1
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Tang P, Zhang J, Li X, Yang F, Zhao Q, Ma J, Hu Z, Sun H, Wang XB, Sun Z, Yang Y. Cryogenic Photoelectron Spectroscopic and Theoretical Study of the Electronic and Geometric Structures of Undercoordinated Osmium Chloride Anions OsCl n- ( n = 3-5). J Phys Chem A 2024; 128:5500-5507. [PMID: 38968614 DOI: 10.1021/acs.jpca.4c01713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2024]
Abstract
A series of anionic transition metal halides, OsCln- (n = 3-5), have been investigated using a newly developed, home-constructed, cryogenic anion cluster photoelectron spectroscopy. The target anionic species are generated through collision-induced dissociation in a two-stage ion funnel. The measured vertical detachment energies (VDEs) are 3.48, 4.54, and 4.81 eV for n = 3, 4, and 5, respectively. Density functional theory calculations at the B3LYP-D3(BJ)//aug-cc-pVTZ(-pp) level predict the lowest energy structures of the atomic form of OsCln- (n = 3-5) to be a quintet triangle, quartet square, and quintet square-based pyramid, respectively. The CCSD(T)-calculated VDEs and corresponding adiabatic detachment energies agree well with our experimental measurements. Analysis of the corresponding frontier molecular orbitals and charge density differences suggests that the d-orbitals of the transition metal Os play a primary role in the single-photon detachment processes, and the detached electrons originating from different molecular orbitals are distinguishable.
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Affiliation(s)
- Peng Tang
- State Key Laboratory of Precision Spectroscopy, and School of Physics and Electron Science, East China Normal University, Shanghai 200241, China
| | - Jian Zhang
- College of Chemistry and Chemical Engineering, Donghua University, Shanghai 201620, China
| | - Xueying Li
- State Key Laboratory of Precision Spectroscopy, and School of Physics and Electron Science, East China Normal University, Shanghai 200241, China
| | - Fan Yang
- State Key Laboratory of Precision Spectroscopy, and School of Physics and Electron Science, East China Normal University, Shanghai 200241, China
| | - Qixu Zhao
- State Key Laboratory of Precision Spectroscopy, and School of Physics and Electron Science, East China Normal University, Shanghai 200241, China
| | - Junyang Ma
- State Key Laboratory of Precision Spectroscopy, and School of Physics and Electron Science, East China Normal University, Shanghai 200241, China
| | - Zhubin Hu
- State Key Laboratory of Precision Spectroscopy, and School of Physics and Electron Science, East China Normal University, Shanghai 200241, China
| | - Haitao Sun
- State Key Laboratory of Precision Spectroscopy, and School of Physics and Electron Science, East China Normal University, Shanghai 200241, China
| | - Xue-Bin Wang
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Zhenrong Sun
- State Key Laboratory of Precision Spectroscopy, and School of Physics and Electron Science, East China Normal University, Shanghai 200241, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Yan Yang
- State Key Laboratory of Precision Spectroscopy, and School of Physics and Electron Science, East China Normal University, Shanghai 200241, China
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Lighvan ZM, Khonakdar HA, Akbari A, Jahromi MD, Ramezanpour A, Kermagoret A, Heydari A, Jabbari E. Synthesis and biological evaluation of novel tetranuclear cyclopalladated complex bearing thiosemicarbazone scaffold ligand: Interactions with double‐strand DNA, coronavirus, and molecular modeling studies. Appl Organomet Chem 2021. [DOI: 10.1002/aoc.6502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Zohreh Mehri Lighvan
- Department of Polymer Processing Iran Polymer and Petrochemical Institute Tehran Iran
| | - Hossein Ali Khonakdar
- Department of Polymer Processing Iran Polymer and Petrochemical Institute Tehran Iran
- Leibniz‐Institut für Polymerforschung Dresdene. V Dresden Germany
| | - Ali Akbari
- Solid Tumor Research Center, Cellular and Molecular Medicine Research Institute Urmia University of Medical Sciences Urmia Iran
| | | | - Azar Ramezanpour
- Department of Chemistry Isfahan University of Technology Isfahan Iran
| | | | - Abolfazl Heydari
- Polymer Institute of the Slovak Academy of Sciences Bratislava Slovakia
| | - Esmaiel Jabbari
- Department of Chemical Engineering University of South Carolina Columbia South Carolina USA
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3
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Fantoni NZ, Brown T, Kellett A. DNA-Targeted Metallodrugs: An Untapped Source of Artificial Gene Editing Technology. Chembiochem 2021; 22:2184-2205. [PMID: 33570813 DOI: 10.1002/cbic.202000838] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 02/09/2021] [Indexed: 12/20/2022]
Abstract
DNA binding metal complexes are synonymous with anticancer drug discovery. Given the array of structural and chemical reactivity properties available through careful design, metal complexes have been directed to bind nucleic acid structures through covalent or noncovalent binding modes. Several recognition modes - including crosslinking, intercalation, and oxidation - are central to the clinical success of broad-spectrum anticancer metallodrugs. However, recent progress in nucleic acid click chemistry coupled with advancement in our understanding of metal complex-nucleic acid interactions has opened up new avenues in genetic engineering and targeted therapies. Several of these applications are enabled by the hybridisation of oligonucleotide or polyamine probes to discrete metal complexes, which facilitate site-specific reactivity at the nucleic acid interface under the guidance of the probe. This Review focuses on recent advancements in hybrid design and, by way of an introduction to this topic, we provide a detailed overview of nucleic acid structures and metal complex-nucleic acid interactions. Our aim is to provide readers with an insight on the rational design of metal complexes with DNA recognition properties and an understanding of how the sequence-specific targeting of these interactions can be achieved for gene engineering applications.
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Affiliation(s)
- Nicolò Zuin Fantoni
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Tom Brown
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Andrew Kellett
- School of Chemical Sciences and National Institute for, Cellular Biotechnology and Nano Research Facility, Dublin City University, Glasnevin, Dublin, 9, Ireland
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Feng B, Sundin E, Lincoln P, Mårtensson AKF. DNA threading intercalation of enantiopure [Ru(phen) 2bidppz] 2+ induced by hydrophobic catalysis. Phys Chem Chem Phys 2021; 23:2238-2244. [PMID: 33439155 DOI: 10.1039/d0cp00845a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The enantiomers of a novel mononuclear ruthenium(ii) complex [Ru(phen)2bidppz]2+ with an elongated dppz moiety were synthesized. Surprisingly, the complex showed no DNA intercalating capability in an aqueous environment. However, by the addition of water-miscible polyethylene glycol ether PEG-400, self-aggregation of the hydrophobic ruthenium(ii) complexes was counter-acted, thus strongly promoting the DNA intercalation binding mode. This mild alteration of the environment surrounding the DNA polymer does not damage or alter the DNA structure but instead enables more efficient binding characterization studies of potential DNA binding drugs.
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Affiliation(s)
- Bobo Feng
- Department of Chemistry and Chemical Engineering, Kemigården 4, SE-412 96 Gothenburg, Sweden.
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Shahabadi N, Shiri F, Hadidi S, Farshadfar K, Sajadimajd S, Roe SM. Equilibrium and site selective analysis for DNA threading intercalation of a new phosphine copper(I) complex: Insights from X-ray analysis, spectroscopic and molecular modeling studies. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 235:118280. [PMID: 32248034 DOI: 10.1016/j.saa.2020.118280] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 03/18/2020] [Accepted: 03/18/2020] [Indexed: 06/11/2023]
Abstract
To clarify the interaction of phosphine copper(I) complex with DNA, our study reports the synthesis of a new phosphine copper(I) complex, along with a detailed analysis of the geometry characterization and its interaction with double-stranded DNA. The triclinic phase Cu(PPh3)2(L)(I) with a tetrahedral geometry was identified as the product of the reaction of copper(I) iodide with (E,E)-N,N'-1,2-Ethanediylbis[1-(3-pyridinyl)methanimine] ligand and triphenylphosphine by single-crystal X-ray analysis. Molecular interaction of the synthesized complex with the calf thymus deoxyribonucleic acid (ct-DNA) was investigated in the physiological buffer (pH 7.4) by multi-spectroscopic approaches associated with a competitive displacement towards Hoechst 33258 and methylene blue (MB) as groove and intercalator probes. The fluorescence and UV/Vis results detected the formation of a complex-DNA adduct in the ground-state with a binding affinity in order of 104 M-1, which is in keeping with both groove binders and intercalators. The thermodynamic parameters, ΔS0 = -200.31 ± 0.08 cal/mol·K and ΔH0 = -63.11 ± 0.24 kcal/mol, confirmed that the van der Waals interaction is the main driving force for the binding process. Moreover, the ionic strength and pH effect experiments demonstrated the electrostatic interactions between the complex and DNA is negligible. Analysis of the molecular docking simulation declared the flat (E,E)-N,N'-1,2-Ethanediylbis[1-(3-pyridinyl)methanimine] part of the complex was inserted between the sequential A…T/A…T base pairs, while the phosphine substituents were located in the groove, i.e. threading intercalation. Besides, the cytotoxicity of the complex against the MCF-7 human breast cancer cells was detected at IC50 = 10 μg/mL.
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Affiliation(s)
- Nahid Shahabadi
- Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran; Medical Biology Research Center (MBRC), Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Farshad Shiri
- Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran; Medical Biology Research Center (MBRC), Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Saba Hadidi
- Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran
| | - Kaveh Farshadfar
- Department of Chemistry, Islamic Azad University, Central Tehran Branch, Poonak, Tehran 1469669191, Iran
| | | | - S Mark Roe
- Department of Chemistry, School of Life Sciences, University of Sussex, Brighton BN1 9QJ, UK
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Zhang SQ, Gao LH, Zhao H, Wang KZ. Recent Progress in Polynuclear Ruthenium Complex-Based DNA Binders/Structural Probes and Anticancer Agents. Curr Med Chem 2020; 27:3735-3752. [DOI: 10.2174/0929867326666181203143422] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 11/22/2018] [Accepted: 11/26/2018] [Indexed: 01/27/2023]
Abstract
Ruthenium complexes have stood out by several mononuclear complexes which have entered
into clinical trials, such as imidazolium [trans-RuCl4(1H-imidazole)(DMSO-S)] (NAMI-A) and
([Ru(II)(4,4'-dimethyl-2,2'-bipyridine)2-(2(2'-,2'':5'',2'''-terthiophene)-imidazo[4,5-f] [1,10]phenanthroline)]
2+) (TLD-1433), opening a new avenue for developing promising ruthenium-based anticancer
drugs alternative to Cisplatin. Polynuclear ruthenium complexes were reported to exhibit synergistic
and/or complementary effects: the enhanced DNA structural recognition and DNA binding as well as
in vitro anticancer activities. This review overviews some representative polynuclear ruthenium
complexes acting as DNA structural probes, DNA binders and in vitro anticancer agents, which were
developed during last decades. These complexes are reviewed according to two main categories of
homo-polynuclear and hetero-polynuclear complexes, each of which is further clarified into the metal
centers linked by rigid and flexible bridging ligands. The perspective, challenges and future efforts
for investigations into these exciting complexes are pointed out or suggested.
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Affiliation(s)
- Si-Qi Zhang
- Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Li-Hua Gao
- School of Science, Beijing Technology and Business University, Key Laboratory of Cosmetic (Beijing Technology and Business University), China National Light Industry, Beijing 100048, China
| | - Hua Zhao
- School of Science, Beijing Technology and Business University, Key Laboratory of Cosmetic (Beijing Technology and Business University), China National Light Industry, Beijing 100048, China
| | - Ke-Zhi Wang
- Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
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Saeed HK, Sreedharan S, Thomas JA. Photoactive metal complexes that bind DNA and other biomolecules as cell probes, therapeutics, and theranostics. Chem Commun (Camb) 2020; 56:1464-1480. [DOI: 10.1039/c9cc09312e] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Using selected transition metal centres and linking ligand “building blocks” a modular approach to the development of cellular imaging agents and therapeutics is discussed and illustrated with examples from research by the Thomas group.
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Affiliation(s)
- Hiwa K Saeed
- Department of Chemistry
- Brooklyn College
- The City University of New York
- Brooklyn
- USA
| | - Sreejesh Sreedharan
- CRUK/MRC Oxford Institute for Radiation Oncology University of Oxford
- Oxford
- UK
| | - Jim A Thomas
- Department of Chemistry
- University of Sheffield
- Sheffield S10 2TN
- UK
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8
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Fairbanks SD, Robertson CC, Keene FR, Thomas JA, Williamson MP. Structural Investigation into the Threading Intercalation of a Chiral Dinuclear Ruthenium(II) Polypyridyl Complex through a B-DNA Oligonucleotide. J Am Chem Soc 2019; 141:4644-4652. [PMID: 30799603 DOI: 10.1021/jacs.8b12280] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Herein we report the separation of the three stereoisomers of the DNA light-switch compound [{Ru(bpy)2}2(tpphz)]4+ (tpphz = tetrapyrido[3,2-a:2',3'-c:3″,2″-h:2‴,3‴-j]phenazine) by column chromatography and the characterization of each stereoisomer by X-ray crystallography. The interaction of these compounds with a DNA octanucleotide d(GCATATCG).d(CGATATGC) has been studied using NMR techniques. Selective deuteration of the bipyridyl rings was needed to provide sufficient spectral resolution to characterize structures. NMR-derived structures for these complexes show a threading intercalation binding mode with slow and chirality-dependent rates. This represents the first solution structure of an intercalated bis-ruthenium ligand. Intriguingly, we find that the binding site selectivity is dependent on the nature of the stereoisomer employed, with Λ RuII centers showing a better intercalation fit.
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Affiliation(s)
- Simon D Fairbanks
- Department of Chemistry , University of Sheffield , Brook Hill , Sheffield , S3 7HF , U.K.,Department of Molecular Biology and Biotechnology , University of Sheffield , Western Bank , Sheffield , S10 2TN , U.K
| | - Craig C Robertson
- Department of Chemistry , University of Sheffield , Brook Hill , Sheffield , S3 7HF , U.K
| | - F Richard Keene
- Department of Chemistry, School of Physical Sciences , University of Adelaide , Adelaide , SA 5005 , Australia
| | - Jim A Thomas
- Department of Chemistry , University of Sheffield , Brook Hill , Sheffield , S3 7HF , U.K
| | - Mike P Williamson
- Department of Molecular Biology and Biotechnology , University of Sheffield , Western Bank , Sheffield , S10 2TN , U.K
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9
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Rubio‐Magnieto J, Kajouj S, Di Meo F, Fossépré M, Trouillas P, Norman P, Linares M, Moucheron C, Surin M. Binding Modes and Selectivity of Ruthenium Complexes to Human Telomeric DNA G‐Quadruplexes. Chemistry 2018; 24:15577-15588. [DOI: 10.1002/chem.201802147] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 07/12/2018] [Indexed: 02/05/2023]
Affiliation(s)
- Jenifer Rubio‐Magnieto
- Laboratory for Chemistry of Novel Materials Center for Innovation in Materials and Polymers University of Mons-UMONS 20 Place du Parc 7000 Mons Belgium
- Current address: Bioinspired Supramolecular Chemistry and Materials group Departament de Química Inorgànica i Orgànica Universitat Jaume I Avda Sos Baynat s/n E-12071 Castelló Spain
| | - Sofia Kajouj
- Chimie Organique et Photochimie CP160/08 Université libre de Bruxelles 50 avenue F. D. Roosevelt 1050 Bruxelles Belgium
| | - Florent Di Meo
- INSERM U1248 IPPRITT University of Limoges School of Pharmacy 2 rue du Dr. Marcland 87025 Limoges France
| | - Mathieu Fossépré
- Laboratory for Chemistry of Novel Materials Center for Innovation in Materials and Polymers University of Mons-UMONS 20 Place du Parc 7000 Mons Belgium
| | - Patrick Trouillas
- INSERM U1248 IPPRITT University of Limoges School of Pharmacy 2 rue du Dr. Marcland 87025 Limoges France
- RCPTM Palacký University Faculty of Sciences Šlechtitelů 27 78371 Olomouc Czech Republic
| | - Patrick Norman
- Department of Theoretical Chemistry and Biology School of Engineering Sciences in Chemistry Biotechnology and Health KTH Royal Institute of Technology SE-106 91 Stockholm Sweden
| | - Mathieu Linares
- Department of Theoretical Chemistry and Biology School of Engineering Sciences in Chemistry Biotechnology and Health KTH Royal Institute of Technology SE-106 91 Stockholm Sweden
- Swedish e-Science Research Centre (SeRC) KTH Royal Institute of Technology 104 50 Stockholm Sweden
| | - Cécile Moucheron
- Chimie Organique et Photochimie CP160/08 Université libre de Bruxelles 50 avenue F. D. Roosevelt 1050 Bruxelles Belgium
| | - Mathieu Surin
- Laboratory for Chemistry of Novel Materials Center for Innovation in Materials and Polymers University of Mons-UMONS 20 Place du Parc 7000 Mons Belgium
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Ypsilantis K, Plakatouras JC, Manos MJ, Kourtellaris A, Markopoulos G, Kolettas E, Garoufis A. Stepwise synthesis, characterization, DNA binding properties and cytotoxicity of diruthenium oligopyridine compounds conjugated with peptides. Dalton Trans 2018; 47:3549-3567. [PMID: 29436543 DOI: 10.1039/c7dt04639a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Although the interactions of oligopyridine ruthenium complexes with DNA have been widely studied, the biological activity of similar diruthenium oligopyridine complexes conjugated with peptides has not been investigated. Herein, we report the stepwise synthesis and characterization of diruthenium complexes with the general formula [(La)Ru(tppz)Ru(Lb)]n+ (tppz = 2,3,5,6-tetra(2-pyridyl)pyrazine, La = 2,2':6',2''-terpyridine or 4-phenyl-2,2':6',2''-terpyridine and Lb = 2,2':6',2''-terpyridine-4'-CO(Gly1-Gly2-Gly3-LysCONH2) (5), (6), n = 5; 2,2':6',2''-terpyridine-4'-CO(Gly1-Gly2-Lys1-Lys2CONH2) (7), (8), n = 6; 2,2':6',2''-terpyridine-4'-CO(Ahx-Lys1Lys2CONH2) (9), (10), n = 5, Ahx = 6-aminohexanoic acid). The compounds [(trpy)Ru(tppz)Ru(trpy-CO2H)](PF6)4, (2)(PF6)4, [(ptrpy)Ru(tppz)Ru(trpy-CO2H)](PF6)4, (3)(PF6)4 and [(ptrpy)Ru(tppz)Ru(trpy)](PF6)4, (4)(PF6)4 were also characterized by single crystal X-ray methods. Moreover, the interactions of the chloride salts (5), (6) and (4) with the self-complementary dodecanucleotide duplex d(5'-CGCGAATTCGCG-3')2 were studied by NMR spectroscopic techniques. The results show that complex (4) binds in the central part of the oligonucleotide, from the minor groove through the ligand ptrpy, while the ligand trpy, which was located on the other side of the diruthenium core, does not contribute to the binding. Complex (5) binds similarly, through the ligand ptrpy. However, the induced upfield shifts of the ptrpy proton signals are significantly lower than the corresponding ones in the case of (4), indicating much lower binding affinity. This is clear evidence that the tethered peptide Gly1-Gly2-Gly3-Lys1CONH2 hinders the complex binding, even though it contains groups that are able to assist it (e.g., the positively charged amino group of lysine, the peptidic backbone, the terminal amide). Complex (6) shows a non-specific binding, interacting through electrostatic forces. The chloride salts of (4), (5) and (6) had insignificant effects on the cell cycle distribution and marginal cytotoxicity (IC50 > 750 μM) against human lung cancer cell lines H1299 and H1437, indicating that their binding to the oligonucleotide is not a sufficient condition for their cytotoxicity.
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Affiliation(s)
- Konstantinos Ypsilantis
- Laboratory of Inorganic Chemistry, Department of Chemistry, University of Ioannina, Ioannina 45110, Greece.
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11
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Comparative studies on DNA-binding and in vitro antitumor activity of enantiomeric ruthenium(II) complexes. J Inorg Biochem 2018; 180:54-60. [DOI: 10.1016/j.jinorgbio.2017.11.024] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 10/31/2017] [Accepted: 11/26/2017] [Indexed: 02/07/2023]
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Almaqwashi AA, Andersson J, Lincoln P, Rouzina I, Westerlund F, Williams MC. Dissecting the Dynamic Pathways of Stereoselective DNA Threading Intercalation. Biophys J 2016; 110:1255-63. [PMID: 27028636 DOI: 10.1016/j.bpj.2016.02.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 02/01/2016] [Accepted: 02/08/2016] [Indexed: 02/07/2023] Open
Abstract
DNA intercalators that have high affinity and slow kinetics are developed for potential DNA-targeted therapeutics. Although many natural intercalators contain multiple chiral subunits, only intercalators with a single chiral unit have been quantitatively probed. Dumbbell-shaped DNA threading intercalators represent the next order of structural complexity relative to simple intercalators, and can provide significant insights into the stereoselectivity of DNA-ligand intercalation. We investigated DNA threading intercalation by binuclear ruthenium complex [μ-dppzip(phen)4Ru2](4+) (Piz). Four Piz stereoisomers are defined by the chirality of the intercalating subunit (Ru(phen)2dppz) and the distal subunit (Ru(phen)2ip), respectively, each of which can be either right-handed (Δ) or left-handed (Λ). We used optical tweezers to measure single DNA molecule elongation due to threading intercalation, revealing force-dependent DNA intercalation rates and equilibrium dissociation constants. The force spectroscopy analysis provided the zero-force DNA binding affinity, the equilibrium DNA-ligand elongation Δxeq, and the dynamic DNA structural deformations during ligand association xon and dissociation xoff. We found that Piz stereoisomers exhibit over 20-fold differences in DNA binding affinity, from a Kd of 27 ± 3 nM for (Δ,Λ)-Piz to a Kd of 622 ± 55 nM for (Λ,Δ)-Piz. The striking affinity decrease is correlated with increasing Δxeq from 0.30 ± 0.02 to 0.48 ± 0.02 nm and xon from 0.25 ± 0.01 to 0.46 ± 0.02 nm, but limited xoff changes. Notably, the affinity and threading kinetics is 10-fold enhanced for right-handed intercalating subunits, and 2- to 5-fold enhanced for left-handed distal subunits. These findings demonstrate sterically dispersed transition pathways and robust DNA structural recognition of chiral intercalators, which are critical for optimizing DNA binding affinity and kinetics.
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Affiliation(s)
- Ali A Almaqwashi
- Department of Physics, Northeastern University, Boston, Massachusetts
| | - Johanna Andersson
- Department of Chemistry-BMC, Uppsala University, Uppsala, Sweden; Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Per Lincoln
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Ioulia Rouzina
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, Ohio
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Mark C Williams
- Department of Physics, Northeastern University, Boston, Massachusetts.
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Shahabadi N, Shiri F. Multispectroscopic studies on the interaction of a copper(ii) complex of ibuprofen drug with calf thymus DNA. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2016; 36:83-106. [PMID: 27835056 DOI: 10.1080/15257770.2016.1223305] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The interaction of copper(II)-ibuprofenato complex with calf thymus DNA (ct-DNA) has been explored following, UV-visible spectrophotometry, fluorescence measurement, dynamic viscosity measurements, and circular dichroism spectroscopy. In spectrophotometric studies of ct-DNA it was found that [Cu(ibp)2]2 can form a complex with double-helical DNA. The association constant of [Cu(ibp)2]2 with DNA from UV-Vis study was found to be 6.19 × 104 L mol-1. The values of Kf from fluorescence measurement clearly underscore the high affinity of [Cu(ibp)2]2 to DNA. The experimental results showed that the conformational changes in DNA helix induced by [Cu(ibp)2]2 are the reason for the fluorescence quenching of the DNA-Hoechst system. In addition, the fluorescence emission spectra of intercalated methylene blue (MB) with increasing concentrations of [Cu(ibp)2]2 represented a significant increase of MB intensity as to release MB from MB-DNA system. The results of circular dichroism (CD) suggested that copper(II)-ibuprofenato complex can change the conformation of DNA. In addition, the results of viscosity measurements suggest that copper(II)-ibuprofenato complex may bind with non-classical intercalative mode. From spectroscopic and hydrodynamic studies, it has been found that [Cu(ibp)2]2 interacts with DNA by partial intercalation mode which contains intercalation and groove properties.
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Affiliation(s)
- Nahid Shahabadi
- a Inorganic Chemistry Department , Faculty of Chemistry, Razi University , Kermanshah , Iran.,b Medical Biology Research Center (MBRC) Kermanshah University of Medical Sciences , Kermanshah , Iran
| | - Farshad Shiri
- a Inorganic Chemistry Department , Faculty of Chemistry, Razi University , Kermanshah , Iran
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Banerjee T, Banerjee S, Sett S, Ghosh S, Rakshit T, Mukhopadhyay R. Discriminating Intercalative Effects of Threading Intercalator Nogalamycin, from Classical Intercalator Daunomycin, Using Single Molecule Atomic Force Spectroscopy. PLoS One 2016; 11:e0154666. [PMID: 27183010 PMCID: PMC4868319 DOI: 10.1371/journal.pone.0154666] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 04/18/2016] [Indexed: 11/24/2022] Open
Abstract
DNA threading intercalators are a unique class of intercalating agents, albeit little biophysical information is available on their intercalative actions. Herein, the intercalative effects of nogalamycin, which is a naturally-occurring DNA threading intercalator, have been investigated by high-resolution atomic force microscopy (AFM) and spectroscopy (AFS). The results have been compared with those of the well-known chemotherapeutic drug daunomycin, which is a non-threading classical intercalator bearing structural similarity to nogalamycin. A comparative AFM assessment revealed a greater increase in DNA contour length over the entire incubation period of 48 h for nogalamycin treatment, whereas the contour length increase manifested faster in case of daunomycin. The elastic response of single DNA molecules to an externally applied force was investigated by the single molecule AFS approach. Characteristic mechanical fingerprints in the overstretching behaviour clearly distinguished the nogalamycin/daunomycin-treated dsDNA from untreated dsDNA—the former appearing less elastic than the latter, and the nogalamycin-treated DNA distinguished from the daunomycin-treated DNA—the classically intercalated dsDNA appearing the least elastic. A single molecule AFS-based discrimination of threading intercalation from the classical type is being reported for the first time.
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Affiliation(s)
- T. Banerjee
- Department of Biological Chemistry, Indian Association for the Cultivation of Science, Kolkata, 700 032, India
| | - S. Banerjee
- Department of Biological Chemistry, Indian Association for the Cultivation of Science, Kolkata, 700 032, India
| | - S. Sett
- Department of Biological Chemistry, Indian Association for the Cultivation of Science, Kolkata, 700 032, India
| | - S. Ghosh
- Department of Biological Chemistry, Indian Association for the Cultivation of Science, Kolkata, 700 032, India
| | - T. Rakshit
- Department of Biological Chemistry, Indian Association for the Cultivation of Science, Kolkata, 700 032, India
| | - R. Mukhopadhyay
- Department of Biological Chemistry, Indian Association for the Cultivation of Science, Kolkata, 700 032, India
- * E-mail:
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15
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Almaqwashi AA, Paramanathan T, Rouzina I, Williams MC. Mechanisms of small molecule-DNA interactions probed by single-molecule force spectroscopy. Nucleic Acids Res 2016; 44:3971-88. [PMID: 27085806 PMCID: PMC4872107 DOI: 10.1093/nar/gkw237] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 03/24/2016] [Indexed: 12/31/2022] Open
Abstract
There is a wide range of applications for non-covalent DNA binding ligands, and optimization of such interactions requires detailed understanding of the binding mechanisms. One important class of these ligands is that of intercalators, which bind DNA by inserting aromatic moieties between adjacent DNA base pairs. Characterizing the dynamic and equilibrium aspects of DNA-intercalator complex assembly may allow optimization of DNA binding for specific functions. Single-molecule force spectroscopy studies have recently revealed new details about the molecular mechanisms governing DNA intercalation. These studies can provide the binding kinetics and affinity as well as determining the magnitude of the double helix structural deformations during the dynamic assembly of DNA–ligand complexes. These results may in turn guide the rational design of intercalators synthesized for DNA-targeted drugs, optical probes, or integrated biological self-assembly processes. Herein, we survey the progress in experimental methods as well as the corresponding analysis framework for understanding single molecule DNA binding mechanisms. We discuss briefly minor and major groove binding ligands, and then focus on intercalators, which have been probed extensively with these methods. Conventional mono-intercalators and bis-intercalators are discussed, followed by unconventional DNA intercalation. We then consider the prospects for using these methods in optimizing conventional and unconventional DNA-intercalating small molecules.
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Affiliation(s)
- Ali A Almaqwashi
- Department of Physics, Northeastern University, Boston, MA 02115, USA
| | | | - Ioulia Rouzina
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210, USA
| | - Mark C Williams
- Department of Physics, Northeastern University, Boston, MA 02115, USA
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16
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Recatalá D, Llusar R, Galindo F, Brylev KA, Gushchin AL. Heteroleptic Phenanthroline Complexes of Trinuclear Molybdenum Clusters with Luminescent Properties. Eur J Inorg Chem 2015. [DOI: 10.1002/ejic.201403228] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- David Recatalá
- Departament de Química Física i Analítica, Universitat Jaume I, Av. Sos Baynat s/n, 12071 Castelló, Spain, http://www.grupo‐rllusar.uji.es
| | - Rosa Llusar
- Departament de Química Física i Analítica, Universitat Jaume I, Av. Sos Baynat s/n, 12071 Castelló, Spain, http://www.grupo‐rllusar.uji.es
| | - Francisco Galindo
- Departament de Química Inorgànica i Orgànica, Universitat Jaume I, Av. Sos Baynat s/n, 12071 Castelló, Spain
| | - Konstantin A. Brylev
- Nikolaev Institute of Inorganic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Artem L. Gushchin
- Departament de Química Física i Analítica, Universitat Jaume I, Av. Sos Baynat s/n, 12071 Castelló, Spain, http://www.grupo‐rllusar.uji.es
- Nikolaev Institute of Inorganic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Novosibirsk State University, 630090 Novosibirsk, Russia
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17
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Kaur N, Kaur K, Raj T, Kaur G, Singh A, Aree T, Park SJ, Kim TJ, Singh N, Jang DO. One-pot synthesis of tricyclic dihydropyrimidine derivatives and their biological evaluation. Tetrahedron 2015. [DOI: 10.1016/j.tet.2014.11.039] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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18
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Le VH, McGuire MR, Ahuja P, MacDonnell FM, Lewis EA. Thermodynamic Investigations of [(phen)2Ru(tatpp)Ru(phen)2]4+ Interactions with B-DNA. J Phys Chem B 2014; 119:65-71. [DOI: 10.1021/jp509569s] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Vu H. Le
- Department
of Chemistry, Mississippi State University, Mississippi State, Mississippi 39762, United States
| | - Matthew R. McGuire
- Department
of Chemistry, Mississippi State University, Mississippi State, Mississippi 39762, United States
| | - Pooja Ahuja
- Department
of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas 76019, United States
| | - Frederick M. MacDonnell
- Department
of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas 76019, United States
| | - Edwin A. Lewis
- Department
of Chemistry, Mississippi State University, Mississippi State, Mississippi 39762, United States
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19
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Almaqwashi AA, Paramanathan T, Lincoln P, Rouzina I, Westerlund F, Williams MC. Strong DNA deformation required for extremely slow DNA threading intercalation by a binuclear ruthenium complex. Nucleic Acids Res 2014; 42:11634-41. [PMID: 25245944 PMCID: PMC4191423 DOI: 10.1093/nar/gku859] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
DNA intercalation by threading is expected to yield high affinity and slow dissociation, properties desirable for DNA-targeted therapeutics. To measure these properties, we utilize single molecule DNA stretching to quantify both the binding affinity and the force-dependent threading intercalation kinetics of the binuclear ruthenium complex Δ,Δ-[μ‐bidppz‐(phen)4Ru2]4+ (Δ,Δ-P). We measure the DNA elongation at a range of constant stretching forces using optical tweezers, allowing direct characterization of the intercalation kinetics as well as the amount intercalated at equilibrium. Higher forces exponentially facilitate the intercalative binding, leading to a profound decrease in the binding site size that results in one ligand intercalated at almost every DNA base stack. The zero force Δ,Δ-P intercalation Kd is 44 nM, 25-fold stronger than the analogous mono-nuclear ligand (Δ-P). The force-dependent kinetics analysis reveals a mechanism that requires DNA elongation of 0.33 nm for association, relaxation to an equilibrium elongation of 0.19 nm, and an additional elongation of 0.14 nm from the equilibrium state for dissociation. In cells, a molecule with binding properties similar to Δ,Δ-P may rapidly bind DNA destabilized by enzymes during replication or transcription, but upon enzyme dissociation it is predicted to remain intercalated for several hours, thereby interfering with essential biological processes.
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Affiliation(s)
- Ali A Almaqwashi
- Department of Physics, Northeastern University, Boston, MA 02115, USA
| | - Thayaparan Paramanathan
- Department of Physics, Northeastern University, Boston, MA 02115, USA Department of Physics, Bridgewater State University, Bridgewater, MA 02324, USA
| | - Per Lincoln
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg SE-41296, Sweden
| | - Ioulia Rouzina
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Fredrik Westerlund
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg SE-41296, Sweden
| | - Mark C Williams
- Department of Physics, Northeastern University, Boston, MA 02115, USA
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20
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Zhang S, Ding Y, Wei H. Ruthenium polypyridine complexes combined with oligonucleotides for bioanalysis: a review. Molecules 2014; 19:11933-87. [PMID: 25116805 PMCID: PMC6271144 DOI: 10.3390/molecules190811933] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 07/17/2014] [Accepted: 07/28/2014] [Indexed: 02/01/2023] Open
Abstract
Ruthenium complexes are among the most interesting coordination complexes and they have attracted great attention over the past decades due to their appealing biological, catalytic, electronic and optical properties. Ruthenium complexes have found a unique niche in bioanalysis, as demonstrated by the substantial progress made in the field. In this review, the applications of ruthenium complexes coordinated with polypyridine ligands (and analogues) in bioanalysis are discussed. Three main detection methods based on electrochemistry, electrochemiluminescence, and photoluminscence are covered. The important targets, including DNA and other biologically important targets, are detected by specific biorecognition with the corresponding oligonucleotides as the biorecognition elements (i.e., DNA is probed by its complementary strand and other targets are detected by functional nucleic acids, respectively). Selected examples are provided and thoroughly discussed to highlight the substantial progress made so far. Finally, a brief summary with perspectives is included.
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Affiliation(s)
- Shuyu Zhang
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing 210093, China.
| | - Yubin Ding
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing 210093, China.
| | - Hui Wei
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing 210093, China.
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21
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Banik B, Somyajit K, Hussain A, Nagaraju G, Chakravarty AR. Carbohydrate-appended photocytotoxic (imidazophenanthroline)-oxovanadium(iv) complexes for cellular targeting and imaging. Dalton Trans 2014; 43:1321-31. [DOI: 10.1039/c3dt52087k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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22
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Gong L, Wenzel M, Meggers E. Chiral-auxiliary-mediated asymmetric synthesis of ruthenium polypyridyl complexes. Acc Chem Res 2013; 46:2635-44. [PMID: 23730834 DOI: 10.1021/ar400083u] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
An octahedral metal complex with 6 different monodentate ligands can form 15 diastereomers as pairs of enantiomers. As a result, the elaborate stereochemistry of octahedral coordination geometries provides tremendous opportunities in the fields of catalysis, the materials sciences, and the life sciences. The demand for enantiomerically pure coordination complexes for tasks related to the selective molecular recognition of biomacromolecules led us to develop synthetic methods to control the absolute stereochemistry at octahedral metal centers. A few years ago our laboratory therefore embarked on a project exploring new and general synthetic strategies for the asymmetric synthesis of inert octahedral transition metal complexes. We initially used the example of thermally inert ruthenium polypyridyl complexes and developed a family of chiral bidentate ligands, including salicyloxazolines, (mercaptophenyl)oxazolines, sulfinylphenols, N-acetylsulfinamides, a phosphinohydroxybinaphthyl, and even the amino acid proline to serve as chiral auxiliaries for asymmetric coordination chemistry. All these chiral auxiliaries strongly coordinate to ruthenium(II) in a bidentate, deprotonated fashion, allowing them to control the absolute metal-centered configuration in the course of subsequent ligand exchange reactions. Finally, we can remove them from the metal without any loss of chiral information and without leaving a chemical trace. A key feature of these chiral auxiliary ligands is their switchable binding strength. A chelate effect ensures that the chiral ligands coordinate very tightly to the metal center, placing their carbon-based, sulfur-based, or axial chirality in a well-defined position close to the metal center to efficiently establish the absolute metal-centered configuration. At the same time a coordinating phenolate, carboximidate, carboxylate, or thiophenolate moiety makes the coordination reversible by weakening the binding strength through protonation or methylation. Following this strategy, we synthesized a large number of homoleptic, bis-heteroleptic, and tris-heteroleptic ruthenium polypyridyl complexes in an asymmetric fashion with enantiomeric ratios that routinely reached or exceeded 96:4. Our approach should serve as a blueprint for the asymmetric synthesis of different classes of ruthenium complexes and chiral coordination complexes of other metals.
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Affiliation(s)
- Lei Gong
- Fujian Provincial Key Laboratory of Chemical Biology, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, People’s Republic of China
| | - Marianne Wenzel
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Strasse, 35043 Marburg, Germany
| | - Eric Meggers
- Fujian Provincial Key Laboratory of Chemical Biology, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, People’s Republic of China
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Strasse, 35043 Marburg, Germany
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23
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Wilson T, Costa PJ, Félix V, Williamson MP, Thomas JA. Structural studies on dinuclear ruthenium(II) complexes that bind diastereoselectively to an antiparallel folded human telomere sequence. J Med Chem 2013; 56:8674-83. [PMID: 24088028 PMCID: PMC3835060 DOI: 10.1021/jm401119b] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
We report DNA binding studies of
the dinuclear ruthenium ligand
[{Ru(phen)2}2tpphz]4+ in enantiomerically
pure forms. As expected from previous studies of related complexes,
both isomers bind with similar affinity to B-DNA and have enhanced
luminescence. However, when tested against the G-quadruplex from human
telomeres (which we show to form an antiparallel basket structure
with a diagonal loop across one end), the ΛΛ isomer binds
approximately 40 times more tightly than the ΔΔ, with
a stronger luminescence. NMR studies show that the complex binds at
both ends of the quadruplex. Modeling studies, based on experimentally
derived restraints obtained for the closely related [{Ru(bipy)2}2tpphz]4+, show that the ΛΛ
isomer fits neatly under the diagonal loop, whereas the ΔΔ
isomer is unable to bind here and binds at the lateral loop end. Molecular
dynamics simulations show that the ΔΔ isomer is prevented
from binding under the diagonal loop by the rigidity of the loop.
We thus present a novel enantioselective binding substrate for antiparallel
basket G-quadruplexes, with features that make it a useful tool for
quadruplex studies.
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Affiliation(s)
- Tom Wilson
- Department of Chemistry, University of Sheffield , Dainton Building, Brook Hill, Sheffield S3 7HF, U.K
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24
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Johansson JR, Wang Y, Eng MP, Kann N, Lincoln P, Andersson J. Bridging ligand length controls at selectivity and enantioselectivity of binuclear ruthenium threading intercalators. Chemistry 2013; 19:6246-56. [PMID: 23576496 DOI: 10.1002/chem.201300483] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Indexed: 11/09/2022]
Abstract
The slow dissociation of DNA threading intercalators makes them interesting as model compounds in the search for new DNA targeting drugs, as there appears to be a correlation between slow dissociation and biological activity. Thus, it would be of great value to understand the mechanisms controlling threading intercalation, and for this purpose we have investigated how the length of the bridging ligand of binuclear ruthenium threading intercalators affects their DNA binding properties. We have synthesised a new binuclear ruthenium threading intercalator with slower dissociation kinetics from ct-DNA than has ever been observed for any ruthenium complex with any type of DNA, a property that we attribute to the increased distance between the ruthenium centres of the new complex. By comparison with previously studied ruthenium complexes, we further conclude that elongation of the bridging ligand reduces the sensitivity of the threading interaction to DNA flexibility, resulting in a decreased AT selectivity for the new complex. We also find that the length of the bridging ligand affects the enantioselectivity with increasing preference for the ΔΔ enantiomer as the bridging ligand becomes longer.
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Affiliation(s)
- Johan R Johansson
- Department of Chemical and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
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