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Melidis L, Hill HJ, Coltman NJ, Davies SP, Winczura K, Chauhan T, Craig JS, Garai A, Hooper CAJ, Egan RT, McKeating JA, Hodges NJ, Stamataki Z, Grzechnik P, Hannon MJ. Supramolecular Cylinders Target Bulge Structures in the 5' UTR of the RNA Genome of SARS-CoV-2 and Inhibit Viral Replication. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 133:18292-18299. [PMID: 38505190 PMCID: PMC10947172 DOI: 10.1002/ange.202104179] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Indexed: 01/09/2023]
Abstract
The untranslated regions (UTRs) of viral genomes contain a variety of conserved yet dynamic structures crucial for viral replication, providing drug targets for the development of broad spectrum anti-virals. We combine in vitro RNA analysis with molecular dynamics simulations to build the first 3D models of the structure and dynamics of key regions of the 5' UTR of the SARS-CoV-2 genome. Furthermore, we determine the binding of metallo-supramolecular helicates (cylinders) to this RNA structure. These nano-size agents are uniquely able to thread through RNA junctions and we identify their binding to a 3-base bulge and the central cross 4-way junction located in stem loop 5. Finally, we show these RNA-binding cylinders suppress SARS-CoV-2 replication, highlighting their potential as novel anti-viral agents.
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Affiliation(s)
- Lazaros Melidis
- Physical Sciences for Health CentreUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Harriet J. Hill
- Institute of Immunology and ImmunotherapyUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | | | - Scott P. Davies
- Institute of Immunology and ImmunotherapyUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Kinga Winczura
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Tasha Chauhan
- Physical Sciences for Health CentreUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - James S. Craig
- Physical Sciences for Health CentreUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Aditya Garai
- School of ChemistryUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | | | - Ross T. Egan
- School of ChemistryUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Jane A. McKeating
- Nuffield Department of Medicine & Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI)Oxford UniversityOxfordOX3 7BNUK
| | - Nikolas J. Hodges
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Zania Stamataki
- Institute of Immunology and ImmunotherapyUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Pawel Grzechnik
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Michael J. Hannon
- Physical Sciences for Health CentreUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
- School of ChemistryUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
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2
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Melidis L, Hill HJ, Coltman NJ, Davies SP, Winczura K, Chauhan T, Craig JS, Garai A, Hooper CAJ, Egan RT, McKeating JA, Hodges NJ, Stamataki Z, Grzechnik P, Hannon MJ. Supramolecular Cylinders Target Bulge Structures in the 5' UTR of the RNA Genome of SARS-CoV-2 and Inhibit Viral Replication*. Angew Chem Int Ed Engl 2021; 60:18144-18151. [PMID: 33915014 PMCID: PMC8222931 DOI: 10.1002/anie.202104179] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Indexed: 12/13/2022]
Abstract
The untranslated regions (UTRs) of viral genomes contain a variety of conserved yet dynamic structures crucial for viral replication, providing drug targets for the development of broad spectrum anti-virals. We combine in vitro RNA analysis with molecular dynamics simulations to build the first 3D models of the structure and dynamics of key regions of the 5' UTR of the SARS-CoV-2 genome. Furthermore, we determine the binding of metallo-supramolecular helicates (cylinders) to this RNA structure. These nano-size agents are uniquely able to thread through RNA junctions and we identify their binding to a 3-base bulge and the central cross 4-way junction located in stem loop 5. Finally, we show these RNA-binding cylinders suppress SARS-CoV-2 replication, highlighting their potential as novel anti-viral agents.
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Affiliation(s)
- Lazaros Melidis
- Physical Sciences for Health CentreUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Harriet J. Hill
- Institute of Immunology and ImmunotherapyUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | | | - Scott P. Davies
- Institute of Immunology and ImmunotherapyUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Kinga Winczura
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Tasha Chauhan
- Physical Sciences for Health CentreUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - James S. Craig
- Physical Sciences for Health CentreUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Aditya Garai
- School of ChemistryUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | | | - Ross T. Egan
- School of ChemistryUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Jane A. McKeating
- Nuffield Department of Medicine & Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI)Oxford UniversityOxfordOX3 7BNUK
| | - Nikolas J. Hodges
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Zania Stamataki
- Institute of Immunology and ImmunotherapyUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Pawel Grzechnik
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Michael J. Hannon
- Physical Sciences for Health CentreUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
- School of ChemistryUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
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3
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van Rixel VHS, Busemann A, Wissingh MF, Hopkins SL, Siewert B, van de Griend C, Siegler MA, Marzo T, Papi F, Ferraroni M, Gratteri P, Bazzicalupi C, Messori L, Bonnet S. Induction of a Four-Way Junction Structure in the DNA Palindromic Hexanucleotide 5'-d(CGTACG)-3' by a Mononuclear Platinum Complex. Angew Chem Int Ed Engl 2019; 58:9378-9382. [PMID: 31046177 PMCID: PMC6618160 DOI: 10.1002/anie.201814532] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Indexed: 12/22/2022]
Abstract
Four-way junctions (4WJs) are supramolecular DNA assemblies comprising four interacting DNA strands that in biology are involved in DNA-damage repair. In this study, a new mononuclear platinum(II) complex 1 was prepared that is capable of driving the crystallization of the DNA oligomer 5'-d(CGTACG)-3' specifically into a 4WJ-like motif. In the crystal structure of the 1-CGTACG adduct, the distorted-square-planar platinum complex binds to the core of the 4WJ-like motif through π-π stacking and hydrogen bonding, without forming any platinum-nitrogen coordination bonds. Our observations suggest that the specific molecular properties of the metal complex are crucially responsible for triggering the selective assembly of this peculiar DNA superstructure.
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Affiliation(s)
- Vincent H. S. van Rixel
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 55, PO Box 95022333CCLeidenThe Netherlands
| | - Anja Busemann
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 55, PO Box 95022333CCLeidenThe Netherlands
| | - Mathijs F. Wissingh
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 55, PO Box 95022333CCLeidenThe Netherlands
| | - Samantha L. Hopkins
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 55, PO Box 95022333CCLeidenThe Netherlands
| | - Bianka Siewert
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 55, PO Box 95022333CCLeidenThe Netherlands
| | - Corjan van de Griend
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 55, PO Box 95022333CCLeidenThe Netherlands
| | | | - Tiziano Marzo
- Department of PharmacyUniversity of PisaVia Bonanno Pisano 656126PisaItaly
| | - Francesco Papi
- Department of ChemistryUniversity of FlorenceVia della Lastruccia 350019Sesto Fiorentino (FI)Italy
| | - Marta Ferraroni
- Department of ChemistryUniversity of FlorenceVia della Lastruccia 350019Sesto Fiorentino (FI)Italy
| | - Paola Gratteri
- Department NEUROFARBA—Pharmaceutical and Nutraceutical sectionLaboratory of Molecular Modeling Cheminformatics and QSARUniversity of FlorenceVia Ugo Schiff 650019Sesto Fiorentino (FI)Italy
| | - Carla Bazzicalupi
- Department of ChemistryUniversity of FlorenceVia della Lastruccia 350019Sesto Fiorentino (FI)Italy
| | - Luigi Messori
- Department of Chemistry “Ugo Schiff”University of FlorenceItaly
| | - Sylvestre Bonnet
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 55, PO Box 95022333CCLeidenThe Netherlands
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van Rixel VHS, Busemann A, Wissingh MF, Hopkins SL, Siewert B, van de Griend C, Siegler MA, Marzo T, Papi F, Ferraroni M, Gratteri P, Bazzicalupi C, Messori L, Bonnet S. Induction of a Four‐Way Junction Structure in the DNA Palindromic Hexanucleotide 5′‐d(CGTACG)‐3′ by a Mononuclear Platinum Complex. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201814532] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Vincent H. S. van Rixel
- Leiden Institute of ChemistryLeiden University Einsteinweg 55, PO Box 9502 2333CC Leiden The Netherlands
| | - Anja Busemann
- Leiden Institute of ChemistryLeiden University Einsteinweg 55, PO Box 9502 2333CC Leiden The Netherlands
| | - Mathijs F. Wissingh
- Leiden Institute of ChemistryLeiden University Einsteinweg 55, PO Box 9502 2333CC Leiden The Netherlands
| | - Samantha L. Hopkins
- Leiden Institute of ChemistryLeiden University Einsteinweg 55, PO Box 9502 2333CC Leiden The Netherlands
| | - Bianka Siewert
- Leiden Institute of ChemistryLeiden University Einsteinweg 55, PO Box 9502 2333CC Leiden The Netherlands
| | - Corjan van de Griend
- Leiden Institute of ChemistryLeiden University Einsteinweg 55, PO Box 9502 2333CC Leiden The Netherlands
| | | | - Tiziano Marzo
- Department of PharmacyUniversity of Pisa Via Bonanno Pisano 6 56126 Pisa Italy
| | - Francesco Papi
- Department of ChemistryUniversity of Florence Via della Lastruccia 3 50019 Sesto Fiorentino (FI) Italy
| | - Marta Ferraroni
- Department of ChemistryUniversity of Florence Via della Lastruccia 3 50019 Sesto Fiorentino (FI) Italy
| | - Paola Gratteri
- Department NEUROFARBA—Pharmaceutical and Nutraceutical sectionLaboratory of Molecular Modeling Cheminformatics and QSARUniversity of Florence Via Ugo Schiff 6 50019 Sesto Fiorentino (FI) Italy
| | - Carla Bazzicalupi
- Department of ChemistryUniversity of Florence Via della Lastruccia 3 50019 Sesto Fiorentino (FI) Italy
| | - Luigi Messori
- Department of Chemistry “Ugo Schiff”University of Florence Italy
| | - Sylvestre Bonnet
- Leiden Institute of ChemistryLeiden University Einsteinweg 55, PO Box 9502 2333CC Leiden The Netherlands
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5
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Mandal PK, Baptiste B, Langlois d'Estaintot B, Kauffmann B, Huc I. Multivalent Interactions between an Aromatic Helical Foldamer and a DNA G-Quadruplex in the Solid State. Chembiochem 2016; 17:1911-1914. [DOI: 10.1002/cbic.201600281] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Indexed: 01/20/2023]
Affiliation(s)
- Pradeep K. Mandal
- University of Bordeaux; CBMN; UMR 5248); Institut Européen de Chimie et Biologie; 2 rue Escarpit 33600 Pessac France
- CNRS; CBMN; UMR 5248); 2 rue Escarpit 33600 Pessac France
- Bordeaux Institut National Polytechnique; CBMN; UMR 5248); 2 rue Escarpit 33600 Pessac France
| | - Benoît Baptiste
- University of Bordeaux; CBMN; UMR 5248); Institut Européen de Chimie et Biologie; 2 rue Escarpit 33600 Pessac France
- CNRS; CBMN; UMR 5248); 2 rue Escarpit 33600 Pessac France
- Bordeaux Institut National Polytechnique; CBMN; UMR 5248); 2 rue Escarpit 33600 Pessac France
| | - Béatrice Langlois d'Estaintot
- University of Bordeaux; CBMN; UMR 5248); Institut Européen de Chimie et Biologie; 2 rue Escarpit 33600 Pessac France
- CNRS; CBMN; UMR 5248); 2 rue Escarpit 33600 Pessac France
- Bordeaux Institut National Polytechnique; CBMN; UMR 5248); 2 rue Escarpit 33600 Pessac France
| | - Brice Kauffmann
- University of Bordeaux; IECB; UMS 3033); Institut Européen de Chimie et Biologie; 2 rue Escarpit 33600 Pessac France
- CNRS; IECB; UMS 3033); 2 rue Escarpit 33600 Pessac France
- INSERM; IECB; US001); 2 rue Escarpit 33600 Pessac France
| | - Ivan Huc
- University of Bordeaux; CBMN; UMR 5248); Institut Européen de Chimie et Biologie; 2 rue Escarpit 33600 Pessac France
- CNRS; CBMN; UMR 5248); 2 rue Escarpit 33600 Pessac France
- Bordeaux Institut National Polytechnique; CBMN; UMR 5248); 2 rue Escarpit 33600 Pessac France
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6
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Mishra A, Chang Lee S, Kaushik N, Cook TR, Choi EH, Kumar Kaushik N, Stang PJ, Chi KW. Self-assembled supramolecular hetero-bimetallacycles for anticancer potency by intracellular release. Chemistry 2014; 20:14410-20. [PMID: 25209962 PMCID: PMC5796531 DOI: 10.1002/chem.201403372] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2014] [Indexed: 11/09/2022]
Abstract
Two new tetracationic hetero-bimetallacycles, compounds 4 and 5, have been constructed from an N,N'-bis(4-(pyridin-4-ylethynyl)phenyl)pyridine-2,6-dicarboxamide ligand (1), and cis-blocked complexes [M(dppf)(OTf)2 ] (dppf=1,1'-bis(diphenylphosphino)ferrocene; OTf=trifluoromethanesulfonate; M=Pd (2), Pt (3)) in CH3 NO2 /CH2 Cl2 (1:1) solvent. Both complexes were isolated with adequate yields as triflate salts and were then characterized using (1) H, (13) C, and (31) P NMR spectroscopy, elemental analysis, UV/Vis spectroscopy, and high-resolution electrospray mass spectrometry (HR-ESMS). The molecular structure of 4 was determined by molecular mechanics force-field calculations. The cytotoxic effect of both new complexes were analyzed against T98G (brain tumor), KB (head and neck cancer), SNU-80 (thyroid cancer), and HEK-293 non-malignant cell lines. The cytotoxicity of complexes 4 and 5 were found to be considerably more effective against cancer cells than reference drug cisplatin. Annexin-V/PI staining, caspase-3/7 activity, and the reduction in mitochondrial membrane potential justify a significant level of apoptosis in complex-treated cells.
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Affiliation(s)
- Anurag Mishra
- Department of Chemistry, University of Ulsan, Ulsan 680-749 (Republic of Korea)
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7
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Boer DR, Wu L, Lincoln P, Coll M. Thread Insertion of a Bis(dipyridophenazine) Diruthenium Complex into the DNA Double Helix by the Extrusion of AT Base Pairs and Cross-Linking of DNA Duplexes. Angew Chem Int Ed Engl 2014; 53:1949-52. [DOI: 10.1002/anie.201308070] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 11/15/2013] [Indexed: 11/07/2022]
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8
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Boer DR, Wu L, Lincoln P, Coll M. Thread Insertion of a Bis(dipyridophenazine) Diruthenium Complex into the DNA Double Helix by the Extrusion of AT Base Pairs and Cross-Linking of DNA Duplexes. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201308070] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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9
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Cámara V, Masciocchi N, Gil-Rubio J, Vicente J. Triple Helicates with Golden Strands: Self-Assembly of M2Au6Complexes from Gold(I) Metallaligands and Iron(II), Cobalt(II) or Zinc(II) Cations. Chemistry 2013; 20:1389-402. [DOI: 10.1002/chem.201303744] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Indexed: 11/05/2022]
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10
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Phongtongpasuk S, Paulus S, Schnabl J, Sigel RKO, Spingler B, Hannon MJ, Freisinger E. Binding of a Designed Anti-Cancer Drug to the Central Cavity of an RNA Three-Way Junction. Angew Chem Int Ed Engl 2013; 52:11513-6. [DOI: 10.1002/anie.201305079] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Indexed: 11/08/2022]
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11
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Phongtongpasuk S, Paulus S, Schnabl J, Sigel RKO, Spingler B, Hannon MJ, Freisinger E. Binding of a Designed Anti-Cancer Drug to the Central Cavity of an RNA Three-Way Junction. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201305079] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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12
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Stefan L, Bertrand B, Richard P, Le Gendre P, Denat F, Picquet M, Monchaud D. Assessing the Differential Affinity of Small Molecules for Noncanonical DNA Structures. Chembiochem 2012; 13:1905-12. [DOI: 10.1002/cbic.201200396] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Indexed: 01/19/2023]
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13
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Terenzi A, Ducani C, Blanco V, Zerzankova L, Westendorf AF, Peinador C, Quintela JM, Bednarski PJ, Barone G, Hannon MJ. DNA binding studies and cytotoxicity of a dinuclear PtII diazapyrenium-based metallo-supramolecular rectangular box. Chemistry 2012; 18:10983-90. [PMID: 22806942 DOI: 10.1002/chem.201201519] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Indexed: 11/08/2022]
Abstract
The interaction with native DNA of a 2,7-diazapyrenium-based ligand 1 and its Pt(II) rectangular metallacycle 2 is explored through circular and linear dichroism and fluorescence spectroscopies. The metal-free ligand 1 binds through intercalation, with a binding constant of approximately 5×10(5) M(-1), whereas the metallacycle 2 binds and bends the DNA with a binding constant of 7×10(6) M(-1). PCR assays show that metallo-supramolecular box 2 interferes with DNA transactions in vitro whereas the intercalator 1 does not. The metallacycle is active against four human cancer cell lines, with IC(50) values ranging between 3.1 and 19.2 μM and shows similar levels of efficacy, but a different spectrum of activity, to cisplatin.
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Affiliation(s)
- Alessio Terenzi
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, UK
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14
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Feng L, Zhao C, Xiao Y, Wu L, Ren J, Qu X. Electrochemical DNA three-way junction based sensor for distinguishing chiral metallo-supramolecular complexes. Chem Commun (Camb) 2012; 48:6900-2. [DOI: 10.1039/c2cc32496b] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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15
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Ducani C, Leczkowska A, Hodges NJ, Hannon MJ. Noncovalent DNA-Binding Metallo-Supramolecular Cylinders Prevent DNA Transactions in vitro. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201004471] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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16
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Ducani C, Leczkowska A, Hodges NJ, Hannon MJ. Noncovalent DNA-Binding Metallo-Supramolecular Cylinders Prevent DNA Transactions in vitro. Angew Chem Int Ed Engl 2010; 49:8942-5. [DOI: 10.1002/anie.201004471] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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