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Andrikopoulos N, Li Y, Nandakumar A, Quinn JF, Davis TP, Ding F, Saikia N, Ke PC. Zinc-Epigallocatechin-3-gallate Network-Coated Nanocomposites against the Pathogenesis of Amyloid-Beta. ACS APPLIED MATERIALS & INTERFACES 2023; 15:7777-7792. [PMID: 36724494 PMCID: PMC10037301 DOI: 10.1021/acsami.2c20334] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The aggregation of amyloid beta (Aβ) is a hallmark of Alzheimer's disease (AD), a major cause of dementia and an unmet challenge in modern medicine. In this study, we constructed a biocompatible metal-phenolic network (MPN) comprising a polyphenol epigallocatechin gallate (EGCG) scaffold coordinated by physiological Zn(II). Upon adsorption onto gold nanoparticles, the MPN@AuNP nanoconstruct elicited a remarkable potency against the amyloid aggregation and toxicity of Aβ in vitro. The superior performance of MPN@AuNP over EGCG@AuNP was attributed to the porosity and hence larger surface area of the MPN in comparison with that of EGCG alone. The atomic detail of Zn(II)-EGCG coordination was unraveled by density functional theory calculations and the structure and dynamics of Aβ aggregation modulated by the MPN were further examined by discrete molecular dynamics simulations. As MPN@AuNP also displayed a robust capacity to cross a blood-brain barrier model through the paracellular pathway, and given the EGCG's function as an anti-amyloidosis and antioxidation agent, this MPN-based strategy may find application in regulating the broad AD pathology beyond protein aggregation inhibition.
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Affiliation(s)
- Nicholas Andrikopoulos
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Yuhuan Li
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Fudan University, Shanghai, 200032, China
| | - Aparna Nandakumar
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - John F. Quinn
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- Department of Chemical and Biological Engineering, Faculty of Engineering, Monash University, Clayton, VIC 3800, Australia
| | - Thomas P. Davis
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane Qld 4072, Australia
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
| | - Nabanita Saikia
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
| | - Pu Chun Ke
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- Nanomedicine Center, The Great Bay Area National Institute for Nanotechnology Innovation, 136 Kaiyuan Avenue, Guangzhou, 510700, China
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Neenu Krishna P, Muraleedharan K. Metal chelation ability of Protocatechuic acid anion with 210Po84; A theoretical insight. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2022.113996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Thuy PT, Son NT. Thermodynamic and kinetic studies on antioxidant capacity of amentoflavone: a DFT (density functional theory) computational approach. Free Radic Res 2022; 56:526-535. [PMID: 36370431 DOI: 10.1080/10715762.2022.2146584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Density functional theory (DFT) at the theoretical M06-2X/6-311G(d,p) level was used to assess thermodynamics and kinetics in the antioxidative action of amentoflavone (AF). The antioxidative HAT pathway (H-atom transfer) is assigned to this compound in gas, but the SPL-ET (sequential proton loss-electron transfer) is the main route in polar solvents methanol and water. In all four mediums gas, benzene, methanol, and water, 4‴-OH is the most active site in free radical quenching with the lowest BDE (bond dissociation enthalpy) values of 81.8-84.8 kcal/mol, as well as it exerted the PA (proton affinity) values of 29.8-33.0 kcal/mol in methanol and water. Regarding kinetics, when interacted with •OOH and •NO2 in gas and methanol, 4‴-OH group is also responsible for the lowest ΔG# values (Gibbs free energy of activation), and the highest rate constant K values. Acidic assessment also indicated that 4‴-OH is associated with the strongest acidity (the lowest pKa). Two favorable oriented 4‴-OH and 7-OH groups further exhibited antioxidative activity since they prevented metal ions Zn2+ and Fe2+ from participating in free radical producing processes, in which the most stable complex [FeAF(H2O)4] generated the lowest IE value of -206.2 kcal/mol, and Egap value of 3.491 kcal/mol, but the highest MIA values of 184.6 kcal/mol in methanol.
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Affiliation(s)
- Phan Thi Thuy
- Department of Chemistry, College of Education, Vinh University, Vinh, Vietnam
| | - Ninh The Son
- Institute of Chemistry, Vietnam Academy of Science and Technology (VAST), Caugiay, Vietnam
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Lemilemu F, Bitew M, Demissie TB, Eswaramoorthy R, Endale M. Synthesis, antibacterial and antioxidant activities of Thiazole-based Schiff base derivatives: a combined experimental and computational study. BMC Chem 2021; 15:67. [PMID: 34949213 PMCID: PMC8697436 DOI: 10.1186/s13065-021-00791-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 12/04/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Thiazole-based Schiff base compounds display significant pharmacological potential with an ability to modulate the activity of many enzymes involved in metabolism. They also demonstrated to have antibacterial, antifungal, anti-inflammatory, antioxidant, and antiproliferative activities. In this work, conventional and green approaches using ZnO nanoparticles as catalyst were used to synthesize thiazole-based Schiff base compounds. RESULTS Among the synthesized compounds, 11 showed good activities towards Gram-negative E. coli (14.40 ± 0.04), and Gram-positive S. aureus (15.00 ± 0.01 mm), respectively, at 200 μg/mL compared to amoxicillin (18.00 ± 0.01 mm and 17.00 ± 0.04). Compounds 7 and 9 displayed better DPPH radical scavenging potency with IC50 values of 3.6 and 3.65 μg/mL, respectively, compared to ascorbic acid (3.91 μg/mL). The binding affinity of the synthesized compounds against DNA gyrase B is within - 7.5 to - 6.0 kcal/mol, compared to amoxicillin (- 6.1 kcal/mol). The highest binding affinity was achieved for compounds 9 and 11 (- 6.9, and - 7.5 kcal/mol, respectively). Compounds 7 and 9 displayed the binding affinity values of - 5.3 to - 5.2 kcal/mol, respectively, against human peroxiredoxin 5. These values are higher than that of ascorbic acid (- 4.9 kcal/mol), in good agreement with the experimental findings. In silico cytotoxicity predictions showed that the synthesized compounds Lethal Dose (LD50) value are class three (50 ≤ LD50 ≤ 300), indicating that the compounds could be categorized under toxic class. Density functional theory calculations showed that the synthesized compounds have small band gap energies ranging from 1.795 to 2.242 eV, demonstrating that the compounds have good reactivities. CONCLUSIONS The synthesized compounds showed moderate to high antibacterial and antioxidant activities. The in vitro antibacterial activity and molecular docking analysis showed that compound 11 is a promising antibacterial therapeutics agent against E. coli, whereas compounds 7 and 9 were found to be promising antioxidant agents. Moreover, the green synthesis approach using ZnO nanoparticles as catalyst was found to be a very efficient method to synthesize biologically active compounds compared to the conventional method.
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Affiliation(s)
- Fitsum Lemilemu
- Department of Applied Chemistry, Adama Science and Technology University, P.O. Box 1888, Adama, Ethiopia.
| | - Mamaru Bitew
- Department of Applied Chemistry, Adama Science and Technology University, P.O. Box 1888, Adama, Ethiopia
| | - Taye B Demissie
- Department of Chemistry, University of Botswana, Notwane Rd, P/bag UB 00704, Gaborone, Botswana
| | | | - Milkyas Endale
- Department of Applied Chemistry, Adama Science and Technology University, P.O. Box 1888, Adama, Ethiopia.
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Manzoor S, Ahmed A, Moin ST. Iron coordination to pyochelin siderophore influences dynamics of FptA receptor from Pseudomonas aeruginosa: a molecular dynamics simulation study. Biometals 2021; 34:1099-1119. [PMID: 34357504 DOI: 10.1007/s10534-021-00332-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 07/19/2021] [Indexed: 12/23/2022]
Abstract
FptA is a TonB-dependent transporter that permits the high affinity binding and transport of Fe(III)-pyochelin complex across the outer membrane of Pseudomonas aeruginosa. Molecular dynamics simulations were employed to FptA receptor and its complexes with pyochelin, and co-crystallized Fe(III)-pyochelin-ethanediol and Fe(III)-pyochelin-water embedded in dilauroyl phosphatidyl choline bilayer for the evaluation of their structural and dynamical properties. The evaluation of properties of the receptor bound to pyochelin molecule and Fe(III)-pyochelin complexes helped to figure out the iron coordination effect on the receptor properties. Moreover, comparison of these four simulation systems revealed further information on the dynamical changes occurred in extracellular loops, in particular loop-7 corresponding to the missing amino acid residues including the close-by loop-8 that was largely affected by the metal coordination to pyochelin. The binding of iron to pyochelin molecule affected the overall structure of the receptor therefore, evaluation fo the gyration radii and hydrogen bonding were evaluated as well as analysis of the pore size were also carried out to understand the effect of metal coordination on the dynamics of the helices which form a kind of translocation channel to transport the siderophore across the FptA protein into the periplasmic space. The properties of each component of the molecular systems were therefore observed to be perturbed by the incorporation of iron to the pyochelin molecule thus demonstrating that the bacteria use its receptor to abstract and transport iron from extracellular environment for its survival and that was made possible to understand at the molecular level through successful implementation of molecular dynamics simulations.
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Affiliation(s)
- Sana Manzoor
- Third World Center for Science and Technology, H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Ayaz Ahmed
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Syed Tarique Moin
- Third World Center for Science and Technology, H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan.
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Sharfalddin AA, Emwas A, Jaremko M, Hussien MA. Transition metal complexes of 6‐mercaptopurine: Characterization, Theoretical calculation, DNA‐Binding, molecular docking, and anticancer activity. Appl Organomet Chem 2020. [DOI: 10.1002/aoc.6041] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Abeer A. Sharfalddin
- Department of Chemistry, Faculty of Science King Abdulaziz University Jeddah Saudi Arabia
| | - Abdul‐Hamid Emwas
- Imaging and Characterization Core Lab King Abdullah University of Science and Technology (KAUST) Thuwal Saudi Arabia
| | - Mariusz Jaremko
- Biological and Environmental Science and Engineering (BESE) King Abdullah University of Science and Technology (KAUST) Thuwal Saudi Arabia
| | - Mostafa A. Hussien
- Department of Chemistry, Faculty of Science King Abdulaziz University Jeddah Saudi Arabia
- Department of Chemistry, Faculty of Science Port Said University Port Said Egypt
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A combined molecular dynamics and quantum mechanics study on the interaction of Fe3+ and human serum albumin relevant to iron overload disease. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.113933] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Antioxidant Properties of Lapachol and Its Derivatives and Their Ability to Chelate Iron (II) Cation: DFT and QTAIM Studies. Bioinorg Chem Appl 2020; 2020:2103239. [PMID: 32318101 PMCID: PMC7150675 DOI: 10.1155/2020/2103239] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 06/09/2019] [Accepted: 08/21/2019] [Indexed: 01/06/2023] Open
Abstract
The elucidation of the complexation of lapachol and its derivatives to Fe2+ cation has been done using the density functional theory (DFT). This complexation has been limited to bidentate and tridentate to Fe2+ cation. Geometry optimizations have been implemented in gas and solution phase (water, acetonitrile, chlorobenzene, benzene, and toluene) for ligands at B3LYP/6-311++G (d,p) level of theory using B3LYP/6-31+G(d,p) optimized data as starting point. But, the geometrical optimizations in solution phase of the 22 complexes analyzed of lapachol and its derivatives to Fe2+ cation were restricted to acetonitrile and benzene. The complexation energy and the metal ion affinity (MIA) have also been calculated using the B3LYP method. The results obtained indicated a proportionality between the MIA values and the retained charge on Fe2+ cation for k2-(O1,O2) modes. But, an inverse proportionality has been yielded between these two parameters for k3-(O2, C=C) tridentate modes. For k3-(O3,C=C) tridentate mode coordination, the higher stability has been obtained. In this latter tridentate coordination in gas phase, the topological analysis of complexes exhibits the fact that the electron density is concentrated between the O3 oxygen atom of the ligand attached to Fe2+ and this metal cation. Moreover, the hydrogen bond strength calculated for isolated ligands (situated between 23.92 and 30.15 kJ/mol) is in the range of normal HBs. Collectively, all the complexation processes have shown to be highly exothermic. Our results have also shown that the electron extraction from Fe2+...Lai complexes is more difficult compared to that from free ligands.
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Suručić LT, Janjić GV, Rakić AA, Nastasović AB, Popović AR, Milčić MK, Onjia AE. Theoretical modeling of sorption of metal ions on amino-functionalized macroporous copolymer in aqueous solution. J Mol Model 2019; 25:177. [PMID: 31161265 DOI: 10.1007/s00894-019-4053-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 04/29/2019] [Indexed: 11/26/2022]
Abstract
With regard to the harmful effects of heavy metals on human health and the environment, the demand for synthesis and investigation of macromolecules with large capacity of harmful substances sorption is ever greater. Quantum-chemical methods may be applied in structural modeling, prediction, and characterization of such molecules and reactions. Sorption of metal ions (Cu2+, Cd2+, Co2+, and Ni2+) to triethylenetetramine-functionalized copolymer poly(GMA-co-EGDMA)-teta was successfully modeled by quantum chemical calculations, at the B3LYP//6-311++G**/lanl2dz level. Optimized structures of metal complexes were used for calculation of real binding energy of metal ion within the complex (ΔEr). Solvent and hydrolyzation effects were essential for obtaining the objective values. Solvent effect was included in ΔEr by using the total solvation energy for reaction of formation of tetaOH complex (ΔEs1, the first approach) or by using dehydration energy of free metal ion (ΔEs2, the second approach). Experimental results were confirmed in our theoretical analyses (using the second approach). Graphical abstract Theoretical modeling of divalent metal ions sorption on triethylenetetramine-functionalized copolymer poly(GMA-co-EGDMA)-teta.
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Affiliation(s)
- Ljiljana T Suručić
- University of Banja Luka, Faculty of Medicine, Save Mrkalja 14, 78000, Banja Luka, Republic of Srpska, Bosnia and Herzegovina.
| | - Goran V Janjić
- Institute of Chemistry Technology and Metallurgy, University of Belgrade, Njegoševa 12, Belgrade, 11000, Serbia
| | - Aleksandra A Rakić
- Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16, Belgrade, 11158, Serbia
| | - Aleksandra B Nastasović
- Institute of Chemistry Technology and Metallurgy, University of Belgrade, Njegoševa 12, Belgrade, 11000, Serbia
| | - Aleksandar R Popović
- Faculty of Chemistry, University of Belgrade, Studentski trg 12 - 16, Belgrade, 11000, Serbia
| | - Miloš K Milčić
- Faculty of Chemistry, University of Belgrade, Studentski trg 12 - 16, Belgrade, 11000, Serbia
| | - Antonije E Onjia
- University of Belgrade, Faculty of Technology and Metallurgy, Karnegijeva 4, Belgrade, 11000, Serbia
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The possibility of iron chelation therapy in the presence of different HPOs; a molecular approach to the non-covalent interactions and binding energies. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.04.065] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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