A theoretical study on the antioxidant properties of methoxy-substituted chalcone derivatives: A case study of kanakugiol and pedicellin through their Fe (II and III) coordination ability

2016 ◽  
Vol 15 (06) ◽  
pp. 1650048 ◽  
Author(s):  
Kemoabetswe R. N. Serobatse ◽  
Mwadham M. Kabanda
Keyword(s):  
Metal Binding ◽  
Metal Ion ◽  
Density Functional ◽  
Theoretical Study ◽  
Water Solution ◽  
Antioxidant Properties ◽  
Hydroxyl Group ◽  
Chalcone Derivatives ◽  
Coordination Ability

A theoretical study on the antioxidant properties of two chalcone derivatives, kanakugiol and pedicellin, is performed by considering their Fe[Formula: see text] and Fe[Formula: see text] coordination ability. The objective of the study is to elucidate the factors influencing the stability of the isolated conformers, the nature of the complexes, metal[Formula: see text]ligand stability, metal ion affinities (MIA) and electronic properties of the cations before and after coordination to the ligand. The study is performed using the B3LYP/6–311[Formula: see text]G(2d,p)//B3LYP/6–31[Formula: see text]G(d,p) method. The LANL2DZ pseudopotential is selected to describe the Fe[Formula: see text] ions. Time-dependent density functional theory (TDDFT) method is used to assess the electronic UV–Vis spectra of the isolated chalcones and their complexes with Fe[Formula: see text] ions. The results suggest that the preferred complexes are those in which the Fe ion is coordinated at the hydroxyl-methoxy and hydroxyl-keto sites for kanakugiol and methoxy-keto site for pedicellin. Both kanakugiol and pedicellin have potential to chelate iron ions as demonstrated by their high MIA values in vacuo and in water solution. However, the ability of pedicellin to chelate iron is slightly lower than that of kanakugiol, indicating that the presence of the hydroxyl group has an effect of enhancing the metal binding abilities of the chalcone derivatives. In all the complexes obtained in vacuo, kanakugiol and pedicellin exhibit the ability to reduce the Fe[Formula: see text] ion. In water solution (which mimics the environment in biological systems or studies performed in vivo), Fe[Formula: see text] is reduced to Fe[Formula: see text] upon coordination to the ligand while the oxidation number of Fe[Formula: see text] upon coordination to the ligand remains virtually unchanged.

scholarly journals Crystallographic and X-ray absorption spectroscopic characterization of Helicobacter pylori UreE bound to Ni2+ and Zn2+ reveals a role for the disordered C-terminal arm in metal trafficking

2012 ◽  
Vol 441 (3) ◽  
pp. 1017-1035 ◽  
Author(s):  
Katarzyna Banaszak ◽  
Vlad Martin-Diaconescu ◽  
Matteo Bellucci ◽  
Barbara Zambelli ◽  
Wojciech Rypniewski ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Metal Ions ◽  
Metal Binding ◽  
Metal Ion ◽  
Mutual Influence ◽  
Accurate Information ◽  
Metal Ion Binding ◽  
X Ray ◽  
X Ray Absorption

The survival and growth of the pathogen Helicobacter pylori in the gastric acidic environment is ensured by the activity of urease, an enzyme containing two essential Ni2+ ions in the active site. The metallo-chaperone UreE facilitates in vivo Ni2+ insertion into the apoenzyme. Crystals of apo-HpUreE (H. pylori UreE) and its Ni2+- and Zn2+-bound forms were obtained from protein solutions in the absence and presence of the metal ions. The crystal structures of the homodimeric protein, determined at 2.00 Å (apo), 1.59 Å (Ni2+) and 2.52 Å (Zn2+) resolution, show the conserved proximal and solvent-exposed His102 residues from two adjacent monomers invariably involved in metal binding. The C-terminal regions of the apoprotein are disordered in the crystal, but acquire significant ordering in the presence of the metal ions due to the binding of His152. The analysis of X-ray absorption spectral data obtained using solutions of Ni2+- and Zn2+-bound HpUreE provided accurate information of the metal-ion environment in the absence of solid-state effects. These results reveal the role of the histidine residues at the protein C-terminus in metal-ion binding, and the mutual influence of protein framework and metal-ion stereo-electronic properties in establishing co-ordination number and geometry leading to metal selectivity.

scholarly journals HK97 gp74 Possesses an α-Helical Insertion in the ββα Fold That Affects Its Metal Binding, cos Site Digestion, and In Vivo Activities

2020 ◽  
Vol 202 (8) ◽  
Author(s):  
Sasha A. Weiditch ◽  
Sarah C. Bickers ◽  
Diane Bona ◽  
Karen L. Maxwell ◽  
Voula Kanelis
Keyword(s):  
Metal Binding ◽  
Metal Ion ◽  
Divalent Metal ◽  
Metal Ion Binding ◽  
Divalent Metal Ions ◽  
Nmr Studies ◽  
Phage Dna ◽  
Divalent Metal Ion ◽  
Phage Morphogenesis

ABSTRACT The last gene in the genome of the bacteriophage HK97 encodes gp74, an HNH endonuclease. HNH motifs contain two conserved His residues and an invariant Asn residue, and they adopt a ββα structure. gp74 is essential for phage head morphogenesis, likely because gp74 enhances the specific endonuclease activity of the HK97 terminase complex. Notably, the ability of gp74 to enhance the terminase-mediated cleavage of the phage cos site requires an intact HNH motif in gp74. Mutation of H82, the conserved metal-binding His residue in the HNH motif, to Ala abrogates gp74-mediated stimulation of terminase activity. Here, we present nuclear magnetic resonance (NMR) studies demonstrating that gp74 contains an α-helical insertion in the Ω-loop, which connects the two β-strands of the ββα fold, and a disordered C-terminal tail. NMR data indicate that the Ω-loop insert makes contacts to the ββα fold and influences the ability of gp74 to bind divalent metal ions. Further, the Ω-loop insert and C-terminal tail contribute to gp74-mediated DNA digestion and to gp74 activity in phage morphogenesis. The data presented here enrich our molecular-level understanding of how HNH endonucleases enhance terminase-mediated digestion of the cos site and contribute to the phage replication cycle. IMPORTANCE This study demonstrates that residues outside the canonical ββα fold, namely, the Ω-loop α-helical insert and a disordered C-terminal tail, regulate the activity of the HNH endonuclease gp74. The increased divalent metal ion binding when the Ω-loop insert is removed compared to reduced cos site digestion and phage formation indicates that the Ω-loop insert plays multiple regulatory roles. The data presented here provide insights into the molecular basis of the involvement of HNH proteins in phage DNA packing.

scholarly journals A Theoretical Study of the Adsorption Process of B-aflatoxins Using Pyracantha koidzumii (Hayata) Rehder Biomasses

Toxins ◽  
2020 ◽  
Vol 12 (5) ◽  
pp. 283
Author(s):  
Abraham Méndez-Albores ◽  
René Escobedo-González ◽  
Juan Manuel Aceves-Hernández ◽  
Perla García-Casillas ◽  
María Inés Nicolás-Vázquez ◽  
...  
Keyword(s):  
Functional Groups ◽  
Electrostatic Interactions ◽  
Density Functional ◽  
Ph Value ◽  
Theoretical Calculations ◽  
Basis Set ◽  
Hydroxyl Group ◽  
Biosorption Process

Employing theoretical calculations with density functional theory (DFT) using the B3LYP/6-311++G(d,p) functional and basis set, the interaction of the aflatoxin B1 (AFB1) molecule and the functional groups present in the Pyracantha koidzumii biosorbent was investigated. Dissociation free energy and acidity equilibrium constant values were obtained theoretically both in solution (water) and gas phases. Additionally, the molecular electrostatic potential for the protonated molecules was calculated to verify the reactivity. Thus, methanol (hydroxyl group), methylammonium ion (amino group), acetate ion (carboxyl group), and acetone (carbonyl group), were used as representatives of the substrates present in the biomass; these references were considered using the corresponding protonated or unprotonated forms at a pH value of 5. The experimental infrared spectrophotometric data suggested the participation of these functional groups in the AFB1 biosorption process, indicating that the mechanism was dominated by electrostatic interactions between the charged functional groups and the positively charged AFB1 molecule. The theoretical determination indicated that the carboxylate ion provided the highest interaction energy with the AFB1 molecule. Consequently, an enriched biosorbent with compounds containing carboxyl groups could improve the yield of the AFB1 adsorption when using in vitro and in vivo trials.

THEORETICAL STUDY ON POTENCY AND SELECTIVITY OF NOVEL NONPEPTIDE INHIBITORS OF MATRIX METALLOPROTEINASES MMP-2 AND MMP-9

2009 ◽  
Vol 08 (03) ◽  
pp. 491-506 ◽  
Author(s):  
DAI-LIN LI ◽  
QING-CHUAN ZHENG ◽  
XUE-XUN FANG ◽  
HAI-TAO JI ◽  
JIN-GANG YANG ◽  
...  
Keyword(s):  
Inhibitory Activity ◽  
Density Functional ◽  
Theoretical Study ◽  
Zinc Binding ◽  
Hydroxyl Group ◽  
Interaction Energies ◽  
Binding Modes ◽  
Functional Theory ◽  
Total Interaction ◽  
Binding Affinity Calculations

Two novel matrix metalloproteinase (MMP) inhibitors, myricetin (m) and kaempferol (k), were found and the inhibitory activity is both in decreased order towards MMP-2 and MMP-9. To understand the mechanism during the processes when inhibitors bind to MMP-2 and MMP-9, molecular modeling, docking, and density functional theory (DFT) calculations were performed. The calculated results indicated that the hydroxyls on benzene ring of the inhibitors control the binding modes between inhibitors and MMPs, thus play an important role on the potency and selectivity. Besides coordinating with the N atoms of three His residues, Zn also interacts with a hydroxyl group of inhibitors by O – Zn distances of 2.66–2.78 Å in all of the docked complexes, so that the hydroxyl acts as a weak zinc binding group (ZBG). The DFT calculated results support the above analysis. The binding affinity calculations between inhibitors and MMPs present the total interaction energies in the m-MMP < k-MMP order and the solvation energy of myricetin is less than that of kaempferol, which reflect the experimental inhibitory activity.

Density functional theoretical study on attachment sites of Mg2+ and Ca2+ and metal ion affinity to Crenulatin molecule

2008 ◽  
Vol 19 (3) ◽  
pp. 541-548 ◽  
Author(s):  
Xinlu Cheng ◽  
Xinfang Su ◽  
Xingwen Zhao ◽  
Hengjie Chen
Keyword(s):  
Metal Ion ◽  
Density Functional ◽  
Theoretical Study ◽  
Attachment Sites

scholarly journals Isolation of the Flavonoid from Bamboo Residues and Its Application as Metal Ion Sensor in Vitro

Polymers ◽  
2019 ◽  
Vol 11 (9) ◽  
pp. 1377 ◽  
Author(s):  
Yan Su ◽  
Huiling Dong ◽  
Min Li ◽  
Chenhuan Lai ◽  
Caoxing Huang ◽  
...  
Keyword(s):  
Metal Ion ◽  
Limit Of Detection ◽  
Antioxidant Properties ◽  
Green Emission ◽  
Natural Polymers ◽  
Fluorescence Sensors ◽  
Intracellular Detection ◽  
L02 Cells

Fluorescence sensors prepared from natural polymers have received increasing attention based on their luminescence characteristics for bioimaging, cell imaging, and intracellular detection of inorganic metabolites. In this work, flavonoids isolated from bamboo residues (BRF) were applied as fluorescence sensors for different metal cations’ detection in vitro. Results showed the optimal flavonoids extraction condition of solid to liquid ratio, ethanol concentration, extraction time and temperature were determined at 1:25, 50%, 240 min and 90 °C, respectively, resulting in an extraction yield with 104.7 mg/100 g bamboo residues. The BRF is mainly composed of isoorientin, isovitexin, pinosylvin, tricin and isorhamnetin by liquid chromatography–mass spectrometry (LC-MS) analysis. It is found that the BRF displayed strong blue-green emission as well as notable excitation, which can selectively and sensitively detect Fe3+ with the limit of detection (LOD) as low as 38.0 nM. In the Fe3+ detection was no obvious interference by other cations except for Al3+. In addition, the BRF displayed excellent biocompatibility that can be applied to bioimages of the intracellular detection of Fe3+ in L02 cells. Finally, it is found that the BRF possessed significant antioxidant properties in scavenging H2O2-induced endogenous reactive oxygen species (ROS) in a zebrafish module (in vivo) and L02 cells (in vitro). These results showed that the flavonoid products sustainably isolated from an abundant lignocellulosic waste appear to be effective fluorescent sensors for Fe3+ detection in biological systems with excellent biocompatibility and antioxidant activity.

scholarly journals Antioxidant Properties of Lapachol and Its Derivatives and Their Ability to Chelate Iron (II) Cation: DFT and QTAIM Studies

2020 ◽  
Vol 2020 ◽  
pp. 1-10 ◽  
Author(s):  
Djafarou Ngouh Pajoudoro ◽  
Daniel Lissouck ◽  
Baruch Ateba Amana ◽  
Joseph Zobo Mfomo ◽  
A. E. B. Abdallah ◽  
...  
Keyword(s):  
Metal Ion ◽  
Density Functional ◽  
Topological Analysis ◽  
Antioxidant Properties ◽  
Solution Phase ◽  
B3lyp Method ◽  
Starting Point ◽  
The Density Functional Theory ◽  
Phase Water ◽  
Two Parameters

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.

scholarly journals In Staphylococcus aureus, Fur Is an Interactive Regulator with PerR, Contributes to Virulence, and Is Necessary for Oxidative Stress Resistance through Positive Regulation of Catalase and Iron Homeostasis

2001 ◽  
Vol 183 (2) ◽  
pp. 468-475 ◽  
Author(s):  
Malcolm J. Horsburgh ◽  
Eileen Ingham ◽  
Simon J. Foster
Keyword(s):  
Oxidative Stress ◽  
Staphylococcus Aureus ◽  
Stress Resistance ◽  
Metal Ion ◽  
Iron Homeostasis ◽  
Antioxidant Properties ◽  
Tetracycline Resistance ◽  
Growth Defect ◽  
Oxidative Stress Resistance

ABSTRACT The Staphylococcus aureus genome encodes three ferric uptake repressor (Fur) homologues: Fur, PerR, and Zur. To determine the exact role of Fur in S. aureus, we inactivated thefur gene by allelic replacement using a tetracycline resistance cassette, creating strain MJH010 (fur). The mutant had a growth defect in rich medium, and this defect was exacerbated in metal-depleted CL medium. This growth defect was partially suppressed by manganous ion, a metal ion with known antioxidant properties. This suggests that the fur mutation leads to an oxidative stress condition. Indeed, MJH010 (fur) has reduced levels of catalase activity resulting from decreased katA transcription. Using akatA-lacZ fusion we have determined that Fur functions, either directly or indirectly, as an iron-dependent positive regulator of katA expression. Transcription of katA is coregulated by Fur and PerR, since in MJH010 (fur) transcription was still repressed by manganese while transcription in MJH201 (fur perR) was unresponsive to the presence of iron or manganese. Siderophore biosynthesis was repressed by iron in 8325-4 (wild-type) but in MJH010 (fur) was constitutive. A number of putative Fur-regulated genes were identified in the incomplete genome databases using known S. aureus Fur box sequences. Of those tested, the sstABCD andsirABC operons and the fhuD2 andorf4 genes were found to have Fur-regulated expression. MJH010 (fur) was attenuated (P < 0.04) in a murine skin abscess model of infection, as was double-mutant MJH201 (fur perR) (P < 0.03). This demonstrates the importance in vivo of iron homeostasis and oxidative stress resistance regulation in S. aureus.

A comparative theoretical study on the biological activity, chemical reactivity, and coordination ability of dichloro-substituted (1,3-thiazol-2-yl)acetamides

2014 ◽  
Vol 92 (3) ◽  
pp. 234-239 ◽  
Author(s):  
Ambrish Kumar Srivastava ◽  
Neeraj Misra
Keyword(s):  
Density Functional ◽  
Theoretical Study ◽  
Chemical Reactivity ◽  
Biological Activities ◽  
First Principle ◽  
Reactivity Descriptors ◽  
Natural Bonding Orbital ◽  
Coordination Ability ◽  
Global Reactivity Descriptors ◽  
Orbital Analysis

We present a theoretical study on three dichloro-substituted (1,3-thiazol-2-yl)acetamides using the first principle density functional approach. Natural bonding orbital analysis is used to discuss the coordination ability of molecules and various global reactivity descriptors are calculated to compare their chemical reactivity. Biological activities of all three molecules are also evaluated. We find that the present molecules show potential coordination ability and their chemical reactivity varies with the position of substitution. We also notice that all three molecules show remarkable biological activities and the (3,4)-dichloro-substituted molecule is relatively more active. The study suggests further investigations on these molecules for their pharmacological importance.

scholarly journals Structures of dipotassium rubidium citrate monohydrate, K2RbC6H5O7(H2O), and potassium dirubidium citrate monohydrate, KRb2C6H5O7(H2O), from laboratory X-ray powder diffraction data and DFT calculations

2020 ◽  
Vol 76 (10) ◽  
pp. 1566-1571
Author(s):  
Andrew J. Cigler ◽  
James A. Kaduk
Keyword(s):  
Powder Diffraction ◽  
Diffraction Data ◽  
Metal Ion ◽  
Density Functional ◽  
Three Dimensional ◽  
Hydroxyl Group ◽  
Powder Diffraction Data ◽  
Coordination Polyhedra ◽  
X Ray ◽  
Carboxylate Oxygen

The crystal structures of the isostructural compounds dipotassium rubidium citrate monohydrate, K2RbC6H5O7(H2O), and potassium dirubidium citrate monohydrate, KRb2C6H5O7(H2O), have been solved and refined using laboratory X-ray powder diffraction data, and optimized using density functional techniques. The compounds are isostructural to K3C6H5O7(H2O) and Rb3C6H5O7(H2O), but exhibit different degrees of ordering of the K and Rb cations over the three metal-ion sites. The K and Rb site occupancies correlate well to both the bond-valence sums and the DFT energies of ordered cation systems. The MO6 and MO7 coordination polyhedra share edges to form a three-dimensional framework. The water molecule acts as a donor in two strong charge-assisted O—H...O hydrogen bonds to carboxylate groups. The hydroxyl group of the citrate anion forms an intramolecular hydrogen bond to one of the central carboxylate oxygen atoms.

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