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Silva TUD, Silva ETD, Lima CHDS, Machado SDP. Molecular modeling of [VO(L 1-4)(R)] complexes (R = bipyridine, phenanthroline): DFT study of antioxidant activity, DNA binding and evaluation of electron-donating and -withdrawing substituent groups. J Mol Graph Model 2023; 124:108577. [PMID: 37536232 DOI: 10.1016/j.jmgm.2023.108577] [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: 03/18/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/05/2023]
Abstract
A DFT (density functional theory) study was conducted with eight oxovanadium complexes (C1 - C8) of general formula [VO(L1-4)(R)] (R = bipyridine, phenanthroline; L1-4 = group of ligands derived from dithiocarbamate). The obtained geometries showed a good correlation with the experimental structures. Molecular orbital analysis revealed that the contribution of the L-ligand in the SOMO (single-occupied molecular orbital) of the complexes correlated with the experimental antioxidant activity (IC50), while the contribution of the R-ligand to the LUMO (lowest unoccupied molecular orbital) of the complexes correlated with the experimental complex-DNA interaction (Kb). It has been identified that the presence of an electron-donating substituent group (such as -NH2) in the C5 - C6 structures should enhance these complexes' antioxidant and DNA interaction activities.
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Affiliation(s)
- Talis Uelisson da Silva
- Instituto de Química, Universidade Federal Rural Do Rio de Janeiro, 23890-000, Seropédica, RJ, Brazil; Instituto de Química, Universidade Federal Do Rio de Janeiro, Rio de Janeiro, 21945-970, Brazil.
| | | | | | - Sérgio de Paula Machado
- Instituto de Química, Universidade Federal Do Rio de Janeiro, Rio de Janeiro, 21945-970, Brazil
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Discovery and structure of a widespread bacterial ABC transporter specific for ergothioneine. Nat Commun 2022; 13:7586. [PMID: 36481738 PMCID: PMC9732360 DOI: 10.1038/s41467-022-35277-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 11/22/2022] [Indexed: 12/13/2022] Open
Abstract
L-Ergothioneine (ET), the 2-thioimidazole derivative of trimethylhistidine, is biosynthesized by select fungi and bacteria, notably Mycobacterium tuberculosis, and functions as a scavenger of reactive oxygen species. The extent to which ET broadly functions in bacterial cells unable to synthesize it is unknown. Here we show that spd_1642-1643 in Streptococcus pneumoniae, a Gram-positive respiratory pathogen, encodes an ET uptake ATP-binding cassette (ABC) transporter, designated EgtU. The solute binding domain (SBD) of EgtU, EgtUC, binds ET with high affinity and exquisite specificity in a cleft between the two subdomains, with cation-π interactions engaging the betaine moiety and a network of water molecules that surround the thioimidazole ring. EgtU is highly conserved among known quaternary amine compound-specific transporters and widely distributed in Firmicutes, including the human pathogens Listeria monocytogenes, as BilEB, Enterococcus faecalis and Staphylococcus aureus. ET increases the chemical diversity of the low molecular weight thiol pool in Gram-positive human pathogens and may contribute to antioxidant defenses in the infected host.
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Saab M, Nelson DJ, Leech MC, Lam K, Nolan SP, Nahra F, Van Hecke K. Reactions of N-heterocyclic carbene-based chalcogenoureas with halogens: a diverse range of outcomes. Dalton Trans 2022; 51:3721-3733. [PMID: 35169826 DOI: 10.1039/d2dt00010e] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have investigated the reactions of chalcogenoureas derived from N-heterocyclic carbenes, referred to here as [E(NHC)], with halogens. Depending on the structure of the chalcogenourea and the identity of the halogen, a diverse range of reactivity was observed and a corresponding range of structures was obtained. Cyclic voltammetry was carried out to characterise the oxidation and reduction potentials of these [E(NHC)] species; selenoureas were found to be easier to oxidise than the corresponding thioureas. In some cases, a correlation was found between the oxidation potential of these compounds and the electronic properties of the corresponding NHC. The reactivity of these chalcogenoureas with different halogenating reagents (Br2, SO2Cl2, I2) was then investigated, and products were characterised using NMR spectroscopy and single-crystal X-ray diffraction. X-ray analyses elucidated the solid-state coordination types of the obtained products, showing that a variety of possible adducts can be obtained. In some cases, we were able to extrapolate a structure/activity correlation to explain the observed trends in reactivity and oxidation potentials.
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Affiliation(s)
- Marina Saab
- XStruct, Department of Chemistry, Ghent University, Krijgslaan 281, Building S3, 9000 Ghent, Belgium.
| | - David J Nelson
- WestCHEM Department of Pure & Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow, G1 1XL, Scotland, UK
| | - Matthew C Leech
- School of Science, University of Greenwich, Chatham Maritime ME4 4TB, UK
| | - Kevin Lam
- School of Science, University of Greenwich, Chatham Maritime ME4 4TB, UK
| | - Steven P Nolan
- Department of Chemistry, Ghent University, Krijgslaan 281, Building S3, 9000 Ghent, Belgium
| | - Fady Nahra
- XStruct, Department of Chemistry, Ghent University, Krijgslaan 281, Building S3, 9000 Ghent, Belgium. .,VITO (Flemish Institute for Technological Research), Boeretang 200, 2400 Mol, Belgium.
| | - Kristof Van Hecke
- XStruct, Department of Chemistry, Ghent University, Krijgslaan 281, Building S3, 9000 Ghent, Belgium.
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Chalana A, Kumar Rai R, Karri R, Kumar Jha K, Kumar B, Roy G. Interplay of the intermolecular and intramolecular interactions in stabilizing the thione-based copper(I) complexes and their significance in protecting the biomolecules against metal-mediated oxidative damage. Polyhedron 2022. [DOI: 10.1016/j.poly.2021.115647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Sambade D, Collins C, Parkin G. Structure and Bonding of 1,2,4-Triazole Thiones Derived from Nitron. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Abstract
Scale deposition is a pertinent challenge in the oil and gas industry. Scales formed from iron sulfide are one of the troublous scales, particularly pyrite. Moreover, the use of biodegradable environmentally friendly chemicals reduces the cost compared to the conventional removal process. In this work, the chelating abilities of four novel chemicals, designed using the in silico technique of density functional theory (DFT), are studied as potential iron sulfide scale removers. Only one of the chemicals containing a hydroxamate functional group had a good chelating ability with Fe2+. The chelating strength and ecotoxicological properties of this chemical were compared to diethylenetriaminepentaacetic acid (DTPA), an already established iron sulfide scale remover. The new promising chemical surpassed DTPA in being a safer chemical and having a greater binding affinity to Fe2+ upon optimization, hence, a better choice. The presence of oxime (-NHOH) and carbonyl (C=O) moieties in the new chemical showed that the bidentate form of chelation is favored. Moreover, the presence of an intramolecular hydrogen bond enhanced its chelating ability.
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da Silva TU, Pougy KDC, da Silva ET, Lima CHDS, Machado SDP. Electronic investigation of the effect of substituents on the SOD mimic activity of copper (II) complexes with 8-hydroxyquinoline-derived ligands. J Inorg Biochem 2021; 217:111359. [PMID: 33578252 DOI: 10.1016/j.jinorgbio.2021.111359] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 01/16/2021] [Accepted: 01/17/2021] [Indexed: 02/04/2023]
Abstract
Density functional theory (DFT) calculations were used to study the superoxide dismutase (SOD) mimic activity of two Cu2+ complexes with ligands derived from 8-hydroxyquinoline (8-HQ). Electron-donating and -withdrawing substituent groups were inserted into the structures to verify changes in the reactivity. The theoretical parameters obtained were compared and validated with the experimental data available. The results showed that the reduction process occurs with greater participation of the 8-HQ ligand and the oxidation step occurs with participation of the copper atom in the complexes, where the electron received during the reduction step is used to reduce the Cu2+ to Cu+. The calculated electronic affinity showed good correlation with the experimental mimetic activity, and the analysis of this property, of total charge and of molecular orbitals indicated an increase in the mimetic activity with the insertion of electron-withdrawing substituent groups in the structures.
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Affiliation(s)
- Talis Uelisson da Silva
- Instituto de Química, Universidade Federal do Rio de Janeiro, 21945-970 Rio de Janeiro, RJ, Brazil.
| | - Karina de Carvalho Pougy
- Instituto de Química, Universidade Federal do Rio de Janeiro, 21945-970 Rio de Janeiro, RJ, Brazil
| | - Everton Tomaz da Silva
- Instituto de Química, Universidade Federal do Rio de Janeiro, 21945-970 Rio de Janeiro, RJ, Brazil; Instituto Federal do Rio de Janeiro, 25050-100 Caxias, RJ, Brazil
| | | | - Sérgio de Paula Machado
- Instituto de Química, Universidade Federal do Rio de Janeiro, 21945-970 Rio de Janeiro, RJ, Brazil
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Rai RK, Chalana A, Karri R, Das R, Kumar B, Roy G. Role of Hydrogen Bonding by Thiones in Protecting Biomolecules from Copper(I)-Mediated Oxidative Damage. Inorg Chem 2019; 58:6628-6638. [DOI: 10.1021/acs.inorgchem.8b03212] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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