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Boychuk BTA, Wetmore SD. Assessment of Density Functional Theory Methods for the Structural Prediction of Transition and Post-Transition Metal-Nucleic Acid Complexes. J Chem Theory Comput 2023. [PMID: 37399186 DOI: 10.1021/acs.jctc.3c00127] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2023]
Abstract
Understanding the structure of metal-nucleic acid systems is important for many applications such as the design of new pharmaceuticals, metal detection platforms, and nanomaterials. Herein, we explore the ability of 20 density functional theory (DFT) functionals to reproduce the crystal structure geometry of transition and post-transition metal-nucleic acid complexes identified in the Protein Data Bank and Cambridge Structural Database. The environmental extremes of the gas phase and implicit water were considered, and analysis focused on the global and inner coordination geometry, including the coordination distances. Although gas-phase calculations were unable to describe the structure of 12 out of the 53 complexes in our test set regardless of the DFT functional considered, accounting for the broader environment through implicit solvation or constraining the model truncation points to crystallographic coordinates generally afforded agreement with the experimental structure, suggesting that functional performance for these systems is likely due to the models rather than the methods. For the remaining 41 complexes, our results show that the reliability of functionals depends on the metal identity, with the magnitude of error varying across the periodic table. Furthermore, minimal changes in the geometries of these metal-nucleic acid complexes occur upon use of the Stuttgart-Dresden effective core potential and/or inclusion of an implicit water environment. The overall top three performing functionals are ωB97X-V, ωB97X-D3(BJ), and MN15, which reliably describe the structure of a broad range of metal-nucleic acid systems. Other suitable functionals include MN15-L, which is a cheaper alternative to MN15, and PBEh-3c, which is commonly used in QM/MM calculations of biomolecules. In fact, these five methods were the only functionals tested to reproduce the coordination sphere of Cu2+-containing complexes. For metal-nucleic acid systems that do not contain Cu2+, ωB97X and ωB97X-D are also suitable choices. These top-performing methods can be utilized in future investigations of diverse metal-nucleic acid complexes of relevance to biology and material science.
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Affiliation(s)
- Briana T A Boychuk
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AB T1K 3M4, Canada
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AB T1K 3M4, Canada
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van der Westhuizen D, Bezuidenhout DI, Munro OQ. Cancer molecular biology and strategies for the design of cytotoxic gold(I) and gold(III) complexes: a tutorial review. Dalton Trans 2021; 50:17413-17437. [PMID: 34693422 DOI: 10.1039/d1dt02783b] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
This tutorial review highlights key principles underpinning the design of selected metallodrugs to target specific biological macromolecules (DNA and proteins). The review commences with a descriptive overview of the eukaryotic cell cycle and the molecular biology of cancer, particularly apoptosis, which is provided as a necessary foundation for the discovery, design, and targeting of metal-based anticancer agents. Drugs which target DNA have been highlighted and clinically approved metallodrugs discussed. A brief history of the development of mainly gold-based metallodrugs is presented prior to addressing ligand systems for stabilizing and adding functionality to bio-active gold(I) and gold(III) complexes, particularly in the burgeoning field of anticancer metallodrugs. Concepts such as multi-modal and selective cytotoxic agents are covered where necessary for selected compounds. The emerging role of carbenes as the ligand system of choice to achieve these goals for gold-based metallodrug candidates is highlighted prior to closing the review with comments on some future directions that this research field might follow. The latter section ultimately emphasizes the importance of understanding the fate of metal complexes in cells to garner key mechanistic insights.
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Affiliation(s)
- Danielle van der Westhuizen
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa.
| | - Daniela I Bezuidenhout
- Laboratory of Inorganic Chemistry, Environmental and Chemical Engineering, University of Oulu, P. O. Box 3000, 90014 Oulu, Finland.
| | - Orde Q Munro
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa.
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Unruh C, Van Bavel N, Anikovskiy M, Prenner EJ. Benefits and Detriments of Gadolinium from Medical Advances to Health and Ecological Risks. Molecules 2020; 25:molecules25235762. [PMID: 33297578 PMCID: PMC7730697 DOI: 10.3390/molecules25235762] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 11/30/2020] [Accepted: 12/04/2020] [Indexed: 12/17/2022] Open
Abstract
Gadolinium (Gd)-containing chelates have been established as diagnostics tools. However, extensive use in magnetic resonance imaging has led to increased Gd levels in industrialized parts of the world, adding to natural occurrence and causing environmental and health concerns. A vast amount of data shows that metal may accumulate in the human body and its deposition has been detected in organs such as brain and liver. Moreover, the disease nephrogenic systemic fibrosis has been linked to increased Gd3+ levels. Investigation of Gd3+ effects at the cellular and molecular levels mostly revolves around calcium-dependent proteins, since Gd3+ competes with calcium due to their similar size; other reports focus on interaction of Gd3+ with nucleic acids and carbohydrates. However, little is known about Gd3+ effects on membranes; yet some results suggest that Gd3+ interacts strongly with biologically-relevant lipids (e.g., brain membrane constituents) and causes serious structural changes including enhanced membrane rigidity and propensity for lipid fusion and aggregation at much lower concentrations than other ions, both toxic and essential. This review surveys the impact of the anthropogenic use of Gd emphasizing health risks and discussing debilitating effects of Gd3+ on cell membrane organization that may lead to deleterious health consequences.
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Affiliation(s)
- Colin Unruh
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada; (C.U.); (N.V.B.)
| | - Nicolas Van Bavel
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada; (C.U.); (N.V.B.)
| | - Max Anikovskiy
- Department of Chemistry, University of Calgary, Calgary, AB T2N 1N4, Canada
- Correspondence: (M.A.); (E.J.P.)
| | - Elmar J. Prenner
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada; (C.U.); (N.V.B.)
- Correspondence: (M.A.); (E.J.P.)
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Soliman MY, Medema G, Bonilla BE, Brouns SJ, van Halem D. Inactivation of RNA and DNA viruses in water by copper and silver ions and their synergistic effect. WATER RESEARCH X 2020; 9:100077. [PMID: 33225254 PMCID: PMC7663217 DOI: 10.1016/j.wroa.2020.100077] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 10/19/2020] [Accepted: 11/01/2020] [Indexed: 05/19/2023]
Abstract
Cu and Ag have been used as bactericidal agents since ancient times, yet their antiviral capacity in water remains poorly understood. This study tested the effect of copper (Cu) and silver (Ag) on model RNA and DNA viruses MS2 and PhiX 174 in solution at pH 6-8. Cu caused MS2 inactivation with similar rates at pH 6 and 7 but was inert towards PhiX 174 regardless of pH. Ag inactivated both viruses, causing denaturation of MS2 and loss of capsid spikes in PhiX 174. Ag inactivation rates were pH dependent and increased with increasing pH. At pH 8, 6.5 logs of PhiX were inactivated after 3 h and 3 logs of MS2 after only 10 min. The combined use of Cu and Ag revealed synergy in disinfecting MS2 at pH ≥ 7. Although metal concentrations used were higher than the desired values for drinking water treatment, the results prove a promising potential of Cu and Ag combinations as efficient viricidal agents.
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Affiliation(s)
- Mona Y.M. Soliman
- Department of Water Management, Delft University of Technology, Stevinweg 1, 2628, CN Delft, the Netherlands
- Corresponding author.
| | - Gertjan Medema
- Department of Water Management, Delft University of Technology, Stevinweg 1, 2628, CN Delft, the Netherlands
- KWR Watercycle Research Institute, P.O. Box 1072, 3430 BB, Nieuwegein, the Netherlands
| | - Boris Estrada Bonilla
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629, HZ Delft, the Netherlands
- Fagenbank, Van der Maasweg 9, 2629, HZ Delft, the Netherlands
| | - Stan J.J. Brouns
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629, HZ Delft, the Netherlands
- Fagenbank, Van der Maasweg 9, 2629, HZ Delft, the Netherlands
| | - Doris van Halem
- Department of Water Management, Delft University of Technology, Stevinweg 1, 2628, CN Delft, the Netherlands
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Augspurger EE, Rana M, Yigit MV. Chemical and Biological Sensing Using Hybridization Chain Reaction. ACS Sens 2018; 3:878-902. [PMID: 29733201 DOI: 10.1021/acssensors.8b00208] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Since the advent of its theoretical discovery more than 30 years ago, DNA nanotechnology has been used in a plethora of diverse applications in both the fundamental and applied sciences. The recent prominence of DNA-based technologies in the scientific community is largely due to the programmable features stored in its nucleobase composition and sequence, which allow it to assemble into highly advanced structures. DNA nanoassemblies are also highly controllable due to the precision of natural and artificial base-pairing, which can be manipulated by pH, temperature, metal ions, and solvent types. This programmability and molecular-level control have allowed scientists to create and utilize DNA nanostructures in one, two, and three dimensions (1D, 2D, and 3D). Initially, these 2D and 3D DNA lattices and shapes attracted a broad scientific audience because they are fundamentally captivating and structurally elegant; however, transforming these conceptual architectural blueprints into functional materials is essential for further advancements in the DNA nanotechnology field. Herein, the chemical and biological sensing applications of a 1D DNA self-assembly process known as hybridization chain reaction (HCR) are reviewed. HCR is a one-dimensional (1D) double stranded (ds) DNA assembly process initiated only in the presence of a specific short ssDNA (initiator) and two kinetically trapped DNA hairpin structures. HCR is considered an enzyme-free isothermal amplification process, which shows substantial promise and offers a wide range of applications for in situ chemical and biological sensing. Due to its modular nature, HCR can be programmed to activate only in the presence of highly specific biological and/or chemical stimuli. HCR can also be combined with different types of molecular reporters and detection approaches for various analytical readouts. While the long dsDNA HCR product may not be as structurally attractive as the 2D and 3D DNA networks, HCR is highly instrumental for applied biological, chemical, and environmental sciences, and has therefore been studied to foster a variety of objectives. In this review, we have focused on nucleic acid, protein, metabolite, and heavy metal ion detection using this 1D DNA nanotechnology via fluorescence, electrochemical, and nanoparticle-based methodologies.
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Jeyalakshmi K, Haribabu J, Balachandran C, Bhuvanesh NSP, Emi N, Karvembu R. Synthesis of Ru(ii)–benzene complexes containing aroylthiourea ligands, and their binding with biomolecules and in vitro cytotoxicity through apoptosis. NEW J CHEM 2017. [DOI: 10.1039/c6nj03099h] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Ru(ii)(η6-benzene) complexes containing sulfur donor monodentate aroylthiourea ligands have been synthesized and evaluated for their biological applications.
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Affiliation(s)
| | - Jebiti Haribabu
- Department of Chemistry
- National Institute of Technology
- Tiruchirappalli 620015
- India
| | | | | | - Nobuhiko Emi
- Department of Hematology
- Fujita Health University
- Toyoake
- Japan
| | - Ramasamy Karvembu
- Department of Chemistry
- National Institute of Technology
- Tiruchirappalli 620015
- India
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7
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Synthesis, Characterization and Crystal Structure of a New 3D Cadmium(II) Coordination Polymer: Binding Interaction with DNA and Double Stranded RNA. J Inorg Organomet Polym Mater 2016. [DOI: 10.1007/s10904-016-0383-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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8
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Ferreira BJML, Brandão P, Meireles M, Martel F, Correia-Branco A, Fernandes DM, Santos TM, Félix V. Synthesis, structural characterization, cytotoxic properties and DNA binding of a dinuclear copper(II) complex. J Inorg Biochem 2016; 161:9-17. [PMID: 27157979 DOI: 10.1016/j.jinorgbio.2016.04.026] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 04/12/2016] [Accepted: 04/18/2016] [Indexed: 11/19/2022]
Abstract
In this study a novel dinuclear copper(II) complex with adenine and phenanthroline has been synthesized and its structure determined by single crystal X-ray diffraction. In the dinuclear complex [Cu₂(μ-adenine)₂(phen)₂(H2O)2](NO3)4·0.5H2O (phen=1,10-phenanthroline) (1) the two Cu(II) centres exhibit a distorted square pyramidal coordination geometry linked by two nitrogen donors from adenine bridges leading to a Cu-Cu distance of 3.242(3)Å. Intramolecular and intermolecular π⋯π interactions as well as an H-bonding network were observed. The antitumor capacity of the complex has been tested in vitro against human cancer cell lines, cervical carcinoma (HeLa) and colorectal adenocarcinoma (Caco-2), by metabolic tests, using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-tetrazolium bromide as reagent. The complex 1 has remarkable low IC50 values of 0.87±0.06μM (HeLa) and 0.44±0.06μM (Caco-2), when compared with values for cisplatin against the same cell lines. The interaction of complex 1 with calf thymus DNA (CT DNA) was further investigated by absorption and fluorescence spectroscopic methods. A binding constant of 5.09×10(5)M(-1) was obtained from UV-vis absorption studies.
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Affiliation(s)
- B J M Leite Ferreira
- Departamento de Química, CICECO, Universidade de Aveiro, 3810-193 Aveiro, Portugal
| | - P Brandão
- Departamento de Química, CICECO, Universidade de Aveiro, 3810-193 Aveiro, Portugal.
| | - M Meireles
- Departamento de Química e Bioquímica, Centro de Química e Bioquímica, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Fátima Martel
- Departamento de Bioquímica, Faculdade de Medicina do Porto e I3S, Universidade do Porto, 4200-319 Porto, Portugal
| | - Ana Correia-Branco
- Departamento de Bioquímica, Faculdade de Medicina do Porto e I3S, Universidade do Porto, 4200-319 Porto, Portugal
| | - Diana M Fernandes
- Departamento de Química e Bioquímica, REQUIMTE/LAQV, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal
| | - T M Santos
- Departamento de Química, CICECO, Universidade de Aveiro, 3810-193 Aveiro, Portugal
| | - V Félix
- Departamento de Química, CICECO, Universidade de Aveiro, 3810-193 Aveiro, Portugal; Departamento de Química, IBIMED and CICECO, Universidade de Aveiro, 3810-193 Aveiro, Portugal.
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9
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Pefkianakis EK, Theodossiou TA, Toubanaki DK, Karagouni E, Falaras P, Papadopoulos K, Vougioukalakis GC. A Family of Potent Ru(II) Photosensitizers with Enhanced DNA Intercalation: Bimodal Photokillers. Photochem Photobiol 2015; 91:1191-202. [DOI: 10.1111/php.12485] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 06/08/2015] [Indexed: 12/23/2022]
Affiliation(s)
| | - Theodossis A. Theodossiou
- Institute of Cancer Research, Department of Radiation Biology; The Norwegian Radium Hospital; Oslo University Hospital; Oslo Norway
| | - Dimitra K. Toubanaki
- Laboratory of Cellular Immunology; Department of Microbiology; Hellenic Pasteur Institute; Athens Greece
| | - Evdokia Karagouni
- Laboratory of Cellular Immunology; Department of Microbiology; Hellenic Pasteur Institute; Athens Greece
| | - Polycarpos Falaras
- Division of Physical Chemistry; Institute of Nanoscience and Nanotechnology; NCSR Demokritos; Aghia Paraskevi Greece
| | - Kyriakos Papadopoulos
- Division of Physical Chemistry; Institute of Nanoscience and Nanotechnology; NCSR Demokritos; Aghia Paraskevi Greece
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Reactivity of hexanuclear ruthenium metallaprisms towards nucleotides and a DNA decamer. J Biol Inorg Chem 2015; 20:49-59. [PMID: 25380991 DOI: 10.1007/s00775-014-1208-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 10/12/2014] [Indexed: 01/12/2023]
Abstract
The reactivity of three hexacationic arene ruthenium metallaprisms towards isolated nucleotides and a short DNA strand was investigated using NMR spectroscopy, ESI mass spectrometry, UV/Vis and circular dichroism spectroscopy. The metallaprism built from oxalato-bridging ligands reacts rapidly in the presence of deoxyguanosine monophosphate (dGMP) and deoxyadenosine monophosphate, while the benzoquinonato derivative only reacts with dGMP. On the other hand, the larger metallaprism incorporating naphtoquinonato bridges remains stable in the presence of nucleotides. The reactivity of the three hexacationic metallaprisms with the decameric oligonucleotide d(CGCGATCGCG)2 was also investigated. Analysis of the NMR, MS, UV/Vis and CD data suggests that no adducts are formed between the oligonucleotide and the metallaprisms, but electrostatic interactions, leading to partial unwinding of the double-stranded oligonucleotide, were evidenced.
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Jana SK, Seth SK, Puschmann H, Hossain M, Dalai S. Synthesis and X-ray structure of a new zinc(ii) coordination polymer: interaction with DNA and double stranded RNA and elucidation of the molecular aspects of the binding to bovine serum albumin. RSC Adv 2014. [DOI: 10.1039/c4ra06588c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Synthesis and characterization of [Zn(4-Me-5-CHOIm)2(HCOO)](ClO4) complex and binding with nucleic acids and BSA has been explored by different biophysical techniques with the combination of isothermal titration calorimetry (ITC).
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Affiliation(s)
- Swapan K. Jana
- Department of Chemistry and Chemical Technology
- Vidyasagar University
- Midnapore 721 102, India
| | - Saikat K. Seth
- Department of Physics
- M. G. Mahavidyalaya
- Purba Medinipur, India
| | | | - Maidul Hossain
- Department of Chemistry and Chemical Technology
- Vidyasagar University
- Midnapore 721 102, India
| | - Sudipta Dalai
- Department of Chemistry and Chemical Technology
- Vidyasagar University
- Midnapore 721 102, India
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12
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Singh SK, Pandey DS. Multifaceted half-sandwich arene–ruthenium complexes: interactions with biomolecules, photoactivation, and multinuclearity approach. RSC Adv 2014. [DOI: 10.1039/c3ra44131h] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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