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Pipier A, Chetot T, Kalamatianou A, Martin N, Caroff M, Britton S, Chéron N, Trantírek L, Granzhan A, Monchaud D. Structural Optimization of Azacryptands for Targeting Three-Way DNA Junctions. Angew Chem Int Ed Engl 2024; 63:e202409780. [PMID: 38873877 DOI: 10.1002/anie.202409780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 06/11/2024] [Accepted: 06/14/2024] [Indexed: 06/15/2024]
Abstract
Transient melting of the duplex-DNA (B-DNA) during DNA transactions allows repeated sequences to fold into non-B-DNA structures, including DNA junctions and G-quadruplexes. These noncanonical structures can act as impediments to DNA polymerase progression along the duplex, thereby triggering DNA damage and ultimately jeopardizing genomic stability. Their stabilization by ad hoc ligands is currently being explored as a putative anticancer strategy since it might represent an efficient way to inflict toxic DNA damage specifically to rapidly dividing cancer cells. The relevance of this strategy is only emerging for three-way DNA junctions (TWJs) and, to date, no molecule has been recognized as a reference TWJ ligand, featuring both high affinity and selectivity. Herein, we characterize such reference ligands through a combination of in vitro techniques comprising affinity and selectivity assays (competitive FRET-melting and TWJ Screen assays), functional tests (qPCR and Taq stop assays) and structural analyses (molecular dynamics and NMR investigations). We identify novel azacryptands TrisNP-amphi and TrisNP-ana as the most promising ligands, interacting with TWJs with high affinity and selectivity. These ligands represent new molecular tools to investigate the cellular roles of TWJs and explore how they can be exploited in innovative anticancer therapies.
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Affiliation(s)
- Angélique Pipier
- Institut de Chimie Moléculaire, ICMUB CNRS UMR6302, 9, Avenue Alain Savary, 21078, Dijon, France
| | - Titouan Chetot
- Chemistry and Modelling for the Biology of Cancer (CMBC), CNRS UMR9187, INSERM U1196, Institut Curie, Université Paris Saclay, 91405, Orsay, France
| | - Apollonia Kalamatianou
- Chemistry and Modelling for the Biology of Cancer (CMBC), CNRS UMR9187, INSERM U1196, Institut Curie, Université Paris Saclay, 91405, Orsay, France
| | - Nicolas Martin
- Chemistry and Modelling for the Biology of Cancer (CMBC), CNRS UMR9187, INSERM U1196, Institut Curie, Université Paris Saclay, 91405, Orsay, France
| | - Maëlle Caroff
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
| | - Sébastien Britton
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
| | - Nicolas Chéron
- PASTEUR, Département de chimie, École Normale Supérieure (ENS), PSL University, Sorbonne Université, CNRS UMR8640, 75005, Paris, France
| | - Lukáš Trantírek
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic
| | - Anton Granzhan
- Chemistry and Modelling for the Biology of Cancer (CMBC), CNRS UMR9187, INSERM U1196, Institut Curie, Université Paris Saclay, 91405, Orsay, France
| | - David Monchaud
- Institut de Chimie Moléculaire, ICMUB CNRS UMR6302, 9, Avenue Alain Savary, 21078, Dijon, France
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2
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Malina J, Crowley JD, Brabec V. Interaction of dinuclear Co(III) cylinders with higher-order DNA structures. Chem Biol Interact 2024; 395:111031. [PMID: 38703805 DOI: 10.1016/j.cbi.2024.111031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Revised: 04/20/2024] [Accepted: 05/01/2024] [Indexed: 05/06/2024]
Abstract
Alternative DNA structures play critical roles in fundamental biological processes linked to human diseases. Thus, targeting and stabilizing these structures by specific ligands could affect the progression of cancer and other diseases. Here, we describe, using methods of molecular biophysics, the interactions of two oxidatively locked [Co2L3]6+ cylinders, rac-2 and meso-1, with diverse alternative DNA structures, such as junctions, G quadruplexes, and bulges. This study was motivated by earlier results demonstrating that both Co(III) cylinders exhibit potent and selective activity against cancer cells, accumulate in the nucleus of cancer cells, and prove to be efficient DNA binders. The results show that the bigger cylinder rac-2 stabilizes all DNA structures, while the smaller cylinder meso-1 stabilizes just the Y-shaped three-way junctions. Collectively, the results of this study suggest that the stabilization of alternative DNA structures by Co(III) cylinders investigated in this work might contribute to the mechanism of their biological activity.
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Affiliation(s)
- Jaroslav Malina
- Czech Academy of Sciences, Institute of Biophysics, CZ-61200, Brno, Czech Republic
| | - James D Crowley
- Department of Chemistry, University of Otago, Dunedin, 9016, Otago, New Zealand
| | - Viktor Brabec
- Czech Academy of Sciences, Institute of Biophysics, CZ-61200, Brno, Czech Republic; Department of Biophysics, Faculty of Science, Palacky University, CZ-78371, Olomouc, Czech Republic.
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3
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Podolski-Renić A, Čipak Gašparović A, Valente A, López Ó, Bormio Nunes JH, Kowol CR, Heffeter P, Filipović NR. Schiff bases and their metal complexes to target and overcome (multidrug) resistance in cancer. Eur J Med Chem 2024; 270:116363. [PMID: 38593587 DOI: 10.1016/j.ejmech.2024.116363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 03/15/2024] [Accepted: 03/25/2024] [Indexed: 04/11/2024]
Abstract
Overcoming multidrug resistance (MDR) is one of the major challenges in cancer therapy. In this respect, Schiff base-related compounds (bearing a R1R2CNR3 bond) gained high interest during the past decades. Schiff bases are considered privileged ligands for various reasons, including the easiness of their preparation and the possibility to form complexes with almost all transition metal ions. Schiff bases and their metal complexes exhibit many types of biological activities and are used for the treatment and diagnosis of various diseases. Until now, 13 Schiff bases have been investigated in clinical trials for cancer treatment and hypoxia imaging. This review represents the first collection of Schiff bases and their complexes which demonstrated MDR-reversal activity. The areas of drug resistance covered in this article involve: 1) Modulation of ABC transporter function, 2) Targeting lysosomal ABCB1 overexpression, 3) Circumvention of ABC transporter-mediated drug efflux by alternative routes of drug uptake, 4) Selective activity against MDR cancer models (collateral sensitivity), 5) Targeting GSH-detoxifying systems, 6) Overcoming apoptosis resistance by inducing necrosis and paraptosis, 7) Reactivation of mutated p53, 8) Restoration of sensitivity to DNA-damaging anticancer therapy, and 9) Overcoming drug resistance through modulation of the immune system. Through this approach, we would like to draw attention to Schiff bases and their metal complexes representing highly interesting anticancer drug candidates with the ability to overcome MDR.
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Affiliation(s)
- Ana Podolski-Renić
- Department of Neurobiology, Institute for Biological Research "Siniša Stanković" - National Institute of Republic of Serbia, University of Belgrade, Serbia
| | | | - Andreia Valente
- Centro de Química Estrutural and Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
| | - Óscar López
- Departamento de Química Organica, Facultad de Química, Universidad de Sevilla, Sevilla, Spain
| | - Julia H Bormio Nunes
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria; Center for Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Christian R Kowol
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Petra Heffeter
- Center for Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria.
| | - Nenad R Filipović
- Department of Chemistry and Biochemistry, University of Belgrade, Belgrade, Serbia.
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4
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Alcalde-Ordóñez A, Barreiro-Piñeiro N, McGorman B, Gómez-González J, Bouzada D, Rivadulla F, Vázquez ME, Kellett A, Martínez-Costas J, López MV. A copper(ii) peptide helicate selectively cleaves DNA replication foci in mammalian cells. Chem Sci 2023; 14:14082-14091. [PMID: 38098723 PMCID: PMC10718067 DOI: 10.1039/d3sc03303a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 10/25/2023] [Indexed: 12/17/2023] Open
Abstract
The use of copper-based artificial nucleases as potential anticancer agents has been hampered by their poor selectivity in the oxidative DNA cleavage process. An alternative strategy to solve this problem is to design systems capable of selectively damaging noncanonical DNA structures that play crucial roles in the cell cycle. We designed an oligocationic CuII peptide helicate that selectively binds and cleaves DNA three-way junctions (3WJs) and induces oxidative DNA damage via a ROS-mediated pathway both in vitro and in cellulo, specifically at DNA replication foci of the cell nucleus, where this DNA structure is transiently generated. To our knowledge, this is the first example of a targeted chemical nuclease that can discriminate with high selectivity 3WJs from other forms of DNA both in vitro and in mammalian cells. Since the DNA replication process is deregulated in cancer cells, this approach may pave the way for the development of a new class of anticancer agents based on copper-based artificial nucleases.
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Affiliation(s)
- Ana Alcalde-Ordóñez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela 15782 Santiago de Compostela Spain
| | - Natalia Barreiro-Piñeiro
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Bioquímica e Bioloxía Molecular, Universidade de Santiago de Compostela 15782 Santiago de Compostela Spain
| | - Bríonna McGorman
- SSPC, The SFI Research Centre for Pharmaceuticals, School of Chemical Sciences, Dublin City University Glasnevin Dublin 9 Ireland
| | - Jacobo Gómez-González
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela 15782 Santiago de Compostela Spain
| | - David Bouzada
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela 15782 Santiago de Compostela Spain
| | - Francisco Rivadulla
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Física, Universidade de Santiago de Compostela 15782 Santiago de Compostela Spain
| | - M Eugenio Vázquez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela 15782 Santiago de Compostela Spain
| | - Andrew Kellett
- SSPC, The SFI Research Centre for Pharmaceuticals, School of Chemical Sciences, Dublin City University Glasnevin Dublin 9 Ireland
| | - José Martínez-Costas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Bioquímica e Bioloxía Molecular, Universidade de Santiago de Compostela 15782 Santiago de Compostela Spain
| | - Miguel Vázquez López
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Inorgánica, Universidade de Santiago de Compostela 15782 Santiago de Compostela Spain
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5
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McGorman B, Poole S, López MV, Kellett A. Analysis of non-canonical three- and four-way DNA junctions. Methods 2023; 219:30-38. [PMID: 37690737 DOI: 10.1016/j.ymeth.2023.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 09/01/2023] [Accepted: 09/05/2023] [Indexed: 09/12/2023] Open
Abstract
The development of compounds that can selectively bind with non-canonical DNA structures has expanded in recent years. Junction DNA, including three-way junctions (3WJs) and four-way Holliday junctions (HJs), offer an intriguing target for developmental therapeutics as both 3WJs and HJs are involved in DNA replication and repair processes. However, there are a limited number of assays available for the analysis of junction DNA binding. Here, we describe the design and execution of multiplex fluorescent polyacrylamide gel electrophoresis (PAGE) and microscale thermophoresis (MST) assays that enable evaluation of junction-binding compounds. Two well characterised junction-binding compounds-a C6 linked bis-acridine ligand and an iron(II)-bound peptide helicate, which recognise HJs and 3WJs, respectively-were employed as probes for both MST and PAGE experiments. The multiplex PAGE assay expands beyond previously reported fluorescent PAGE as it uses four individual fluorophores that can be combined to visualise single-strands, pseudo-duplexes, and junction DNA present during 3WJ and HJ formation. The use of MST to identify the binding affinity of junction binding agents is, to our knowledge, first reported example of this technique. The combined use of PAGE and MST provides complementary results for the visualisation of 3WJ and HJ formation and the direct binding affinity (Kd and EC50) of these agents. These assays can be used to aid the discovery and design of new therapeutics targeting non-canonical nucleic acid structures.
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Affiliation(s)
- Bríonna McGorman
- SSPC, the Science Foundation Ireland Research Centre for Pharmaceuticals, School of Chemical Sciences, Dublin City University Glasnevin, Dublin 9, Ireland
| | - Simon Poole
- SSPC, the Science Foundation Ireland Research Centre for Pharmaceuticals, School of Chemical Sciences, Dublin City University Glasnevin, Dublin 9, Ireland
| | - Miguel Vázquez López
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS) and Departamento de Química Inorgánica. Universidade de Santiago de Compostela., Rúa Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
| | - Andrew Kellett
- SSPC, the Science Foundation Ireland Research Centre for Pharmaceuticals, School of Chemical Sciences, Dublin City University Glasnevin, Dublin 9, Ireland.
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6
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Malina J, Kostrhunova H, Scott P, Brabec V. Metallohelices stabilize DNA three-way junctions and induce DNA damage in cancer cells. Nucleic Acids Res 2023; 51:7174-7183. [PMID: 37351627 PMCID: PMC10415117 DOI: 10.1093/nar/gkad536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/31/2023] [Accepted: 06/08/2023] [Indexed: 06/24/2023] Open
Abstract
DNA three-way junctions (3WJ) represent one of the simplest supramolecular DNA structures arising as intermediates in homologous recombination in the absence of replication. They are also formed transiently during DNA replication. Here we examine the ability of Fe(II)-based metallohelices to act as DNA 3WJ binders and induce DNA damage in cells. We investigated the interaction of eight pairs of enantiomerically pure Fe(II) metallohelices with four different DNA junctions using biophysical and molecular biology methods. The results show that the metallohelices stabilize all types of tested DNA junctions, with the highest selectivity for the Y-shaped 3WJ and minimal selectivity for the 4WJ. The potential of the best stabilizer of DNA junctions and, at the same time, the most selective 3WJ binder investigated in this work to induce DNA damage was determined in human colon cancer HCT116 cells. These metallohelices proved to be efficient in killing cancer cells and triggering DNA damage that could yield therapeutic benefits.
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Affiliation(s)
- Jaroslav Malina
- Czech Academy of Sciences, Institute of Biophysics, Brno, CZ-61200, Czech Republic
| | - Hana Kostrhunova
- Czech Academy of Sciences, Institute of Biophysics, Brno, CZ-61200, Czech Republic
| | - Peter Scott
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| | - Viktor Brabec
- Czech Academy of Sciences, Institute of Biophysics, Brno, CZ-61200, Czech Republic
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7
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Craig JS, Melidis L, Williams HD, Dettmer SJ, Heidecker AA, Altmann PJ, Guan S, Campbell C, Browning DF, Sigel RKO, Johannsen S, Egan RT, Aikman B, Casini A, Pöthig A, Hannon MJ. Organometallic Pillarplexes That Bind DNA 4-Way Holliday Junctions and Forks. J Am Chem Soc 2023. [PMID: 37318835 DOI: 10.1021/jacs.3c00118] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Holliday 4-way junctions are key to important biological DNA processes (insertion, recombination, and repair) and are dynamic structures that adopt either open or closed conformations, the open conformation being the biologically active form. Tetracationic metallo-supramolecular pillarplexes display aryl faces about a cylindrical core, an ideal structure to interact with open DNA junction cavities. Combining experimental studies and MD simulations, we show that an Au pillarplex can bind DNA 4-way (Holliday) junctions in their open form, a binding mode not accessed by synthetic agents before. Pillarplexes can bind 3-way junctions too, but their large size leads them to open up and expand that junction, disrupting the base pairing, which manifests in an increased hydrodynamic size and lower junction thermal stability. At high loading, they rearrange both 4-way and 3-way junctions into Y-shaped forks to increase the available junction-like binding sites. Isostructural Ag pillarplexes show similar DNA junction binding behavior but lower solution stability. This pillarplex binding contrasts with (but complements) that of metallo-supramolecular cylinders, which prefer 3-way junctions and can rearrange 4-way junctions into 3-way junction structures. The pillarplexes' ability to bind open 4-way junctions creates exciting possibilities to modulate and switch such structures in biology, as well as in synthetic nucleic acid nanostructures. In human cells, the pillarplexes do reach the nucleus, with antiproliferative activity at levels similar to those of cisplatin. The findings provide a new roadmap for targeting higher-order junction structures using a metallo-supramolecular approach, as well as expanding the toolbox available to design bioactive junction binders into organometallic chemistry.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Roland K O Sigel
- Department of Chemistry, University of Zürich, Winterthurerstr. 190, 8057 Zürich, Switzerland
| | - Silke Johannsen
- Department of Chemistry, University of Zürich, Winterthurerstr. 190, 8057 Zürich, Switzerland
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McQuaid K, Pipier A, Cardin C, Monchaud D. Interactions of small molecules with DNA junctions. Nucleic Acids Res 2022; 50:12636-12656. [PMID: 36382400 PMCID: PMC9825177 DOI: 10.1093/nar/gkac1043] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/13/2022] [Accepted: 10/23/2022] [Indexed: 11/17/2022] Open
Abstract
The four natural DNA bases (A, T, G and C) associate in base pairs (A=T and G≡C), allowing the attached DNA strands to assemble into the canonical double helix of DNA (or duplex-DNA, also known as B-DNA). The intrinsic supramolecular properties of nucleobases make other associations possible (such as base triplets or quartets), which thus translates into a diversity of DNA structures beyond B-DNA. To date, the alphabet of DNA structures is ripe with approximately 20 letters (from A- to Z-DNA); however, only a few of them are being considered as key players in cell biology and, by extension, valuable targets for chemical biology intervention. In the present review, we summarise what is known about alternative DNA structures (what are they? When, where and how do they fold?) and proceed to discuss further about those considered nowadays as valuable therapeutic targets. We discuss in more detail the molecular tools (ligands) that have been recently developed to target these structures, particularly the three- and four-way DNA junctions, in order to intervene in the biological processes where they are involved. This new and stimulating chemical biology playground allows for devising innovative strategies to fight against genetic diseases.
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Affiliation(s)
- Kane T McQuaid
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, UK
| | - Angélique Pipier
- Institut de Chimie Moléculaire de l’Université de Bourgogne (ICMUB), CNRS UMR 6302, UBFC Dijon, 21078 Dijon, France
| | - Christine J Cardin
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, UK
| | - David Monchaud
- Institut de Chimie Moléculaire de l’Université de Bourgogne (ICMUB), CNRS UMR 6302, UBFC Dijon, 21078 Dijon, France
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Filote C, Lanez E, Popa VI, Lanez T, Volf I. Characterization and Bioactivity of Polysaccharides Separated through a (Sequential) Biorefinery Process from Fucus spiralis Brown Macroalgae. Polymers (Basel) 2022; 14:polym14194106. [PMID: 36236054 PMCID: PMC9572633 DOI: 10.3390/polym14194106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 09/12/2022] [Accepted: 09/23/2022] [Indexed: 11/18/2022] Open
Abstract
Marine macroalgae biomass is a valuable renewable resource that can be used for the development of bioeconomy through the valorisation of valuable compounds. The aim of the current study is separate macroalgal polysaccharides with bioactive properties from brown macroalgae Fucus spiralis based on a designed biocascading biorefinery approach. Thus, we applied an integrated processing method for the separation of fucoidan and alginate, in addition to characterization through IR spectroscopy and 1H NMR. The bioactivity potential (antioxidant activity using superoxide anion and DPPH radical scavenging analysis) of the two polysaccharides was evaluated, together with DNA binding studies performed though voltametric techniques and electronic spectroscopy titration. In terms of results, functional groups S=O (1226 cm−1), N=S=O (1136 cm−1) and C-O-SO3 (1024 cm−1), which are characteristic of fucoidan, were identified in the first polysaccharidic extract, whereas guluronic units (G) (1017 cm−1) and mannuronic units (M) (872 and 812 cm−1) confirmed the separation of alginate. The DNA binding studies of the isolated polysaccharides revealed an electrostatic and an intercalation interaction of DNA with fucoidan and alginate, respectively. Both antioxidant activity assays revealed improved antioxidant activity for both fucoidan and alginate compared to the standard α-tocopherol.
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Affiliation(s)
- Cătălina Filote
- Department of Environmental Engineering and Management, Faculty of Chemical Engineering and Environmental Protection, “Gheorghe Asachi” Technical University of Iasi, 73 Prof. D. Mangeron Bldv., 700050 Iasi, Romania
| | - Elhafnaoui Lanez
- VTRS Laboratory, Faculty of Sciences, University of El Oued, B.P. 789, El Oued 39000, Algeria
| | - Valentin I. Popa
- Department of Environmental Engineering and Management, Faculty of Chemical Engineering and Environmental Protection, “Gheorghe Asachi” Technical University of Iasi, 73 Prof. D. Mangeron Bldv., 700050 Iasi, Romania
| | - Touhami Lanez
- VTRS Laboratory, Faculty of Sciences, University of El Oued, B.P. 789, El Oued 39000, Algeria
| | - Irina Volf
- Department of Environmental Engineering and Management, Faculty of Chemical Engineering and Environmental Protection, “Gheorghe Asachi” Technical University of Iasi, 73 Prof. D. Mangeron Bldv., 700050 Iasi, Romania
- Correspondence:
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10
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Ivens E, Cominetti MM, Searcey M. Junctions in DNA: underexplored targets for therapeutic intervention. Bioorg Med Chem 2022; 69:116897. [DOI: 10.1016/j.bmc.2022.116897] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/15/2022] [Accepted: 06/20/2022] [Indexed: 11/02/2022]
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11
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Martinez-Monge A, Pastor I, Bustamante C, Manosas M, Ritort F. Measurement of the specific and non-specific binding energies of Mg 2+ to RNA. Biophys J 2022; 121:3010-3022. [PMID: 35864738 PMCID: PMC9463699 DOI: 10.1016/j.bpj.2022.07.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Determining the non-specific and specific electrostatic contributions of magnesium binding to RNA is a challenging problem. We introduce a single-molecule method based on measuring the folding energy of a native RNA in magnesium and at its equivalent sodium concentration. The latter is defined so that the folding energy in sodium equals the non-specific electrostatic contribution in magnesium. The sodium equivalent can be estimated according to the empirical 100/1 rule (1 M NaCl is equivalent to 10 mM MgCl2), which is a good approximation for most RNAs. The method is applied to an RNA three-way junction (3WJ) that contains specific Mg2+ binding sites and misfolds into a double hairpin structure without binding sites. We mechanically pull the RNA with optical tweezers and use fluctuation theorems to determine the folding energies of the native and misfolded structures in magnesium (10 mM MgCl2) and at the equivalent sodium condition (1 M NaCl). While the free energies of the misfolded structure are equal in magnesium and sodium, they are not for the native structure, the difference being due to the specific binding energy of magnesium to the 3WJ, which equals ΔG≃ 10 kcal/mol. Besides stabilizing the 3WJ, Mg2+ also kinetically rescues it from the misfolded structure over timescales of tens of seconds in a force-dependent manner. The method should generally be applicable to determine the specific binding energies of divalent cations to other tertiary RNAs.
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Affiliation(s)
- A Martinez-Monge
- Small Biosystems Lab, Departament de Física de la Matèria Condensada, Facultat de Física, Universitat de Barcelona, Carrer de Martí i Franquès, 1, 08028 Barcelona, Spain
| | - Isabel Pastor
- Small Biosystems Lab, Departament de Física de la Matèria Condensada, Facultat de Física, Universitat de Barcelona, Carrer de Martí i Franquès, 1, 08028 Barcelona, Spain; Institut de Nanociència i Nanotecnologia (IN2UB), Universitat de Barcelona, 08028 Barcelona, Spain
| | - Carlos Bustamante
- Departments of Chemistry, Physics and Molecular and Cell Biology, University of California Berkeley, Berkeley, California; Howard Hughes Medical Institute University of California Berkeley, Berkeley, California; Kavli Energy Nanosciences Institute, University of California Berkeley, Berkeley, California
| | - Maria Manosas
- Small Biosystems Lab, Departament de Física de la Matèria Condensada, Facultat de Física, Universitat de Barcelona, Carrer de Martí i Franquès, 1, 08028 Barcelona, Spain; Institut de Nanociència i Nanotecnologia (IN2UB), Universitat de Barcelona, 08028 Barcelona, Spain.
| | - Felix Ritort
- Small Biosystems Lab, Departament de Física de la Matèria Condensada, Facultat de Física, Universitat de Barcelona, Carrer de Martí i Franquès, 1, 08028 Barcelona, Spain; Institut de Nanociència i Nanotecnologia (IN2UB), Universitat de Barcelona, 08028 Barcelona, Spain.
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12
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Gómez-González J, Martínez-Castro L, Tolosa-Barrilero J, Alcalde-Ordóñez A, Learte-Aymamí S, Mascareñas JL, García-Martínez JC, Martínez-Costas J, Maréchal JD, Vázquez López M, Vázquez ME. Selective recognition of A/T-rich DNA 3-way junctions with a three-fold symmetric tripeptide. Chem Commun (Camb) 2022; 58:7769-7772. [PMID: 35730795 DOI: 10.1039/d2cc02874c] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Non-canonical DNA structures, particularly 3-Way Junctions (3WJs) that are transiently formed during DNA replication, have recently emerged as promising chemotherapeutic targets. Here, we describe a new approach to target 3WJs that relies on the cooperative and sequence-selective recognition of A/T-rich duplex DNA branches by three AT-Hook peptides attached to a three-fold symmetric and fluorogenic 1,3,5-tristyrylbenzene core.
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Affiliation(s)
- Jacobo Gómez-González
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Spain.
| | - Laura Martínez-Castro
- Insilichem, Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola, Spain
| | - Juan Tolosa-Barrilero
- Department of Inorganic, Organic Chemistry and Biochemistry, Faculty of Pharmacy, University of Castilla-La Mancha, 02071 Albacete, Spain.,Regional Center for Biomedical Research (CRIB), 02071 Albacete, Spain
| | - Ana Alcalde-Ordóñez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Spain.
| | - Soraya Learte-Aymamí
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Spain.
| | - José L Mascareñas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Spain.
| | - Joaquín C García-Martínez
- Department of Inorganic, Organic Chemistry and Biochemistry, Faculty of Pharmacy, University of Castilla-La Mancha, 02071 Albacete, Spain.,Regional Center for Biomedical Research (CRIB), 02071 Albacete, Spain
| | - José Martínez-Costas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Bioquímica y Biología Molecular, Universidade de Santiago de Compostela, Spain
| | - Jean-Didier Maréchal
- Insilichem, Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola, Spain
| | - Miguel Vázquez López
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Inorgánica, Universidade de Santiago de Compostela, Spain
| | - M Eugenio Vázquez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Spain.
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13
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Limarev IP, Zelinskii GE, Belova SA, Dorovatovskii PV, Vologzhanina AV, Lebed EG, Voloshin YZ. Monoribbed‐functionalized macrobicyclic iron(
II
) complexes decorated with terminal reactive and vector groups: synthetic strategy towards, chemical transformations and structural characterization. CHINESE J CHEM 2022. [DOI: 10.1002/cjoc.202200191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Ilya P. Limarev
- Nesmeyanov Institute of Organoelement Compounds of the Russian Academy of Sciences, 28 Vavilova st. 119991 Moscow Russia
- Kurnakov Institute of General and Inorganic Chemistry of the Russian Academy of Sciences, 31 Leninsky pr. 119991 Moscow Russia
| | - Genrikh E. Zelinskii
- Nesmeyanov Institute of Organoelement Compounds of the Russian Academy of Sciences, 28 Vavilova st. 119991 Moscow Russia
- Kurnakov Institute of General and Inorganic Chemistry of the Russian Academy of Sciences, 31 Leninsky pr. 119991 Moscow Russia
| | - Svetlana A. Belova
- Nesmeyanov Institute of Organoelement Compounds of the Russian Academy of Sciences, 28 Vavilova st. 119991 Moscow Russia
- Kurnakov Institute of General and Inorganic Chemistry of the Russian Academy of Sciences, 31 Leninsky pr. 119991 Moscow Russia
| | | | - Anna V. Vologzhanina
- Nesmeyanov Institute of Organoelement Compounds of the Russian Academy of Sciences, 28 Vavilova st. 119991 Moscow Russia
| | - Ekaterina G. Lebed
- Nesmeyanov Institute of Organoelement Compounds of the Russian Academy of Sciences, 28 Vavilova st. 119991 Moscow Russia
- Kurnakov Institute of General and Inorganic Chemistry of the Russian Academy of Sciences, 31 Leninsky pr. 119991 Moscow Russia
| | - Yan Z. Voloshin
- Nesmeyanov Institute of Organoelement Compounds of the Russian Academy of Sciences, 28 Vavilova st. 119991 Moscow Russia
- Kurnakov Institute of General and Inorganic Chemistry of the Russian Academy of Sciences, 31 Leninsky pr. 119991 Moscow Russia
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14
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Joaqui-Joaqui MA, Maxwell Z, Raju MVR, Jiang M, Srivastava K, Shao F, Arriaga EA, Pierre VC. Metallointercalators-DNA Tetrahedron Supramolecular Self-Assemblies with Increased Serum Stability. ACS NANO 2022; 16:2928-2941. [PMID: 35133785 PMCID: PMC8926058 DOI: 10.1021/acsnano.1c10084] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Self-assembly of metallointercalators into DNA nanocages is a rapid and facile approach to synthesize discrete bioinorganic host/guest structures with a high load of metal complexes. Turberfield's DNA tetrahedron can accommodate one intercalator for every two base pairs, which corresponds to 48 metallointercalators per DNA tetrahedron. The affinity of the metallointercalator for the DNA tetrahedron is a function of both the structure of the intercalating ligand and the overall charge of the complex, with a trend in affinity [Ru(bpy)2(dppz)]2+ > [Tb-DOTAm-Phen]3+ ≫ Tb-DOTA-Phen. Intercalation of the metal complex stabilizes the DNA tetrahedron, resulting in an increase of its melting temperature and, importantly, a significant increase in its stability in the presence of serum. [Ru(bpy)2(dppz)]2+, which has a greater affinity for DNA than [Tb-DOTAm-Phen]3+, increases the melting point and decreases degradation in serum to a greater extent than the TbIII complex. In the presence of Lipofectamine, the metallointercalator@DNA nanocage assemblies substantially increase the cell uptake of their respective metal complex. Altogether, the facile incorporation of a large number of metal complexes per assembly, the higher stability in serum, and the increased cell penetration of metallointercalator@DNA make these self-assemblies well-suited as metallodrugs.
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Affiliation(s)
- M. Andrey Joaqui-Joaqui
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, United States of America
| | - Zoe Maxwell
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, United States of America
| | | | - Min Jiang
- Zhejiang University-University of Illinois at Urbana-Champaign Institute, Zhejiang University, Haining, 314400, China
| | - Kriti Srivastava
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, United States of America
| | - Fangwei Shao
- Zhejiang University-University of Illinois at Urbana-Champaign Institute, Zhejiang University, Haining, 314400, China
| | - Edgar A. Arriaga
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, United States of America
| | - Valérie C. Pierre
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, United States of America
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15
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Affiliation(s)
- Xin‐Xin Peng
- Beijing National Laboratory for Molecular Sciences State Key Laboratory of Rare Earth Materials Chemistry and Applications College of Chemistry and Molecular Engineering Peking University Chengfu Road 292, Haidian district Beijing 100871 R. P. China
| | - Song Gao
- Beijing National Laboratory for Molecular Sciences State Key Laboratory of Rare Earth Materials Chemistry and Applications College of Chemistry and Molecular Engineering Peking University Chengfu Road 292, Haidian district Beijing 100871 R. P. China
- Chemistry and Chemical Engineering Guangdong Laboratory Shantou 515031 P. R. China
- Spin-X Institute, School of Chemistry and Chemical Engineering South China University of Technology Guangzhou 510641 P. R. China
- Guangdong-Hong Kong-Macao Joint Laboratory of Optoelectronic and Magnetic Functional Materials Guangzhou 510641 P. R. China
| | - Jun‐Long Zhang
- Beijing National Laboratory for Molecular Sciences State Key Laboratory of Rare Earth Materials Chemistry and Applications College of Chemistry and Molecular Engineering Peking University Chengfu Road 292, Haidian district Beijing 100871 R. P. China
- Chemistry and Chemical Engineering Guangdong Laboratory Shantou 515031 P. R. China
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16
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Ragab MS, Shehata MR, Shoukry MM, Haukka M, Ragheb MA. Oxidative DNA cleavage mediated by a new unexpected [Pd(BAPP)][PdCl 4] complex (BAPP = 1,4-bis(3-aminopropyl)piperazine): crystal structure, DNA binding and cytotoxic behavior. RSC Adv 2022; 12:1871-1884. [PMID: 35425175 PMCID: PMC8979008 DOI: 10.1039/d1ra07793g] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 12/17/2021] [Indexed: 12/30/2022] Open
Abstract
A novel Pd(ii) double complex, [Pd(BAPP)][PdCl4], containing the 1,4-bis(3-aminopropyl)piperazine (BAPP) ligand is investigated. X-ray crystallography of a single crystal confirmed the structure of the [Pd(BAPP)][PdCl4] complex. The spectroscopic behavior was also elucidated using elemental analysis, nuclear magnetic resonance and Fourier-transform infrared spectroscopy, and mass spectrometry. The antimicrobial susceptibility of the [Pd(BAPP)][PdCl4] complex against all tested microbial strains was lower than that of the BAPP ligand except for C. albicans. The cytotoxic impacts of the BAPP ligand and its [Pd(BAPP)][PdCl4] complex were evaluated in vitro for HepG2, CaCo-2 and MCF7 cell lines as well as the WI-38 normal cell line. The anticancer activity was markedly improved by the complexation. The [Pd(BAPP)][PdCl4] complex could selectively inhibit the tested cancer cells in a safe way to the non-tumorigenic cell (WI-38). From the DNA binding studies with ultraviolet-visible spectrophotometry, the [Pd(BAPP)][PdCl4] complex interacts more efficiently with the calf thymus DNA than its BAPP ligand through the intercalative binding mode. In the absence of an external reductant, the [Pd(BAPP)][PdCl4] complex cleaved the intact supercoiled pBR322 DNA under physiological conditions in a concentration-dependent manner. Additionally, electrophoretic experiments were performed in the presence of different radical scavengers, namely DMSO, NaN3 and KI, and ruled out the hydrolytic mechanistic pathway of the reaction and suggested that the oxidative mechanism is the preferred one. The results of the binding affinity of the [Pd(BAPP)][PdCl4] complex to human DNA were modeled using a molecular docking study showing that the complex interacts more strongly with human DNA than the ligand. Finally, an in vitro pharmacokinetic study was assessed through in silico ADME predictions.
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Affiliation(s)
- Mona S Ragab
- Department of Chemistry, Faculty of Science, Cairo University Giza 12613 Egypt
| | - Mohamed R Shehata
- Department of Chemistry, Faculty of Science, Cairo University Giza 12613 Egypt
| | - Mohamed M Shoukry
- Department of Chemistry, Faculty of Science, Cairo University Giza 12613 Egypt
| | - Matti Haukka
- Department of Chemistry, University of Jyväskylä P.O. Box 35 FI-40014 Jyväskylä Finland
| | - Mohamed A Ragheb
- Department of Chemistry (Biochemistry Division), Faculty of Science, Cairo University Giza Egypt
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17
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Malina J, Kostrhunova H, Brabec V. Dinuclear nickel( ii) supramolecular helicates down-regulate gene expression in human cells by stabilizing DNA G-quadruplexes formed in the promoter regions. Inorg Chem Front 2022. [DOI: 10.1039/d2qi01435a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Dinuclear nickel(ii) supramolecular helicates selectively stabilize DNA G-quadruplexes and suppress G-quadruplex-regulated genes.
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Affiliation(s)
- Jaroslav Malina
- Czech Academy of Sciences, Institute of Biophysics, Kralovopolska 135, CZ-61265 Brno, Czech Republic
| | - Hana Kostrhunova
- Czech Academy of Sciences, Institute of Biophysics, Kralovopolska 135, CZ-61265 Brno, Czech Republic
| | - Viktor Brabec
- Czech Academy of Sciences, Institute of Biophysics, Kralovopolska 135, CZ-61265 Brno, Czech Republic
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18
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Takezawa Y, Sakakibara S, Shionoya M. Bipyridine-Modified DNA Three-Way Junctions with Amide linkers: Metal-Dependent Structure Induction and Self-Sorting. Chemistry 2021; 27:16626-16633. [PMID: 34623721 DOI: 10.1002/chem.202102977] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Indexed: 11/12/2022]
Abstract
DNA three-way junction (3WJ) structures are essential building blocks for the construction of DNA nanoarchitectures. We have synthesized a bipyridine (bpy)-modified DNA 3WJ by using a newly designed bpy-modified nucleoside, Ubpy -3, in which a bpy ligand is tethered via a stable amide linker. The thermal stability of the bpy-modified 3WJ was greatly enhanced by the formation of an interstrand NiII (bpy)3 complex at the junction core (ΔTm =+17.7 °C). Although the stereochemistry of the modification site differs from that of the previously reported bpy-modified nucleoside Ubpy -2, the degree of the NiII -mediated stabilization observed with Ubpy -3 was comparable to that of Ubpy -2. Structure induction of the 3WJs and the duplexes was carried out by the addition or removal of NiII ions. Furthermore, NiII -mediated self-sorting of 3WJs was performed by using the bpy-modified strands and their unmodified counterparts. Both transformations were driven by the formation of NiII (bpy)3 complexes. The structural induction and self-sorting of bpy-modified 3WJs are expected to have many potential applications in the development of metal-responsive DNA materials.
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Affiliation(s)
- Yusuke Takezawa
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Shiori Sakakibara
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Mitsuhiko Shionoya
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
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19
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McStay N, Slator C, Singh V, Gibney A, Westerlund F, Kellett A. Click and Cut: a click chemistry approach to developing oxidative DNA damaging agents. Nucleic Acids Res 2021; 49:10289-10308. [PMID: 34570227 PMCID: PMC8501983 DOI: 10.1093/nar/gkab817] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 09/01/2021] [Accepted: 09/07/2021] [Indexed: 01/04/2023] Open
Abstract
Metallodrugs provide important first-line treatment against various forms of human cancer. To overcome chemotherapeutic resistance and widen treatment possibilities, new agents with improved or alternative modes of action are highly sought after. Here, we present a click chemistry strategy for developing DNA damaging metallodrugs. The approach involves the development of a series of polyamine ligands where three primary, secondary or tertiary alkyne-amines were selected and 'clicked' using the copper-catalysed azide-alkyne cycloaddition reaction to a 1,3,5-azide mesitylene core to produce a family of compounds we call the 'Tri-Click' (TC) series. From the isolated library, one dominant ligand (TC1) emerged as a high-affinity copper(II) binding agent with potent DNA recognition and damaging properties. Using a range of in vitro biophysical and molecular techniques-including free radical scavengers, spin trapping antioxidants and base excision repair (BER) enzymes-the oxidative DNA damaging mechanism of copper-bound TC1 was elucidated. This activity was then compared to intracellular results obtained from peripheral blood mononuclear cells exposed to Cu(II)-TC1 where use of BER enzymes and fluorescently modified dNTPs enabled the characterisation and quantification of genomic DNA lesions produced by the complex. The approach can serve as a new avenue for the design of DNA damaging agents with unique activity profiles.
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Affiliation(s)
- Natasha McStay
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
- Synthesis and Solid-State Pharmaceutical Centre, School of Chemical Sciences, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Creina Slator
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Vandana Singh
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Alex Gibney
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
- Synthesis and Solid-State Pharmaceutical Centre, School of Chemical Sciences, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Andrew Kellett
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
- Synthesis and Solid-State Pharmaceutical Centre, School of Chemical Sciences, Dublin City University, Glasnevin, Dublin 9, Ireland
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20
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Zell J, Duskova K, Chouh L, Bossaert M, Chéron N, Granzhan A, Britton S, Monchaud D. Dual targeting of higher-order DNA structures by azacryptands induces DNA junction-mediated DNA damage in cancer cells. Nucleic Acids Res 2021; 49:10275-10288. [PMID: 34551430 PMCID: PMC8501980 DOI: 10.1093/nar/gkab796] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 08/16/2021] [Accepted: 09/01/2021] [Indexed: 12/11/2022] Open
Abstract
DNA is intrinsically dynamic and folds transiently into alternative higher-order structures such as G-quadruplexes (G4s) and three-way DNA junctions (TWJs). G4s and TWJs can be stabilised by small molecules (ligands) that have high chemotherapeutic potential, either as standalone DNA damaging agents or combined in synthetic lethality strategies. While previous approaches have claimed to use ligands that specifically target either G4s or TWJs, we report here on a new approach in which ligands targeting both TWJs and G4s in vitro demonstrate cellular effects distinct from that of G4 ligands, and attributable to TWJ targeting. The DNA binding modes of these new, dual TWJ-/G4-ligands were studied by a panel of in vitro methods and theoretical simulations, and their cellular properties by extensive cell-based assays. We show here that cytotoxic activity of TWJ-/G4-ligands is mitigated by the DNA damage response (DDR) and DNA topoisomerase 2 (TOP2), making them different from typical G4-ligands, and implying a pivotal role of TWJs in cells. We designed and used a clickable ligand, TrisNP-α, to provide unique insights into the TWJ landscape in cells and its modulation upon co-treatments. This wealth of data was exploited to design an efficient synthetic lethality strategy combining dual ligands with clinically relevant DDR inhibitors.
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Affiliation(s)
- Joanna Zell
- Institut de Chimie Moléculaire de l’Université de Bourgogne (ICMUB), CNRS UMR 6302, UBFC Dijon, 21078 Dijon, France
| | - Katerina Duskova
- Institut de Chimie Moléculaire de l’Université de Bourgogne (ICMUB), CNRS UMR 6302, UBFC Dijon, 21078 Dijon, France
| | - Leïla Chouh
- Institut Curie, CNRS UMR 9187, INSERM U1196, PSL Research University, 91405 Orsay, France
- Université Paris Saclay, CNRS UMR 9187, INSERM U1196, 91405 Orsay, France
| | - Madeleine Bossaert
- Institut de Pharmacologie et de Biologie Structurale (IPBS), CNRS UMR 5089, Université de Toulouse, UPS, Équipe labellisée la Ligue Contre le Cancer, 31077 Toulouse, France
| | - Nicolas Chéron
- Pasteur, Département de chimie, École Normale Supérieure (ENS), CNRS UMR8640, PSL Research University, Sorbonne Université, 75005 Paris, France
| | - Anton Granzhan
- Institut Curie, CNRS UMR 9187, INSERM U1196, PSL Research University, 91405 Orsay, France
- Université Paris Saclay, CNRS UMR 9187, INSERM U1196, 91405 Orsay, France
| | - Sébastien Britton
- Institut de Pharmacologie et de Biologie Structurale (IPBS), CNRS UMR 5089, Université de Toulouse, UPS, Équipe labellisée la Ligue Contre le Cancer, 31077 Toulouse, France
| | - David Monchaud
- Institut de Chimie Moléculaire de l’Université de Bourgogne (ICMUB), CNRS UMR 6302, UBFC Dijon, 21078 Dijon, France
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21
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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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22
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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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23
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Xu J, Wang J, Ye J, Jiao J, Liu Z, Zhao C, Li B, Fu Y. Metal-Coordinated Supramolecular Self-Assemblies for Cancer Theranostics. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2101101. [PMID: 34145984 PMCID: PMC8373122 DOI: 10.1002/advs.202101101] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/25/2021] [Indexed: 05/07/2023]
Abstract
Metal-coordinated supramolecular nanoassemblies have recently attracted extensive attention as materials for cancer theranostics. Owing to their unique physicochemical properties, metal-coordinated supramolecular self-assemblies can bridge the boundary between traditional inorganic and organic materials. By tailoring the structural components of the metal ions and binding ligands, numerous multifunctional theranostic nanomedicines can be constructed. Metal-coordinated supramolecular nanoassemblies can modulate the tumor microenvironment (TME), thus facilitating the development of TME-responsive nanomedicines. More importantly, TME-responsive organic-inorganic hybrid nanomaterials can be constructed in vivo by exploiting the metal-coordinated self-assembly of a variety of functional ligands, which is a promising strategy for enhancing the tumor accumulation of theranostic molecules. In this review, recent advancements in the design and fabrication of metal-coordinated supramolecular nanomedicines for cancer theranostics are highlighted. These supramolecular compounds are classified according to the order in which the coordinated metal ions appear in the periodic table. Furthermore, the prospects and challenges of metal-coordinated supramolecular self-assemblies for both technical advances and clinical translation are discussed. In particular, the superiority of TME-responsive nanomedicines for in vivo coordinated self-assembly is elaborated, with an emphasis on strategies that enhance the accumulation of functional components in tumors for an ideal theranostic outcome.
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Affiliation(s)
- Jiating Xu
- Key Laboratory of Forest Plant EcologyMinistry of EducationCollege of ChemistryChemical Engineering and Resource UtilizationNortheast Forestry UniversityHarbin150040P. R. China
| | - Jun Wang
- Key Laboratory of Forest Plant EcologyMinistry of EducationCollege of ChemistryChemical Engineering and Resource UtilizationNortheast Forestry UniversityHarbin150040P. R. China
| | - Jin Ye
- Key Laboratory of Forest Plant EcologyMinistry of EducationCollege of ChemistryChemical Engineering and Resource UtilizationNortheast Forestry UniversityHarbin150040P. R. China
| | - Jiao Jiao
- Key Laboratory of Forest Plant EcologyMinistry of EducationCollege of ChemistryChemical Engineering and Resource UtilizationNortheast Forestry UniversityHarbin150040P. R. China
| | - Zhiguo Liu
- Key Laboratory of Forest Plant EcologyMinistry of EducationCollege of ChemistryChemical Engineering and Resource UtilizationNortheast Forestry UniversityHarbin150040P. R. China
| | - Chunjian Zhao
- Key Laboratory of Forest Plant EcologyMinistry of EducationCollege of ChemistryChemical Engineering and Resource UtilizationNortheast Forestry UniversityHarbin150040P. R. China
| | - Bin Li
- Key Laboratory of Forest Plant EcologyMinistry of EducationCollege of ChemistryChemical Engineering and Resource UtilizationNortheast Forestry UniversityHarbin150040P. R. China
| | - Yujie Fu
- Key Laboratory of Forest Plant EcologyMinistry of EducationCollege of ChemistryChemical Engineering and Resource UtilizationNortheast Forestry UniversityHarbin150040P. R. China
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24
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Gómez-González J, Bouzada D, Pérez-Márquez LA, Sciortino G, Maréchal JD, Vázquez López M, Vázquez ME. Stereoselective Self-Assembly of DNA Binding Helicates Directed by the Viral β-Annulus Trimeric Peptide Motif. Bioconjug Chem 2021; 32:1564-1569. [PMID: 34320309 PMCID: PMC8485332 DOI: 10.1021/acs.bioconjchem.1c00312] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
![]()
Combining
coordination chemistry and peptide engineering offers
extraordinary opportunities for developing novel molecular (supra)structures.
Here, we demonstrate that the β-annulus motif is capable of
directing the stereoselective assembly of designed peptides containing
2,2′-bipyridine ligands into parallel three-stranded chiral
peptide helicates, and that these helicates selectively bind with
high affinity to three-way DNA junctions.
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Affiliation(s)
- Jacobo Gómez-González
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Inorgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - David Bouzada
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Lidia A Pérez-Márquez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Inorgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Giuseppe Sciortino
- Insilichem, Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola, Spain
| | - Jean-Didier Maréchal
- Insilichem, Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola, Spain
| | - Miguel Vázquez López
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Inorgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - M Eugenio Vázquez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
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25
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Ćoćić D, Jovanović-Stević S, Jelić R, Matić S, Popović S, Djurdjević P, Baskić D, Petrović B. Homo- and hetero-dinuclear Pt(II)/Pd(II) complexes: studies of hydrolysis, nucleophilic substitution reactions, DNA/BSA interactions, DFT calculations, molecular docking and cytotoxic activity. Dalton Trans 2021; 49:14411-14431. [PMID: 33043330 DOI: 10.1039/d0dt02906h] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Three dinuclear complexes [Pd2(tpbd)Cl2]Cl2 (PP1), [Pt2(tpbd)Cl2]Cl2 (PP2) and [PdPt(tpbd)Cl2]Cl2 (PP3) (tpbd = N,N,N',N'-tetrakis(2-pyridylmethyl)benzene-1,4-diamine) have been synthesized and characterized and the protonation constants of their corresponding diaqua analogues have been determined. Also, in water solution, the aqua analogues of these complexes exist as mono-hydroxo, di-hydroxo and dimer μ-hydroxo complexes in the pH between 3.0 and 11.0. Substitution reactions with sulfur- and nitrogen-donor nucleophiles, such as thiourea (Tu), l-methionine (l-Met), glutathione (GSH) and guanosine-5'-monophosphate (5'-GMP), were studied at pH 7.2 by conventional and stopped-flow UV-Vis spectrophotometry and the observed reactivity follows the order: Tu > l-Met > GSH > 5'-GMP. Also, the interactions with calf thymus DNA (CT-DNA) and bovine serum albumin (BSA) were investigated. Competitive studies with DNA were performed in the presence of ethidium bromide and Hoechst dye 33258 as well. The complexes possess the strong ability to react with CT-DNA exhibiting intercalation and more preferable minor groove binding. Nevertheless, all complexes showed a good binding affinity toward BSA with relatively high binding constants. The nature of the binding forces between complexes and biomolecules has been identified as hydrophobic. Experimental results were compared with the molecular docking results, while the relative stability and thermodynamic properties of dinuclear complexes were compared with their mononuclear units by DFT calculations. Among three tested complexes, PP2 showed the most powerful cytotoxic effect on HTB140 and H460 cancer cell lines after 48 h of treatment and exerted a strong long-term influence on the proliferation potential of both tested cell lines. PP2 induced the inhibition of autophagy, G2/M cell cycle arrest and mitotic catastrophe.
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Affiliation(s)
- Dušan Ćoćić
- University of Kragujevac, Faculty of Science, Radoja Domanovića 12, 34000 Kragujevac, Serbia.
| | - SneŽana Jovanović-Stević
- University of Kragujevac, Institute of Information Technologies, Jovana Cvijića bb, 34000 Kragujevac, Serbia
| | - Ratomir Jelić
- University of Kragujevac, Faculty of Medical Sciences, Department of Pharmacy, Svetozara Markovića 69, 34000 Kragujevac, Serbia
| | - Sanja Matić
- University of Kragujevac, Faculty of Medical Sciences, Department of Pharmacy, Svetozara Markovića 69, 34000 Kragujevac, Serbia
| | - Suzana Popović
- University of Kragujevac, Faculty of Medical Sciences, Centre for Molecular Medicine and Stem Cell Research, Svetozara Markovića 69, 34000 Kragujevac, Serbia
| | - Predrag Djurdjević
- University of Kragujevac, Faculty of Medical Sciences, Department of Internal medicine, Svetozara Markovića 69, 34000 Kragujevac, Serbia and Clinic for Haematology, Clinical Centre Kragujevac, Zmaj Jovina 30, 34000 Kragujevac, Serbia
| | - Dejan Baskić
- University of Kragujevac, Faculty of Medical Sciences, Centre for Molecular Medicine and Stem Cell Research, Svetozara Markovića 69, 34000 Kragujevac, Serbia and Public Health Institute, Nikole Pašića 1, 34000 Kragujevac, Serbia
| | - Biljana Petrović
- University of Kragujevac, Faculty of Science, Radoja Domanovića 12, 34000 Kragujevac, Serbia.
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26
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Lisboa LS, Riisom M, Vasdev RAS, Jamieson SMF, Wright LJ, Hartinger CG, Crowley JD. Cavity-Containing [Fe 2L 3] 4+ Helicates: An Examination of Host-Guest Chemistry and Cytotoxicity. Front Chem 2021; 9:697684. [PMID: 34307299 PMCID: PMC8292671 DOI: 10.3389/fchem.2021.697684] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 06/16/2021] [Indexed: 02/04/2023] Open
Abstract
Two new di(2,2′-bipyridine) ligands, 2,6-bis([2,2′-bipyridin]-5-ylethynyl)pyridine (L1) and bis(4-([2,2′-bipyridin]-5-ylethynyl)phenyl)methane (L2) were synthesized and used to generate two metallosupramolecular [Fe2(L)3](BF4)4 cylinders. The ligands and cylinders were characterized using elemental analysis, electrospray ionization mass spectrometry, UV-vis, 1H-, 13C and DOSY nuclear magnetic resonance (NMR) spectroscopies. The molecular structures of the [Fe2(L)3](BF4)4 cylinders were confirmed using X-ray crystallography. Both the [Fe2(L1)3](BF4)4 and [Fe2(L2)3](BF4)4 complexes crystallized as racemic (rac) mixtures of the ΔΔ (P) and ΛΛ (M) helicates. However, 1H NMR spectra showed that in solution the larger [Fe2(L2)3](BF4)4 was a mixture of the rac-ΔΔ/ΛΛ and meso-ΔΛ isomers. The host-guest chemistry of the helicates, which both feature a central cavity, was examined with several small drug molecules. However, none of the potential guests were found to bind within the helicates. In vitro cytotoxicity assays demonstrated that both helicates were active against four cancer cell lines. The smaller [Fe2(L1)3](BF4)4 system displayed low μM activity against the HCT116 (IC50 = 7.1 ± 0.5 μM) and NCI-H460 (IC50 = 4.9 ± 0.4 μM) cancer cells. While the antiproliferative effects against all the cell lines examined were less than the well-known anticancer drug cisplatin, their modes of action would be expected to be very different.
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Affiliation(s)
- Lynn S Lisboa
- Department of Chemistry, University of Otago, Dunedin, New Zealand
| | - Mie Riisom
- School of Chemical Sciences, University of Auckland, Auckland, New Zealand.,Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand
| | - Roan A S Vasdev
- Department of Chemistry, University of Otago, Dunedin, New Zealand
| | - Stephen M F Jamieson
- Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand
| | - L James Wright
- School of Chemical Sciences, University of Auckland, Auckland, New Zealand
| | | | - James D Crowley
- Department of Chemistry, University of Otago, Dunedin, New Zealand
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27
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28
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Tran NM, Yoo H. Recent advances in heteroleptic multiple-stranded metallosupramolecules. Dalton Trans 2021; 49:11819-11827. [PMID: 32797124 DOI: 10.1039/d0dt02243h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Well-ordered combination of defined coordination spheres and multiple types of ligands (heteroleptic) in a given structure can expand the structural complexity and functional diversity of the resulting metallosupramolecules. Such heteroleptic metallosupramolecular architectures are expected to afford advanced utility in a variety of applications. In this concise review article, recent advances in the development of multi-nuclear-cluster-based heteroleptic multiple-stranded (HLMS) metallosupramolecules are summarized and demonstrated. To construct HLMS metallosupramolecules, one type of multitopic ligands can be employed for building up multiple strands, while another type of ligands can be utilized to construct multi-nuclear clusters. Most HLMS metallosupramolecules adopt helical geometries and have high molecular symmetry, which can be key factors for the structural completion. HLMS metallosupramolecules can be used as basic building blocks for the fabrication of higher-order polymeric or discrete assembly architectures with well-defined geometries.
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Affiliation(s)
- Ngoc Minh Tran
- Department of Materials Science and Chemical Engineering, Hanyang University, Ansan, Gyeonggi-do 15588, Republic of Korea.
| | - Hyojong Yoo
- Department of Materials Science and Chemical Engineering, Hanyang University, Ansan, Gyeonggi-do 15588, Republic of Korea.
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29
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van der Westhuizen D, Slabber CA, Fernandes MA, Joubert DF, Kleinhans G, van der Westhuizen CJ, Stander A, Munro OQ, Bezuidenhout DI. A Cytotoxic Bis(1,2,3-triazol-5-ylidene)carbazolide Gold(III) Complex Targets DNA by Partial Intercalation. Chemistry 2021; 27:8295-8307. [PMID: 33822431 PMCID: PMC8251726 DOI: 10.1002/chem.202100598] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Indexed: 12/13/2022]
Abstract
The syntheses of bis(triazolium)carbazole precursors and their corresponding coinage metal (Au, Ag) complexes are reported. For alkylated triazolium salts, di- or tetranuclear complexes with bridging ligands were isolated, while the bis(aryl) analogue afforded a bis(carbene) AuI -CNC pincer complex suitable for oxidation to the redox-stable [AuIII (CNC)Cl]+ cation. Although the ligand salt and the [AuIII (CNC)Cl]+ complex were both notably cytotoxic toward the breast cancer cell line MDA-MB-231, the AuIII complex was somewhat more selective. Electrophoresis, viscometry, UV-vis, CD and LD spectroscopy suggest the cytotoxic [AuIII (CNC)Cl]+ complex behaves as a partial DNA intercalator. In silico screening indicated that the [AuIII (CNC)Cl]+ complex can target DNA three-way junctions with good specificity, several other regular B-DNA forms, and Z-DNA. Multiple hydrophobic π-type interactions involving T and A bases appear to be important for B-form DNA binding, while phosphate O⋅⋅⋅Au interactions evidently underpin Z-DNA binding. The CNC ligand effectively stabilizes the AuIII ion, preventing reduction in the presence of glutathione. Both the redox stability and DNA affinity of the hit compound might be key factors underpinning its cytotoxicity in vitro.
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Affiliation(s)
| | - Cathryn A. Slabber
- Molecular Sciences InstituteSchool of ChemistryUniversity of the Witwatersrand2050JohannesburgSouth Africa
| | - Manuel A. Fernandes
- Molecular Sciences InstituteSchool of ChemistryUniversity of the Witwatersrand2050JohannesburgSouth Africa
| | - Daniël F. Joubert
- Department of PhysiologyUniversity of Pretoria0031PretoriaSouth Africa
| | - George Kleinhans
- Molecular Sciences InstituteSchool of ChemistryUniversity of the Witwatersrand2050JohannesburgSouth Africa
- Chemistry DepartmentUniversity of Pretoria0028PretoriaSouth Africa
| | - C. Johan van der Westhuizen
- Chemistry DepartmentUniversity of Pretoria0028PretoriaSouth Africa
- Future Production: ChemicalsPharmaceutical Technologies Research GroupCouncil for Scientific and Industrial Research (CSIR)0184PretoriaSouth Africa
| | - André Stander
- Department of PhysiologyUniversity of Pretoria0031PretoriaSouth Africa
| | - Orde Q. Munro
- Molecular Sciences InstituteSchool of ChemistryUniversity of the Witwatersrand2050JohannesburgSouth Africa
| | - Daniela I. Bezuidenhout
- Molecular Sciences InstituteSchool of ChemistryUniversity of the Witwatersrand2050JohannesburgSouth Africa
- Laboratory of Inorganic ChemistryEnvironmental and Chemical EngineeringUniversity of Oulu3000OuluFinland
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30
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Zhou XQ, Carbo-Bague I, Siegler MA, Hilgendorf J, Basu U, Ott I, Liu R, Zhang L, Ramu V, IJzerman AP, Bonnet S. Rollover Cyclometalation vs Nitrogen Coordination in Tetrapyridyl Anticancer Gold(III) Complexes: Effect on Protein Interaction and Toxicity. JACS AU 2021; 1:380-395. [PMID: 34056633 PMCID: PMC8154207 DOI: 10.1021/jacsau.0c00104] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Indexed: 05/05/2023]
Abstract
In this work, a pair of gold(III) complexes derived from the analogous tetrapyridyl ligands H2biqbpy1 and H2biqbpy2 was prepared: the rollover, bis-cyclometalated [Au(biqbpy1)Cl ([1]Cl) and its isomer [Au(biqbpy2)Cl ([2]Cl). In [1]+, two pyridyl rings coordinate to the metal via a Au-C bond (C∧N∧N∧C coordination) and the two noncoordinated amine bridges of the ligand remain protonated, while in [2]+ all four pyridyl rings of the ligand coordinate to the metal via a Au-N bond (N∧N∧N∧N coordination), but both amine bridges are deprotonated. As a result, both complexes are monocationic, which allowed comparison of the sole effect of cyclometalation on the chemistry, protein interaction, and anticancer properties of the gold(III) compounds. Due to their identical monocationic charge and similar molecular shape, both complexes [1]Cl and [2]Cl displaced reference radioligand [3H]dofetilide equally well from cell membranes expressing the Kv11.1 (hERG) potassium channel, and more so than the tetrapyridyl ligands H2biqbpy1 and H2biqbpy2. By contrast, cyclometalation rendered [1]Cl coordinatively stable in the presence of biological thiols, while [2]Cl was reduced by a millimolar concentration of glutathione into metastable Au(I) species releasing the free ligand H2biqbpy2 and TrxR-inhibiting Au+ ions. The redox stability of [1]Cl dramatically decreased its thioredoxin reductase (TrxR) inhibition properties, compared to [2]Cl. On the other hand, unlike [2]Cl, [1]Cl aggregated into nanoparticles in FCS-containing medium, which resulted in much more efficient gold cellular uptake. [1]Cl had much more selective anticancer properties than [2]Cl and cisplatin, as it was almost 10 times more cytotoxic to human cancer cells (A549, A431, A375, and MCF7) than to noncancerous cells (MRC5). Mechanistic studies highlight the strikingly different mode of action of the two compounds: while for [1]Cl high gold cellular uptake, nuclear DNA damage, and interaction with hERG may contribute to cell killing, for [2]Cl extracellular reduction released TrxR-inhibiting Au+ ions that were taken up in minute amounts in the cytosol, and a toxic tetrapyridyl ligand also capable of binding to hERG. These results demonstrate that bis-cyclometalation is an appealing method to improve the redox stability of Au(III) compounds and to develop gold-based cytotoxic compounds that do not rely on TrxR inhibition to kill cancer cells.
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Affiliation(s)
- Xue-Quan Zhou
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Imma Carbo-Bague
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
- Department
of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Maxime A. Siegler
- Department
of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Jonathan Hilgendorf
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Uttara Basu
- Institute
of Medicinal and Pharmaceutical Chemistry, Technische Universität Braunschweig, Beethovenstrasse 55, 38106 Braunschweig, Germany
| | - Ingo Ott
- Institute
of Medicinal and Pharmaceutical Chemistry, Technische Universität Braunschweig, Beethovenstrasse 55, 38106 Braunschweig, Germany
| | - Rongfang Liu
- Division
of Drug Discovery & Safety, Leiden Academic Centre for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands
| | - Liyan Zhang
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Vadde Ramu
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Adriaan P. IJzerman
- Division
of Drug Discovery & Safety, Leiden Academic Centre for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands
| | - Sylvestre Bonnet
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
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31
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Melidis L, Styles IB, Hannon MJ. Targeting structural features of viral genomes with a nano-sized supramolecular drug. Chem Sci 2021; 12:7174-7184. [PMID: 34123344 PMCID: PMC8153246 DOI: 10.1039/d1sc00933h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 04/05/2021] [Indexed: 11/21/2022] Open
Abstract
RNA targeting is an exciting frontier for drug design. Intriguing targets include functional RNA structures in structurally-conserved untranslated regions (UTRs) of many lethal viruses. However, computational docking screens, valuable in protein structure targeting, fail for inherently flexible RNA. Herein we harness MD simulations with Markov state modeling to enable nanosize metallo-supramolecular cylinders to explore the dynamic RNA conformational landscape of HIV-1 TAR untranslated region RNA (representative for many viruses) replicating experimental observations. These cylinders are exciting as they have unprecedented nucleic acid binding and are the first supramolecular helicates shown to have anti-viral activity in cellulo: the approach developed in this study provides additional new insight about how such viral UTR structures might be targeted with the cylinder binding into the heart of an RNA-bulge cavity, how that reduces the conformational flexibility of the RNA and molecular details of the insertion mechanism. The approach and understanding developed represents a new roadmap for design of supramolecular drugs to target RNA structural motifs across biology and nucleic acid nanoscience.
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Affiliation(s)
- Lazaros Melidis
- Physical Sciences for Health Centre, University of Birmingham Edgbaston Birmingham B15 2TT UK
| | - Iain B Styles
- Physical Sciences for Health Centre, University of Birmingham Edgbaston Birmingham B15 2TT UK
- School of Computer Science, University of Birmingham Edgbaston Birmingham B15 2TT UK
- Centre of Membrane Proteins and Receptors, The Universities of Birmingham and Nottingham The Midlands UK
- Alan Turing Institute London UK
| | - Michael J Hannon
- Physical Sciences for Health Centre, University of Birmingham Edgbaston Birmingham B15 2TT UK
- School of Chemistry, University of Birmingham Edgbaston Birmingham B15 2TT UK
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32
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Dey N, Haynes CJE. Supramolecular Coordination Complexes as Optical Biosensors. Chempluschem 2021; 86:418-433. [PMID: 33665986 DOI: 10.1002/cplu.202100004] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/15/2021] [Indexed: 12/11/2022]
Abstract
In recent years, luminescent supramolecular coordination complexes (SCCs), including 2D-metallacycles and 3D-metallacages have been utilised for biomolecular analysis. Unlike small-molecular probes, the dimensions, size, shape, and flexibility of these complexes can easily be tuned by combining ligands designed with particular geometries, symmetries and denticity with metal ions with strong geometrical binding preferences. The well-defined cavities that result, in combination with the other non-covalent interactions that can be programmed into the ligand design, facilitate great selectivity towards guest binding. In this Review we will discuss the application of luminescent metallacycles and cages in the binding and detection of a wide range of biomolecules, such as carbohydrates, proteins, amino acids, and biogenic amines. We aim to explore the effect of the structural diversity of SCCs on the extent of biomolecular sensing, expressed in terms of sensitivity, selectivity and detection range.
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Affiliation(s)
- Nilanjan Dey
- Graduate School of Science, Kyoto University, Japan
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33
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Zell J, Rota Sperti F, Britton S, Monchaud D. DNA folds threaten genetic stability and can be leveraged for chemotherapy. RSC Chem Biol 2021; 2:47-76. [PMID: 35340894 PMCID: PMC8885165 DOI: 10.1039/d0cb00151a] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 09/20/2020] [Indexed: 12/22/2022] Open
Abstract
Damaging DNA is a current and efficient strategy to fight against cancer cell proliferation. Numerous mechanisms exist to counteract DNA damage, collectively referred to as the DNA damage response (DDR) and which are commonly dysregulated in cancer cells. Precise knowledge of these mechanisms is necessary to optimise chemotherapeutic DNA targeting. New research on DDR has uncovered a series of promising therapeutic targets, proteins and nucleic acids, with application notably via an approach referred to as combination therapy or combinatorial synthetic lethality. In this review, we summarise the cornerstone discoveries which gave way to the DNA being considered as an anticancer target, and the manipulation of DDR pathways as a valuable anticancer strategy. We describe in detail the DDR signalling and repair pathways activated in response to DNA damage. We then summarise the current understanding of non-B DNA folds, such as G-quadruplexes and DNA junctions, when they are formed and why they can offer a more specific therapeutic target compared to that of canonical B-DNA. Finally, we merge these subjects to depict the new and highly promising chemotherapeutic strategy which combines enhanced-specificity DNA damaging and DDR targeting agents. This review thus highlights how chemical biology has given rise to significant scientific advances thanks to resolutely multidisciplinary research efforts combining molecular and cell biology, chemistry and biophysics. We aim to provide the non-specialist reader a gateway into this exciting field and the specialist reader with a new perspective on the latest results achieved and strategies devised.
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Affiliation(s)
- Joanna Zell
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon France
| | - Francesco Rota Sperti
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon France
| | - Sébastien Britton
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS Toulouse France
- Équipe Labellisée la Ligue Contre le Cancer 2018 Toulouse France
| | - David Monchaud
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon France
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34
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Gómez-González J, Pérez Y, Sciortino G, Roldan-Martín L, Martínez-Costas J, Maréchal JD, Alfonso I, Vázquez López M, Vázquez ME. Dynamic Stereoselection of Peptide Helicates and Their Selective Labeling of DNA Replication Foci in Cells*. Angew Chem Int Ed Engl 2021; 60:8859-8866. [PMID: 33290612 DOI: 10.1002/anie.202013039] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 11/12/2020] [Indexed: 01/03/2023]
Abstract
Although largely overlooked in peptide engineering, coordination chemistry offers a new set of interactions that opens unexplored design opportunities for developing complex molecular structures. In this context, we report new artificial peptide ligands that fold into chiral helicates in the presence of labile metal ions such as FeII and CoII . Heterochiral β-turn-promoting sequences encode the stereoselective folding of the peptide ligands and define the physicochemical properties of their corresponding metal complexes. Circular dichroism and NMR spectroscopy in combination with computational methods allowed us to identify and determine the structure of two isochiral ΛΛ-helicates, folded as topological isomers. Finally, in addition to the in-vitro characterization of their selective binding to DNA three-way junctions, cell-microscopy experiments demonstrated that a rhodamine-labeled FeII helicate was internalized and selectively stains DNA replication factories in functional cells.
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Affiliation(s)
- Jacobo Gómez-González
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Spain
| | - Yolanda Pérez
- NMR Facility, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, 08034, Barcelona, Spain
| | - Giuseppe Sciortino
- Departament de Química, Universitat Autònoma de Barcelona, 08193, Cerdanyola, Spain.,Institute of Chemical Research of Catalonia (ICIQ), Avgda. Països Catalans, 16, 43007, Tarragona, Spain
| | - Lorena Roldan-Martín
- Departament de Química, Universitat Autònoma de Barcelona, 08193, Cerdanyola, Spain
| | - José Martínez-Costas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Bioquímica y Biología Molecular, Universidade de Santiago de Compostela, Spain
| | - Jean-Didier Maréchal
- Departament de Química, Universitat Autònoma de Barcelona, 08193, Cerdanyola, Spain
| | - Ignacio Alfonso
- Department of Biological Chemistry, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, 08034, Barcelona, Spain
| | - Miguel Vázquez López
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Inorgánica, Universidade de Santiago de Compostela, Spain
| | - M Eugenio Vázquez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Spain
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35
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Gómez‐González J, Pérez Y, Sciortino G, Roldan‐Martín L, Martínez‐Costas J, Maréchal J, Alfonso I, Vázquez López M, Vázquez ME. Dynamic Stereoselection of Peptide Helicates and Their Selective Labeling of DNA Replication Foci in Cells**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202013039] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Jacobo Gómez‐González
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS) Departamento de Química Orgánica Universidade de Santiago de Compostela Spain
| | - Yolanda Pérez
- NMR Facility Institute for Advanced Chemistry of Catalonia (IQAC-CSIC) Jordi Girona 18–26 08034 Barcelona Spain
| | - Giuseppe Sciortino
- Departament de Química Universitat Autònoma de Barcelona 08193 Cerdanyola Spain
- Institute of Chemical Research of Catalonia (ICIQ) Avgda. Països Catalans, 16 43007 Tarragona Spain
| | | | - José Martínez‐Costas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS) Departamento de Bioquímica y Biología Molecular Universidade de Santiago de Compostela Spain
| | | | - Ignacio Alfonso
- Department of Biological Chemistry Institute for Advanced Chemistry of Catalonia (IQAC-CSIC) Jordi Girona 18–26 08034 Barcelona Spain
| | - Miguel Vázquez López
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS) Departamento de Química Inorgánica Universidade de Santiago de Compostela Spain
| | - M. Eugenio Vázquez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS) Departamento de Química Orgánica Universidade de Santiago de Compostela Spain
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36
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Song H, Postings M, Scott P, Rogers NJ. Metallohelices emulate the properties of short cationic α-helical peptides. Chem Sci 2021; 12:1620-1631. [PMID: 34163922 PMCID: PMC8179244 DOI: 10.1039/d0sc06412b] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 12/24/2020] [Indexed: 12/15/2022] Open
Abstract
Naturally occurring peptides in many living systems perform antimicrobial and anticancer host defence roles, but their potential for clinical application is limited by low metabolic stability and relatively high costs of goods. Self-assembled helical metal complexes provide an attractive synthetic platform for non-peptidic architectures that can emulate some of the properties of short cationic α-helical peptides, with tuneable charge, shape, size and amphipathicity. Correspondingly there is a growing body of evidence demonstrating that these supramolecular architectures exhibit bioactivity that emulates that of the natural systems. We review that evidence in the context of synthetic advances in the area, driven by the potential for biomedical applications. We note some design considerations for new biologically-relevant metallohelices, and give our outlook on the future of these compounds as therapeutic peptidomimetics.
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37
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Shao J, Yan ZY, Tang M, Huang CH, Sheng ZG, Chen J, Shao B, Zhu BZ. Potent oxidation of DNA by Ru(ii) tri(polypyridyl) complexes under visible light irradiation via a singlet oxygen-mediated mechanism. Inorg Chem Front 2021. [DOI: 10.1039/d0qi01518k] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The irradiation of Ru(ii) tri(polypridyl) complexes with visible light can induce potent oxidation of DNA mediated by 1O2via a type II photosensitization mechanism.
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Affiliation(s)
- Jie Shao
- State Key Laboratory of Environmental Chemistry and Eco-toxicology
- Research Centre for Eco-environmental Sciences and University of the Chinese Academy of Sciences
- the Chinese Academy of Sciences
- Beijing 100085
- PR China
| | - Zhu-Ying Yan
- State Key Laboratory of Environmental Chemistry and Eco-toxicology
- Research Centre for Eco-environmental Sciences and University of the Chinese Academy of Sciences
- the Chinese Academy of Sciences
- Beijing 100085
- PR China
| | - Miao Tang
- State Key Laboratory of Environmental Chemistry and Eco-toxicology
- Research Centre for Eco-environmental Sciences and University of the Chinese Academy of Sciences
- the Chinese Academy of Sciences
- Beijing 100085
- PR China
| | - Chun-Hua Huang
- State Key Laboratory of Environmental Chemistry and Eco-toxicology
- Research Centre for Eco-environmental Sciences and University of the Chinese Academy of Sciences
- the Chinese Academy of Sciences
- Beijing 100085
- PR China
| | - Zhi-Guo Sheng
- State Key Laboratory of Environmental Chemistry and Eco-toxicology
- Research Centre for Eco-environmental Sciences and University of the Chinese Academy of Sciences
- the Chinese Academy of Sciences
- Beijing 100085
- PR China
| | - Jing Chen
- State Key Laboratory of Environmental Chemistry and Eco-toxicology
- Research Centre for Eco-environmental Sciences and University of the Chinese Academy of Sciences
- the Chinese Academy of Sciences
- Beijing 100085
- PR China
| | - Bo Shao
- State Key Laboratory of Environmental Chemistry and Eco-toxicology
- Research Centre for Eco-environmental Sciences and University of the Chinese Academy of Sciences
- the Chinese Academy of Sciences
- Beijing 100085
- PR China
| | - Ben-Zhan Zhu
- State Key Laboratory of Environmental Chemistry and Eco-toxicology
- Research Centre for Eco-environmental Sciences and University of the Chinese Academy of Sciences
- the Chinese Academy of Sciences
- Beijing 100085
- PR China
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38
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Percástegui E, Ronson TK, Nitschke JR. Design and Applications of Water-Soluble Coordination Cages. Chem Rev 2020; 120:13480-13544. [PMID: 33238092 PMCID: PMC7760102 DOI: 10.1021/acs.chemrev.0c00672] [Citation(s) in RCA: 238] [Impact Index Per Article: 59.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Indexed: 12/23/2022]
Abstract
Compartmentalization of the aqueous space within a cell is necessary for life. In similar fashion to the nanometer-scale compartments in living systems, synthetic water-soluble coordination cages (WSCCs) can isolate guest molecules and host chemical transformations. Such cages thus show promise in biological, medical, environmental, and industrial domains. This review highlights examples of three-dimensional synthetic WSCCs, offering perspectives so as to enhance their design and applications. Strategies are presented that address key challenges for the preparation of coordination cages that are soluble and stable in water. The peculiarities of guest binding in aqueous media are examined, highlighting amplified binding in water, changing guest properties, and the recognition of specific molecular targets. The properties of WSCC hosts associated with biomedical applications, and their use as vessels to carry out chemical reactions in water, are also presented. These examples sketch a blueprint for the preparation of new metal-organic containers for use in aqueous solution, as well as guidelines for the engineering of new applications in water.
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Affiliation(s)
- Edmundo
G. Percástegui
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
- Instituto
de Química, Ciudad UniversitariaUniversidad
Nacional Autónoma de México, Ciudad de México 04510, México
- Centro
Conjunto de Investigación en Química Sustentable, UAEM-UNAM, Carretera Toluca-Atlacomulco Km 14.5, Toluca, 50200 Estado de México, México
| | - Tanya K. Ronson
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
| | - Jonathan R. Nitschke
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
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39
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Hooper CAJ, Cardo L, Craig JS, Melidis L, Garai A, Egan RT, Sadovnikova V, Burkert F, Male L, Hodges NJ, Browning DF, Rosas R, Liu F, Rocha FV, Lima MA, Liu S, Bardelang D, Hannon MJ. Rotaxanating Metallo-supramolecular Nano-cylinder Helicates to Switch DNA Junction Binding. J Am Chem Soc 2020; 142:20651-20660. [DOI: 10.1021/jacs.0c07750] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Catherine A. J. Hooper
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Lucia Cardo
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - James S. Craig
- Physical Sciences for Health Centre, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Lazaros Melidis
- Physical Sciences for Health Centre, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Aditya Garai
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Ross T. Egan
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Viktoriia Sadovnikova
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Florian Burkert
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Louise Male
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Nikolas J. Hodges
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Douglas F. Browning
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Roselyne Rosas
- Aix Marseille Univ, CNRS, Centrale Marseille, FSCM, Spectropole, Marseille 13007, France
| | - Fengbo Liu
- The State Key Laboratory of Refractories and Metallurgy, School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, P. R. China
| | - Fillipe V. Rocha
- Department of Chemistry, Federal University of São Carlos, São Carlos 13565-905, Brazil
| | - Mauro A. Lima
- Department of Chemistry, Federal University of São Carlos, São Carlos 13565-905, Brazil
| | - Simin Liu
- The State Key Laboratory of Refractories and Metallurgy, School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, P. R. China
| | | | - Michael J. Hannon
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
- Physical Sciences for Health Centre, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
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40
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Tan DJY, Winnerdy FR, Lim KW, Phan AT. Coexistence of two quadruplex-duplex hybrids in the PIM1 gene. Nucleic Acids Res 2020; 48:11162-11171. [PMID: 32976598 PMCID: PMC7641742 DOI: 10.1093/nar/gkaa752] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 08/26/2020] [Accepted: 08/31/2020] [Indexed: 12/31/2022] Open
Abstract
The triple-negative breast cancer (TNBC), a subtype of breast cancer which lacks of targeted therapies, exhibits a poor prognosis. It was shown recently that the PIM1 oncogene is highly related to the proliferation of TNBC cells. A quadruplex-duplex hybrid (QDH) forming sequence was recently found to exist near the transcription start site of PIM1. This structure could be an attractive target for regulation of the PIM1 gene expression and thus the treatment of TNBC. Here, we present the solution structures of two QDHs that could coexist in the human PIM1 gene. Form 1 is a three-G-tetrad-layered (3+1) G-quadruplex containing a propeller loop, a lateral loop and a stem-loop made up of three G•C Watson-Crick base pairs. On the other hand, Form 2 is an anti-parallel G-quadruplex comprising two G-tetrads and a G•C•G•C tetrad; the structure has three lateral loops with the middle stem-loop made up of two Watson-Crick G•C base pairs. These structures provide valuable information for the design of G-quadruplex-specific ligands for PIM1 transcription regulation.
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Affiliation(s)
- Derrick J Y Tan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Fernaldo Richtia Winnerdy
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Kah Wai Lim
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, Singapore 636921, Singapore
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41
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Metallosupramolecular helices constructed from nickel(II) and multidentate “click” triazole ligands. Polyhedron 2020. [DOI: 10.1016/j.poly.2020.114805] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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42
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Dong Y, Yao C, Zhu Y, Yang L, Luo D, Yang D. DNA Functional Materials Assembled from Branched DNA: Design, Synthesis, and Applications. Chem Rev 2020; 120:9420-9481. [DOI: 10.1021/acs.chemrev.0c00294] [Citation(s) in RCA: 168] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Yuhang Dong
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
| | - Chi Yao
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
| | - Yi Zhu
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
| | - Lu Yang
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
| | - Dan Luo
- Department of Biological & Environmental Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Dayong Yang
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
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43
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Li X, Shi Z, Wu J, Wu J, He C, Hao X, Duan C. Lighting up metallohelices: from DNA binders to chemotherapy and photodynamic therapy. Chem Commun (Camb) 2020; 56:7537-7548. [PMID: 32573609 DOI: 10.1039/d0cc02194f] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The design of novel agents that specifically target DNA and interrupt its normal biological processes is an attractive goal in drug design. Among the promising metallodrugs, metal-directed self-assembled metallohelices with defined three-dimensional stereochemical structures display unique structure-inherent and unprecedented noncovalent targeting abilities towards DNA, resulting in excellent anticancer or antibiotic activities. A newly burgeoning hotspot is focusing on lighting them up by embedding luminescent metal ions as the vertices. The photoactive metallohelices that combine strong interactions toward DNA targets and efficient 1O2 quantum yield may provide new motivation in diagnostic and photodynamic therapy (PDT) areas. This perspective focuses on research progress on metallohelices as DNA binders and chemotherapeutic agents, and highlights recent advances in fabricating luminescent examples for PDT. The relative assembly strategies are also discussed and compared. Finally, perspectives on the future development of the lit-up metallohelices are presented.
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Affiliation(s)
- Xuezhao Li
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian, 116024, China.
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44
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Crlikova H, Malina J, Novohradsky V, Kostrhunova H, Vasdev RAS, Crowley JD, Kasparkova J, Brabec V. Antiproliferative Activity and Associated DNA Interactions of [Co2L3]6+ Cylinders Derived from Bis(bidentate) 2-Pyridyl-1,2,3-triazole Ligands. Organometallics 2020. [DOI: 10.1021/acs.organomet.0c00146] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hana Crlikova
- Department of Biophysics, Faculty of Science, Palacky University, Slechtitelu 27, CZ-783-71 Olomouc, Czech Republic
| | - Jaroslav Malina
- Czech Academy of Sciences, Institute of Biophysics, Kralovopolska 135, CZ-61265 Brno, Czech Republic
| | - Vojtech Novohradsky
- Czech Academy of Sciences, Institute of Biophysics, Kralovopolska 135, CZ-61265 Brno, Czech Republic
| | - Hana Kostrhunova
- Czech Academy of Sciences, Institute of Biophysics, Kralovopolska 135, CZ-61265 Brno, Czech Republic
| | - Roan A. S. Vasdev
- Department of Chemistry, University of Otago, P.O. Box 56, Dunedin 9016, Otago, New Zealand
| | - James D. Crowley
- Department of Chemistry, University of Otago, P.O. Box 56, Dunedin 9016, Otago, New Zealand
| | - Jana Kasparkova
- Department of Biophysics, Faculty of Science, Palacky University, Slechtitelu 27, CZ-783-71 Olomouc, Czech Republic
- Czech Academy of Sciences, Institute of Biophysics, Kralovopolska 135, CZ-61265 Brno, Czech Republic
| | - Viktor Brabec
- Czech Academy of Sciences, Institute of Biophysics, Kralovopolska 135, CZ-61265 Brno, Czech Republic
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45
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Takezawa Y, Shionoya M. Supramolecular DNA Three-Way Junction Motifs With a Bridging Metal Center. Front Chem 2020; 7:925. [PMID: 32010671 PMCID: PMC6974547 DOI: 10.3389/fchem.2019.00925] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 12/18/2019] [Indexed: 12/15/2022] Open
Abstract
Various nano-sized supramolecular architectures have been constructed from DNA molecules via sequence-dependent self-assembly. A DNA three-way junction (3WJ), consisting of three oligonucleotides that are partially complementary to each other, is one of the simplest DNA supramolecular structures. This minireview covers studies on DNA 3WJ motifs bridged by an interstrand metal complex with some related works. The incorporation of interstrand metal complexes into DNA has attracted increasing attention because it potentially allows for metal-dependent regulation of the thermal stability and the structure of DNA supramolecules. Metal-bridged DNA 3WJs were synthesized from three DNA strands containing a bipyridine (bpy)-modified nucleotide in the presence of appropriate metal ions. The bpy-modified DNA strands were crosslinked by an interstrand 3:1 metal complex [NiII(bpy)3 etc.] at the junction core. As a result, the thermal stability of the 3WJs was significantly enhanced upon metal complexation. Furthermore, metal-mediated structural transformation between DNA duplexes and 3WJs was demonstrated by using the same bpy-modified DNA strands. A mixture of bpy-modified strands and their natural complementary strands were self-assembled exclusively into duplexes in the absence of any transition metal ions. In contrast, addition of NiII ions induced the formation of 3WJs through the formation of an interstrand NiII(bpy)3 complex, which served as a template for the 3WJ assembly. Because DNA 3WJ structures are essential structural motifs for DNA-based nanoarchitectures, the metal-mediated stabilization and structural induction of metal-locked 3WJs would lead to many potential applications to artificial DNA architectures.
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Affiliation(s)
- Yusuke Takezawa
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Mitsuhiko Shionoya
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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46
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Chaudhari KR, Kunwar A, Bhuvanesh N, Dey S. Synthesis and anti-proliferative activities of amine capped Pd and Pt macrocycles of 4,4′-dipyridylselenides. NEW J CHEM 2020. [DOI: 10.1039/c9nj06052a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Symmetric macrocyclic complexes characterized as dimeric and their oligomeric form in water and the solid state exhibit high in vitro anticancer activities.
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Affiliation(s)
- K. R. Chaudhari
- Chemistry Division
- Bhabha Atomic Research Centre
- Mumbai 400 085
- India
| | - A. Kunwar
- Homi Bhabha National Institute
- Training School Complex
- Mumbai 400 094
- India
- Radiation and Photo Chemistry Division
| | - N. Bhuvanesh
- Department of Chemistry
- Texas A&M University
- College Station
- USA
| | - S. Dey
- Chemistry Division
- Bhabha Atomic Research Centre
- Mumbai 400 085
- India
- Homi Bhabha National Institute
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47
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Kench T, Vilar R. Metal complexes as G-quadruplex binders. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 2020. [DOI: 10.1016/bs.armc.2020.05.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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48
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Duskova K, Lejault P, Benchimol É, Guillot R, Britton S, Granzhan A, Monchaud D. DNA Junction Ligands Trigger DNA Damage and Are Synthetic Lethal with DNA Repair Inhibitors in Cancer Cells. J Am Chem Soc 2019; 142:424-435. [PMID: 31833764 DOI: 10.1021/jacs.9b11150] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Translocation of DNA and RNA polymerases along their duplex substrates results in DNA supercoiling. This torsional stress promotes the formation of plectonemic structures, including three-way DNA junction (TWJ), which can block DNA transactions and lead to DNA damage. While cells have evolved multiple mechanisms to prevent the accumulation of such structures, stabilizing TWJ through ad hoc ligands offer an opportunity to trigger DNA damage in cells with high levels of transcription and replication, such as cancer cells. Here, we develop a series of azacryptand-based TWJ ligands, we thoroughly characterize their TWJ-interacting properties in vitro and demonstrate their capacity to trigger DNA damage in rapidly dividing human cancer cells. We also demonstrate that TWJ ligands are amenable to chemically induced synthetic lethality strategies upon association with inhibitors of DNA repair, thus paving the way toward innovative drug combinations to fight cancers.
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Affiliation(s)
- Katerina Duskova
- Institut de Chimie Moléculaire de l'Université de Bourgogne (ICMUB), CNRS UMR 6302 , UBFC Dijon , 21078 Dijon , France
| | - Pauline Lejault
- Institut de Chimie Moléculaire de l'Université de Bourgogne (ICMUB), CNRS UMR 6302 , UBFC Dijon , 21078 Dijon , France
| | - Élie Benchimol
- Institut Curie, CNRS UMR 9187, INSERM U1196 , PSL Research University , 91405 Orsay , France.,Université Paris Saclay, CNRS UMR 9187, INSERM U1196 , Université Paris-Sud , 91405 Orsay , France
| | - Régis Guillot
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), CNRS UMR 8182, Université Paris-Sud , Université Paris Saclay , 91405 Orsay , France
| | - Sébastien Britton
- Institut de Pharmacologie et de Biologie Structurale (IPBS), CNRS UMR 5089, Université de Toulouse , UPS , Equipe labellisée la Ligue Contre le Cancer , 31077 Toulouse , France
| | - Anton Granzhan
- Institut Curie, CNRS UMR 9187, INSERM U1196 , PSL Research University , 91405 Orsay , France.,Université Paris Saclay, CNRS UMR 9187, INSERM U1196 , Université Paris-Sud , 91405 Orsay , France
| | - David Monchaud
- Institut de Chimie Moléculaire de l'Université de Bourgogne (ICMUB), CNRS UMR 6302 , UBFC Dijon , 21078 Dijon , France
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Eskandari A, Kundu A, Ghosh S, Suntharalingam K. A Triangular Platinum(II) Multinuclear Complex with Cytotoxicity Towards Breast Cancer Stem Cells. Angew Chem Int Ed Engl 2019; 58:12059-12064. [DOI: 10.1002/anie.201905389] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Indexed: 12/21/2022]
Affiliation(s)
- Arvin Eskandari
- Department of ChemistryKing's College London London SE1 1DB UK
| | - Arunangshu Kundu
- Department of ChemistryGauhati University Guwahati Assam 781014 India
| | - Sushobhan Ghosh
- Department of ChemistryGauhati University Guwahati Assam 781014 India
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Lejault P, Duskova K, Bernhard C, Valverde IE, Romieu A, Monchaud D. The Scope of Application of Macrocyclic Polyamines Beyond Metal Chelation. European J Org Chem 2019. [DOI: 10.1002/ejoc.201900870] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Pauline Lejault
- CNRS UMR6302, Université Bourgogne Franche-Comté (UBFC); Institut de Chimie Moleculaire de l'Université de Bourgogne (ICMUB); 9, Avenue Alain Savary 21078 Dijon France
| | - Katerina Duskova
- CNRS UMR6302, Université Bourgogne Franche-Comté (UBFC); Institut de Chimie Moleculaire de l'Université de Bourgogne (ICMUB); 9, Avenue Alain Savary 21078 Dijon France
| | - Claire Bernhard
- CNRS UMR6302, Université Bourgogne Franche-Comté (UBFC); Institut de Chimie Moleculaire de l'Université de Bourgogne (ICMUB); 9, Avenue Alain Savary 21078 Dijon France
| | - Ibai E. Valverde
- CNRS UMR6302, Université Bourgogne Franche-Comté (UBFC); Institut de Chimie Moleculaire de l'Université de Bourgogne (ICMUB); 9, Avenue Alain Savary 21078 Dijon France
| | - Anthony Romieu
- CNRS UMR6302, Université Bourgogne Franche-Comté (UBFC); Institut de Chimie Moleculaire de l'Université de Bourgogne (ICMUB); 9, Avenue Alain Savary 21078 Dijon France
| | - David Monchaud
- CNRS UMR6302, Université Bourgogne Franche-Comté (UBFC); Institut de Chimie Moleculaire de l'Université de Bourgogne (ICMUB); 9, Avenue Alain Savary 21078 Dijon France
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