protocols for future blind and low-vision graduate students in computational chemistry.
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Affiliation(s)
- Mona S. Minkara
- Department
of Chemistry Quantum Theory Project, University
of Florida, 2328 New
Physics Building, Gainesville, Florida 32611-8435, United States
| | - Michael N. Weaver
- Department
of Chemistry Quantum Theory Project, University
of Florida, 2328 New
Physics Building, Gainesville, Florida 32611-8435, United States
| | - Jim Gorske
- Disability Resource Center, University of Florida Reid Hall P.O. Box 114085, Gainesville, Florida 32611, United States
| | - Clifford R. Bowers
- Department
of Chemistry Quantum Theory Project, University
of Florida, 2328 New
Physics Building, Gainesville, Florida 32611-8435, United States
| | - Kenneth M. Merz
- Department of Chemistry Department of Biochemistry
and Molecular Biology, Michigan State University 578 South Shaw Lane, East Lansing, Michigan 48824-1322, United States
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27
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Cáceres-Delpiano J, Teneb J, Mansilla R, García A, Salas-Burgos A. Variations in periplasmic loop interactions determine the pH-dependent activity of the hexameric urea transporter UreI from Helicobacter pylori: a molecular dynamics study. BMC STRUCTURAL BIOLOGY 2015; 15:11. [PMID: 26112768 PMCID: PMC4482100 DOI: 10.1186/s12900-015-0038-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 06/15/2015] [Indexed: 11/17/2022]
Abstract
Background Helicobacter pylori is an important factor in the development of diseases such as ulcer and gastric cancer. This bacterium uses a periplasmic transporter, UreI, to deliver urea to the intracelullar space, where later it is transformed into ammonia by the cytoplasmic enzyme urease to survive the acidic condition of the human stomach. The UreI transporter presents a pH-dependent activity, where this pH-dependence remains unknown at a structural level. Althought the existance of several protonable residues in the periplasmic loops are related to the pH-dependent activity, we find interesting to have a clear view of the conformational changes involved in this phenomena through a molecular dynamic study. Results Molecular dynamic simulations of the UreI transporter at three different pH conditions were performed, revealing two main pH-dependent conformations, which we present as the open and close states. We find that salt bridges between the periplasmic loops are crucial interactions that stabilize these conformations. Besides, a cooperative behaviour exists between the six subunits of the system that is necessary to fulfill the activity of this transporter. Conclusions We found different pH-dependent conformations of the urea transporter UreI from Helicobacter pylori, which are related to salt-bridge interactions in the periplasmic regions. The behaviour of every channel in the system is not independent, given the existance of a cooperative behaviour through the formation of salt-bridges between the subunits of the hexameric system. We believe that our results will be related to the generation of new eradication therapies using this transporter as an attractive target, denoting that the knowledge of the possible pH-dependent conformations adopted for this transporter are important for the development of rational drug design approximations. Electronic supplementary material The online version of this article (doi:10.1186/s12900-015-0038-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Javier Cáceres-Delpiano
- Department of Pharmacology, School of Sciences, University of Concepción, Concepción, Chile.
| | - Jaime Teneb
- Department of Pharmacology, School of Sciences, University of Concepción, Concepción, Chile.
| | - Rodrigo Mansilla
- Department of Pharmacology, School of Sciences, University of Concepción, Concepción, Chile.
| | - Apolinaria García
- Department of Microbiology, School of Sciences, University of Concepción, Concepción, Chile.
| | - Alexis Salas-Burgos
- Department of Pharmacology, School of Sciences, University of Concepción, Concepción, Chile.
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Minkara MS, Weaver MN, Merz KM. Effect of 10.5 M Aqueous Urea on Helicobacter pylori Urease: A Molecular Dynamics Study. Biochemistry 2015; 54:4121-30. [DOI: 10.1021/acs.biochem.5b00078] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mona S. Minkara
- Department
of Chemistry, Quantum Theory Project, University of Florida, 2328 New Physics Building, Gainesville, Florida 32611-8435, United States
- Department
of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, 578 South Shaw Lane, East
Lansing, Michigan 48824-1322, United States
| | - Michael N. Weaver
- Department
of Chemistry, Quantum Theory Project, University of Florida, 2328 New Physics Building, Gainesville, Florida 32611-8435, United States
- Department
of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, 578 South Shaw Lane, East
Lansing, Michigan 48824-1322, United States
| | - Kenneth M. Merz
- Department
of Chemistry, Quantum Theory Project, University of Florida, 2328 New Physics Building, Gainesville, Florida 32611-8435, United States
- Department
of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, 578 South Shaw Lane, East
Lansing, Michigan 48824-1322, United States
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29
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Li P, Song LF, Merz KM. Parameterization of highly charged metal ions using the 12-6-4 LJ-type nonbonded model in explicit water. J Phys Chem B 2014; 119:883-95. [PMID: 25145273 PMCID: PMC4306492 DOI: 10.1021/jp505875v] [Citation(s) in RCA: 210] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
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Highly charged metal ions act as
catalytic centers and structural
elements in a broad range of chemical complexes. The nonbonded model
for metal ions is extensively used in molecular simulations due to
its simple form, computational speed, and transferability. We have
proposed and parametrized a 12-6-4 LJ (Lennard-Jones)-type nonbonded
model for divalent metal ions in previous work, which showed a marked
improvement over the 12-6 LJ nonbonded model. In the present study,
by treating the experimental hydration free energies and ion–oxygen
distances of the first solvation shell as targets for our parametrization,
we evaluated 12-6 LJ parameters for 18 M(III) and 6 M(IV) metal ions
for three widely used water models (TIP3P, SPC/E, and TIP4PEW). As expected, the interaction energy underestimation of the 12-6
LJ nonbonded model increases dramatically for the highly charged metal
ions. We then parametrized the 12-6-4 LJ-type nonbonded model for
these metal ions with the three water models. The final parameters
reproduced the target values with good accuracy, which is consistent
with our previous experience using this potential. Finally, tests
were performed on a protein system, and the obtained results validate
the transferability of these nonbonded model parameters.
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Affiliation(s)
- Pengfei Li
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Michigan State University , 578 S. Shaw Lane, East Lansing, Michigan 48824-1322, United States
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