1
|
Gao X, Zhang S, Wang P, Jaroniec M, Zheng Y, Qiao SZ. Urea catalytic oxidation for energy and environmental applications. Chem Soc Rev 2024; 53:1552-1591. [PMID: 38168798 DOI: 10.1039/d3cs00963g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Urea is one of the most essential reactive nitrogen species in the nitrogen cycle and plays an indispensable role in the water-energy-food nexus. However, untreated urea or urine wastewater causes severe environmental pollution and threatens human health. Electrocatalytic and photo(electro)catalytic urea oxidation technologies under mild conditions have become promising methods for energy recovery and environmental remediation. An in-depth understanding of the reaction mechanisms of the urea oxidation reaction (UOR) is important to design efficient electrocatalysts/photo(electro)catalysts for these technologies. This review provides a critical appraisal of the recent advances in the UOR by means of both electrocatalysis and photo(electro)catalysis, aiming to comprehensively assess this emerging field from fundamentals and materials, to practical applications. The emphasis of this review is on the design and development strategies for electrocatalysts/photo(electro)catalysts based on reaction pathways. Meanwhile, the UOR in natural urine is discussed, focusing on the influence of impurity ions. A particular emphasis is placed on the application of the UOR in energy and environmental fields, such as hydrogen production by urea electrolysis, urea fuel cells, and urea/urine wastewater remediation. Finally, future directions, prospects, and remaining challenges are discussed for this emerging research field. This critical review significantly increases the understanding of current progress in urea conversion and the development of a sustainable nitrogen economy.
Collapse
Affiliation(s)
- Xintong Gao
- School of Chemical Engineering, The University of Adelaide, Adelaide, SA 5005, Australia.
| | - Shuai Zhang
- School of Chemical Engineering, The University of Adelaide, Adelaide, SA 5005, Australia.
| | - Pengtang Wang
- School of Chemical Engineering, The University of Adelaide, Adelaide, SA 5005, Australia.
| | - Mietek Jaroniec
- Department of Chemistry and Biochemistry & Advanced Materials and Liquid Crystal Institute, Kent State University, Kent, OH 44242, USA
| | - Yao Zheng
- School of Chemical Engineering, The University of Adelaide, Adelaide, SA 5005, Australia.
| | - Shi-Zhang Qiao
- School of Chemical Engineering, The University of Adelaide, Adelaide, SA 5005, Australia.
| |
Collapse
|
2
|
Zahra FT, Saeed A, Ahmed A, Ismail H, Ijaz MU, Albericio F. Synthesis of amantadine clubbed N-aryl amino thiazoles as potent urease, α-amylase & α-glucosidase inhibitors, kinetic and molecular docking studies. RSC Adv 2023; 13:24988-25001. [PMID: 37614781 PMCID: PMC10442672 DOI: 10.1039/d3ra05330j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 08/15/2023] [Indexed: 08/25/2023] Open
Abstract
A series of ten novel compounds were synthesized by incorporating a 1,3 thiazole core into amantadine and their structures were validated using different analytical and spectral methods such as FTIR, EI-MS, 1H NMR, and 13C NMR. The antibacterial and enzyme inhibitory properties of these newly synthesized compounds were evaluated. Remarkably, the compounds exhibited significant antibacterial activity against Escherichia coli and Bacillus subtilis. Additionally, the in vitro inhibitory activities of the synthesized compounds, against α-amylase, α-glucosidase, and urease were investigated. Among the tested compounds, compound 6d demonstrated potent and selective inhibition of α-amylase IC50 = 97.37 ± 1.52 μM, while acarbose was used as positive control and exhibited IC50 = 5.17 ± 0.25 μM. Compound 6d and 6e exhibited prominent inhibition against α-glucosidase IC50 = 38.73 ± 0.80 μM and 41.63 ± 0.26 μM respectively. Furthermore, compound 6d inhibited urease with exceptional efficacy IC50 = 32.76 μM, while positive control thiourea showed more prominent activity having IC50 = 1.334 μM. Molecular docking studies disclosed the binding mechanism and affinity of these new inhibitors within the binding sites of various amino acids. To investigate the association between molecular structural characteristics and inhibitory actions of synthesized derivatives, preliminary structure-activity relationship (SAR) studies were performed. These findings indicated that compounds 6a, 6c, 6d and 6e are potential candidates for hit-to-lead follow-up in the drug-discovery process for treating diabetes and hyperglycemia.
Collapse
Affiliation(s)
- Fatima Tuz Zahra
- Department of Chemistry, Quaid-i-Azam University 45320 Islamabad Pakistan +92-51-9064-2241 +92-51-9064-2128
| | - Aamer Saeed
- Department of Chemistry, Quaid-i-Azam University 45320 Islamabad Pakistan +92-51-9064-2241 +92-51-9064-2128
| | - Atteeque Ahmed
- Department of Chemistry, Quaid-i-Azam University 45320 Islamabad Pakistan +92-51-9064-2241 +92-51-9064-2128
| | - Hammad Ismail
- Department of Biochemistry and Biotechnology, University of Gujrat Gujrat 50700 Pakistan
| | - Muhammad Umar Ijaz
- Department of Zoology, Wildlife and Fisheries, University of Agriculture Faisalabad 38040 Pakistan
| | - Fernando Albericio
- Peptides Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal Westville Durban 4000 South Africa
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Department of Organic Chemistry, University of Barcelona 08028 Barcelona Spain
| |
Collapse
|
3
|
Yuvarajan S, Hameed A, Bhagwath Arun A, Kanekar S, Rekha PD. Urease-negative uropathogen Kalamiella piersonii YU22 metabolizes urea by urea carboxylase and allophanate hydrolase enzyme system. Microbiol Res 2022; 263:127142. [DOI: 10.1016/j.micres.2022.127142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 07/18/2022] [Accepted: 07/21/2022] [Indexed: 10/16/2022]
|
4
|
Espinosa-Chávez B, Ramírez-Vives F, Zeeman G, Monroy-Hermosillo O. Start-up and performance of a downflow fluidised bed reactor for biological treatment of yellow wastewater and nutrient recovery. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2022; 85:3208-3224. [PMID: 35704406 DOI: 10.2166/wst.2022.167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The treatment of yellow water (human urine) in a downflow fluidised bed reactor (DFFBR) was investigated to evaluate biological ureolysis and nutrient recovery. The reactor was operated at 30±4 °C in batch mode, and reaction time = 1 d. The average immobilised biomass (as volatile solids, IVS) in the reactor was 2.5±0.9 g L-1support, and specific ureolytic activity was 121 g Urea-N g-1 IVS d-1. The kinetic parameters were 0.152 mol L-1 (Km) and 8 mol g-1 IVS d-1 (Vmax). The ureolysis efficiency was 93.4% and chemical oxygen demand removal efficiency was 31.2%, while total ammonium nitrogen (NH4+-N) production rate was 7 g L-1 d-1 and phosphate removal reached 26%. Precipitates recovery during biological treatment was 1.72±0.8 g. These results suggest that the treatment of yellow water in a DFFBR is a viable option for partial recovery of N and P.
Collapse
Affiliation(s)
- Belem Espinosa-Chávez
- Institute of Ecology, Universidad del Mar, Ciudad Universitaria, 70902 Puerto Ángel, Oaxaca, México E-mail: ; Department of Biotechnology, Universidad Autónoma Metropolitana, Av. San Rafael Atlixco. 186. Col. Vicentina, 09340 Iztapalapa, México City, México
| | - Florina Ramírez-Vives
- Department of Biotechnology, Universidad Autónoma Metropolitana, Av. San Rafael Atlixco. 186. Col. Vicentina, 09340 Iztapalapa, México City, México
| | | | - Oscar Monroy-Hermosillo
- Department of Biotechnology, Universidad Autónoma Metropolitana, Av. San Rafael Atlixco. 186. Col. Vicentina, 09340 Iztapalapa, México City, México
| |
Collapse
|
5
|
Lee ZR, Quinn LJ, Jones CW, Hayes SE, Dixon DA. Predicting the Mechanism and Products of CO 2 Capture by Amines in the Presence of H 2O. J Phys Chem A 2021; 125:9802-9818. [PMID: 34748350 DOI: 10.1021/acs.jpca.1c05950] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An extensive correlated molecular orbital theory study of the reactions of CO2 with a range of substituted amines and H2O in the gas phase and aqueous solution was performed at the G3(MP2) level with a self-consistent reaction field approach. The G3(MP2) calculations were benchmarked at the CCSD(T)/CBS level for NH3 reactions. A catalytic NH3 reduces the energy barrier more than a catalytic H2O for the formation of H2NCOOH and H2CO3. In aqueous solution, the barriers to form both H2NCOOH and H2CO3 are reduced, with HCO3- formation possible with one amine present and H2NCOO- formation possible only with two amines. Further reactions of H2NCOOH to form HNCO and urea via the Bazarov reaction have high barriers and are unlikely in both the gas phase and aqueous solution. Reaction coordinates for CH3NH2, CH3CH2NH2, (CH3)2NH, CH3CH2CH2NH2, (CH3)3N, and DMAP were also calculated. The barrier for proton transfer correlates with amine basicity for alkylammonium carbamate (ΔG‡aq < 15 kcal/mol) and alkylammonium bicarbonate (ΔG‡aq < 30 kcal/mol) formation. In aqueous solution, carbamic acids, carbamates, and bicarbonates can all form in small amounts with ammonium carbamates dominating for primary and secondary alkylamines. These results have implications for CO2 capture by amines in both the gas phase and aqueous solution as well as in the solid state, if enough water is present.
Collapse
Affiliation(s)
- Zachary R Lee
- Department of Chemistry and Biochemistry, University of Alabama, Tuscaloosa, Alabama 35487, United States.,Department of Biology and Chemistry, Morehead State University, Morehead, Kentucky 40351, United States
| | - La'Darious J Quinn
- Department of Chemistry and Biochemistry, University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Christopher W Jones
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive, Atlanta, Georgia 30332, United States
| | - Sophia E Hayes
- Department of Chemistry, Washington University, 1 Brookings Drive, Saint Louis, Missouri 63130, United States
| | - David A Dixon
- Department of Chemistry and Biochemistry, University of Alabama, Tuscaloosa, Alabama 35487, United States
| |
Collapse
|
6
|
Gratzfeld D, Heitkämper J, Debailleul J, Olzmann M. On the influence of water on urea condensation reactions: a theoretical study. Z PHYS CHEM 2020. [DOI: 10.1515/zpch-2020-1658] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
The influence of water molecules on the kinetics of urea condensation reactions was studied with high-level quantum chemical methods and statistical rate theory. The study focuses on the production of biuret, triuret, and cyanuric acid from urea because of their relevance as unwanted byproducts in the urea-based selective catalytic reduction (urea-SCR) exhaust after treatment of Diesel engines. In order to characterize the potential energy surfaces and molecular reaction pathways, calculations with explicitly-correlated coupled-cluster methods were performed. It turned out that the reactions proceed via pre-reactive complexes and the inclusion of one or two water molecules into the condensation mechanisms leads to a decrease of the energy barriers. This effect is particularly pronounced in the production of biuret. Due to the pre-reactive equilibria, the rates of the overall reactions can increase or decrease by incorporating water into the mechanism, depending on the temperature and water concentration. Under the conditions of urea-SCR, the studied reactions are too slow to contribute to the observed byproduct formation.
Collapse
Affiliation(s)
- Dennis Gratzfeld
- Institut für Physikalische Chemie, Karlsruher Institut für Technologie (KIT) , Kaiserstr. 12 , 76131 Karlsruhe , Germany
| | - Juliane Heitkämper
- Institut für Physikalische Chemie, Karlsruher Institut für Technologie (KIT) , Kaiserstr. 12 , 76131 Karlsruhe , Germany
| | - Julien Debailleul
- Institut für Physikalische Chemie, Karlsruher Institut für Technologie (KIT) , Kaiserstr. 12 , 76131 Karlsruhe , Germany
| | - Matthias Olzmann
- Institut für Physikalische Chemie, Karlsruher Institut für Technologie (KIT) , Kaiserstr. 12 , 76131 Karlsruhe , Germany
| |
Collapse
|
7
|
Hydrazine clubbed 1,3-thiazoles as potent urease inhibitors: design, synthesis and molecular docking studies. Mol Divers 2020; 25:1-13. [PMID: 32095975 DOI: 10.1007/s11030-020-10057-7] [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: 11/29/2019] [Accepted: 02/17/2020] [Indexed: 10/24/2022]
Abstract
Synthesis of a novel series of hydrazine clubbed 1,3-thiazoles (5a-m) has been described by reacting hydrazine-1-carbothioamides (3a-k) with α-chloro- or bromo-acetophenones (4a-d) in refluxing ethanol in good to excellent yields (65-86%). Structural confirmation was based upon spectroscopic techniques such as 1H-NMR, 13C-NMR, FT-IR and mass spectrometry. The biological application of these motifs has been demonstrated in terms of their strong urease inhibition activity. The results of in vitro study revealed that all the compounds are the potent inhibitors of urease. The IC50 (ranging in between 110 and 440 nM) values were higher as compared to that of standard, i.e., thiourea (IC50 = 490 ± 10 nM). The synthesized compounds were docked at the active sites of the Jack bean urease enzyme in order to explore the possible binding interactions of enzyme-ligand complexes; the results reinforced the in vitro biological activity results.
Collapse
|
8
|
van Gelder MK, Jong JAW, Folkertsma L, Guo Y, Blüchel C, Verhaar MC, Odijk M, Van Nostrum CF, Hennink WE, Gerritsen KGF. Urea removal strategies for dialysate regeneration in a wearable artificial kidney. Biomaterials 2020; 234:119735. [PMID: 31958714 DOI: 10.1016/j.biomaterials.2019.119735] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 12/05/2019] [Accepted: 12/25/2019] [Indexed: 12/31/2022]
Abstract
The availability of a wearable artificial kidney (WAK) that provides dialysis outside the hospital would be an important advancement for dialysis patients. The concept of a WAK is based on regeneration of a small volume of dialysate in a closed-loop. Removal of urea, the primary waste product of nitrogen metabolism, is the major challenge for the realization of a WAK since it is a molecule with low reactivity that is difficult to adsorb while it is the waste solute with the highest daily molar production. Currently, no efficient urea removal technology is available that allows for miniaturization of the WAK to a size and weight that is acceptable for patients to carry. Several urea removal strategies have been explored, including enzymatic hydrolysis by urease, electro-oxidation and sorbent systems. However, thus far, these methods have toxic side effects, limited removal capacity or slow removal kinetics. This review discusses different urea removal strategies for application in a wearable dialysis device, from both a chemical and a medical perspective.
Collapse
Affiliation(s)
- Maaike K van Gelder
- Department of Nephrology and Hypertension, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, the Netherlands
| | - Jacobus A W Jong
- Department of Nephrology and Hypertension, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, the Netherlands; Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, the Netherlands
| | - Laura Folkertsma
- Department of Nephrology and Hypertension, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, the Netherlands; BIOS-Lab on a Chip Group, MESA+ Institute of Nanotechnology, Technical Medical Center, Max Planck Center for Complex Fluid Dynamics, University of Twente, 7522 NH, Enschede, the Netherlands
| | - Yong Guo
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, the Netherlands
| | | | - Marianne C Verhaar
- Department of Nephrology and Hypertension, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, the Netherlands
| | - Mathieu Odijk
- BIOS-Lab on a Chip Group, MESA+ Institute of Nanotechnology, Technical Medical Center, Max Planck Center for Complex Fluid Dynamics, University of Twente, 7522 NH, Enschede, the Netherlands
| | - Cornelus F Van Nostrum
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, the Netherlands
| | - Wim E Hennink
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, the Netherlands
| | - Karin G F Gerritsen
- Department of Nephrology and Hypertension, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, the Netherlands.
| |
Collapse
|
9
|
Polino D, Parrinello M. Kinetics of Aqueous Media Reactions via Ab Initio Enhanced Molecular Dynamics: The Case of Urea Decomposition. J Phys Chem B 2019; 123:6851-6856. [PMID: 31286763 DOI: 10.1021/acs.jpcb.9b05271] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Aqueous solutions provide a medium for many important reactions in chemical synthesis, industrial processes, environmental chemistry, and biological functions. It is an accepted fact that aqueous solvents can be direct participants in the reaction process and not act only as simple passive dielectrics. Assisting water molecules and proton wires are thus essential for the efficiency of many reactions. Here, we study the decomposition of urea into ammonia and isocyanic acid by means of enhanced ab initio molecular dynamics simulations. We highlight the role of the solvent molecules and their interactions with the reactants providing a proper description of the reaction mechanism and how the water hydrogen-bond network affects the reaction dynamics. Reaction free energy and rates have been calculated taking into account this important effect.
Collapse
Affiliation(s)
- Daniela Polino
- Department of Chemistry and Applied Biosciences , ETH Zurich , c/o USI Campus, Via Giuseppe Buffi 13 , CH-6900 Lugano , Switzerland.,Facoltà di Informatica, Istituto di Scienze Computazionali , Università della Svizzera Italiana , Via Giuseppe Buffi 13 , CH-6900 Lugano , Switzerland
| | - Michele Parrinello
- Department of Chemistry and Applied Biosciences , ETH Zurich , c/o USI Campus, Via Giuseppe Buffi 13 , CH-6900 Lugano , Switzerland.,Facoltà di Informatica, Istituto di Scienze Computazionali , Università della Svizzera Italiana , Via Giuseppe Buffi 13 , CH-6900 Lugano , Switzerland.,Istituto Italiano di Tecnologia , Via Morego 30 , 16163 Genova , Italy
| |
Collapse
|
10
|
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: 110] [Impact Index Per Article: 18.3] [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.
Collapse
Affiliation(s)
- Paweł Kafarski
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | | |
Collapse
|
11
|
Overbury SH, Kolesnikov AI, Brown GM, Zhang Z, Nair GS, Sacci RL, Lotfi R, van Duin ACT, Naguib M. Complexity of Intercalation in MXenes: Destabilization of Urea by Two-Dimensional Titanium Carbide. J Am Chem Soc 2018; 140:10305-10314. [DOI: 10.1021/jacs.8b05913] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | | | | | | | | | - Roghayyeh Lotfi
- Department of Mechanical & Nuclear Engineering, Penn State University, University Park, Pennsylvania 16802, United States
| | - Adri C. T. van Duin
- Department of Mechanical & Nuclear Engineering, Penn State University, University Park, Pennsylvania 16802, United States
| | - Michael Naguib
- Department of Physics and Engineering Physics, Tulane University, New Orleans, Louisiana 70118, United States
| |
Collapse
|
12
|
Decomposition of 8 mol·L−1 Urea Solution at 298.15 K. J SOLUTION CHEM 2018. [DOI: 10.1007/s10953-018-0762-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
13
|
Wei D, Huang X, Qiao Y, Rao J, Wang L, Liao F, Zhan CG. Catalytic Mechanisms for Cofactor-Free Oxidase-Catalyzed Reactions: Reaction Pathways of Uricase-Catalyzed Oxidation and Hydration of Uric Acid. ACS Catal 2017; 7:4623-4636. [PMID: 28890842 DOI: 10.1021/acscatal.7b00901] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
First-principles quantum mechanical/molecular mechanical (QM/MM)-free energy calculations have been performed to uncover how uricase catalyzes metabolic reactions of uric acid (UA), demonstrating that the entire reaction process of UA in uricase consists of two stages-oxidation followed by hydration. The oxidation consists of four steps: (1) chemical transformation from 8-hydroxyxythine to an anionic radical via a proton transfer along with an electron transfer, which is different from the previously proposed electron-transfer mechanism that involves a dianion intermediate (UA2-) during the catalytic reaction process; (2) proton transfer to the O2- anion (radical); (3) diradical recombination to form a peroxo intermediate; (4) dissociation of H2O2 to generate the dehydrourate. Hydration, for the most favorable pathway, is initiated by the nucleophilic attack of a water molecule on dehydrourate, along with a concerted proton transfer through residue Thr69 in the catalytic site. According to the calculated free energy profile, the hydration is the rate-determining step, and the corresponding free energy barrier of 16.2 kcal/mol is consistent with that derived from experimental kinetic data, suggesting that the computational insights into the catalytic mechanisms are reasonable. The mechanistic insights not only provide a mechanistic base for future rational design of uricase mutants with improved catalytic activity against uric acid as an improved enzyme therapy, but also are valuable for understanding a variety of other cofactor-free oxidase-catalyzed reactions involving an oxygen molecule.
Collapse
Affiliation(s)
- Donghui Wei
- College
of Chemistry and Molecular Engineering, Zhengzhou University, 100 Science Avenue, Zhengzhou, Henan 450001, P. R. China
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States,
| | - Xiaoqin Huang
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States,
- Center
for Theoretical Biological Physics, and Center for Research Computing, Rice University, Houston, Texas 77030, United States,
| | - Yan Qiao
- College
of Chemistry and Molecular Engineering, Zhengzhou University, 100 Science Avenue, Zhengzhou, Henan 450001, P. R. China
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States,
| | - Jingjing Rao
- Key
Laboratory of Medical Laboratory Diagnostics of the Education Ministry,
College of Laboratory Medicine, Chongqing Medical University, No.1, Yixueyuan Road, Chongqing 400016, China
| | - Lu Wang
- Key
Laboratory of Medical Laboratory Diagnostics of the Education Ministry,
College of Laboratory Medicine, Chongqing Medical University, No.1, Yixueyuan Road, Chongqing 400016, China
| | - Fei Liao
- Key
Laboratory of Medical Laboratory Diagnostics of the Education Ministry,
College of Laboratory Medicine, Chongqing Medical University, No.1, Yixueyuan Road, Chongqing 400016, China
| | - Chang-Guo Zhan
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States,
- Molecular
Modeling and Biopharmaceutical Center, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States
| |
Collapse
|
14
|
Wei D, Tang M, Zhan CG. Fundamental reaction pathway and free energy profile of proteasome inhibition by syringolin A (SylA). Org Biomol Chem 2016; 13:6857-65. [PMID: 26018983 DOI: 10.1039/c5ob00737b] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this study, molecular dynamics (MD) simulations and first-principles quantum mechanical/molecular mechanical free energy (QM/MM-FE) calculations have been performed to uncover the fundamental reaction pathway of proteasome with a representative inhibitor syringolin A (SylA). The calculated results reveal that the reaction process consists of three steps. The first step is a proton transfer process, activating Thr1-O(γ) directly by Thr1-N(z) to form a zwitterionic intermediate. The next step is a nucleophilic attack on the olefin carbon of SylA by the negatively charged Thr1-O(γ) atom. The last step is a proton transfer from Thr1-N(z) to another olefin carbon of SylA to complete the inhibition reaction process. The calculated free energy profile demonstrates that the second step should be the rate-determining step and has the highest free energy barrier of 24.6 kcal mol(-1), which is reasonably close to the activation free energy (∼22.4-23.0 kcal mol(-1)) derived from the available experimental kinetic data. In addition, our computational results indicate that no water molecule can assist the rate-determining step, since the second step is not involved in a proton transfer process. The obtained mechanistic insights should be valuable for understanding the inhibition process of proteasome by SylA and structurally related inhibitors at a molecular level, and thus provide a solid mechanistic base and valuable clues for future rational design of novel, more potent inhibitors of proteasome.
Collapse
Affiliation(s)
- Donghui Wei
- Department of Chemistry, Zhengzhou University, Daxue Road, Zhengzhou, Henan 450052, China
| | | | | |
Collapse
|
15
|
Abstract
To accurately predict the free energy barrier for urea elimination in aqueous solution, we examined the reaction coordinates for the direct and water-assisted elimination pathways, and evaluated the corresponding free energy barriers by using the surface and volume polarization for electrostatics (SVPE) model-based first-principles electronic-structure calculations. Based on the computational results, the water-assisted elimination pathway is dominant for urea elimination in aqueous solution, and the corresponding free energy barrier is 25.3 kcal/mol. The free energy barrier of 25.3 kcal/mol predicted for the dominant reaction pathway of urea elimination in aqueous solution is in good agreement with available experimental kinetic data.
Collapse
|
16
|
Belzile MN, Neverov AA, Brown RS. Cu(II)-Ion-Catalyzed Solvolysis of N,N-Bis(2-picolyl)ureas in Alcohol Solvents: Evidence for Cleavage Involving Nucleophilic Addition and Strong Assistance of Bis(2-picolyl)amine Leaving Group Departure. Inorg Chem 2014; 53:7916-25. [DOI: 10.1021/ic500620k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mei-Ni Belzile
- Department
of Chemistry, Queen’s University, Kingston, Ontario, Canada K7L 3N6
| | - Alexei. A. Neverov
- Department
of Chemistry, Queen’s University, Kingston, Ontario, Canada K7L 3N6
| | - R. Stan Brown
- Department
of Chemistry, Queen’s University, Kingston, Ontario, Canada K7L 3N6
| |
Collapse
|
17
|
Dana AG, Shter GE, Grader GS. Thermal analysis of aqueous urea ammonium nitrate alternative fuel. RSC Adv 2014. [DOI: 10.1039/c4ra04381b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
TGA/DTA/MS and DSC under high pressure of aqueous urea ammonium nitrate alternative fuel is reported.
Collapse
Affiliation(s)
- Alon Grinberg Dana
- The Nancy and Stephen Grand Technion Energy Program
- Technion – Israel Institute of Technology
- Haifa 3200003, Israel
| | - Gennady E. Shter
- The Wolfson Department of Chemical Engineering
- Technion – Israel Institute of Technology
- Haifa 3200003, Israel
| | - Gideon S. Grader
- The Wolfson Department of Chemical Engineering
- Technion – Israel Institute of Technology
- Haifa 3200003, Israel
| |
Collapse
|