1
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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:e202409780. [PMID: 38873877 DOI: 10.1002/anie.202409780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [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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Pruška A, Harrison JA, Granzhan A, Marchand A, Zenobi R. Solution and Gas-Phase Stability of DNA Junctions from Temperature-Controlled Electrospray Ionization and Surface-Induced Dissociation. Anal Chem 2023; 95:14384-14391. [PMID: 37699589 DOI: 10.1021/acs.analchem.3c02742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
Abstract
DNA three-way junction (TWJ) structures transiently form during key cellular processes such as transcription, replication, and DNA repair. Despite their significance, the thermodynamics of TWJs, including the influence of strand length, base pair composition, and ligand binding on TWJ stability and dissociation mechanisms, are poorly understood. To address these questions, we interfaced temperature-controlled nanoelectrospray ionization mass spectrometry (TC-nESI-MS) with a cyclic ion mobility spectrometry (cIMS) instrument that was also equipped with a surface-induced dissociation (SID) stage. This novel combination allowed us to investigate the structural intermediates of three TWJ complexes and examine the effects of GC base pairs on their dissociation pathways. We found that two TWJ-specific ligands, 2,7-tris-naphthalene (2,7-TrisNP) and tris-phenoxybenzene (TrisPOB), lead to TWJ stabilization, revealed by an increase in the melting temperature (Tm) by 13 or 26 °C, respectively. To gain insights into conformational changes in the gas phase, we employed cIMS and SID to analyze TWJs and their complexes with ligands. Analysis of IM arrival distributions suggested a single-step dissociation of TWJs and their intermediates for the three studied TWJ complexes. Upon ligand binding, a higher SID energy by 3 V (2,7-TrisNP) and 5 V (TrisPOB) was required to induce 50% dissociation of TWJ, compared to 38 V in the absence of ligands. Our results demonstrate the power of utilizing TC-nESI-MS in combination with cIMS and SID for thermodynamic characterization of TWJ complexes and investigation of ligand binding. These techniques are essential for the TWJ design and development as drug targets, aptamers, and structural units for functional biomaterials.
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Affiliation(s)
- Adam Pruška
- Department of Chemistry and Applied Biosciences, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Julian A Harrison
- Department of Chemistry and Applied Biosciences, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Anton Granzhan
- CNRS UMR9187, Inserm U1196, Institut Curie, Paris Saclay University, F-91405 Orsay, France
| | - Adrien Marchand
- Department of Chemistry and Applied Biosciences, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, ETH Zurich, CH-8093 Zurich, Switzerland
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3
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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: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [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
- Correspondence may also be addressed to Christine J. Cardin. Tel: +44 118 378 8215;
| | - David Monchaud
- To whom correspondence should be addressed. Tel: +33 380 399 043;
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4
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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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Song Q, Hu Y, Yin A, Wang H, Yin Q. DNA Holliday Junction: History, Regulation and Bioactivity. Int J Mol Sci 2022; 23:ijms23179730. [PMID: 36077130 PMCID: PMC9456528 DOI: 10.3390/ijms23179730] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 08/16/2022] [Accepted: 08/18/2022] [Indexed: 11/16/2022] Open
Abstract
DNA Holliday junction (HJ) is a four-way stranded DNA intermediate that formed in replication fork regression, homology-dependent repair and mitosis, performing a significant role in genomic stability. Failure to remove HJ can induce an acceptable replication fork stalling and DNA damage in normal cells, leading to a serious chromosomal aberration and even cell death in HJ nuclease-deficient tumor cells. Thus, HJ is becoming an attractive target in cancer therapy. However, the development of HJ-targeting ligand faces great challenges because of flexile cavities on the center of HJs. This review introduces the discovery history of HJ, elucidates the formation and dissociation procedures of HJ in corresponding bio-events, emphasizes the importance of prompt HJ-removing in genome stability, and summarizes recent advances in HJ-based ligand discovery. Our review indicate that target HJ is a promising approach in oncotherapy.
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Affiliation(s)
- Qinqin Song
- State/Key Laboratory of Microbial Technology, Shandong University, 72 Jimo Binhai Road, Qingdao 266237, China
| | - Yuemiao Hu
- Key Laboratory of Molecular Pharmacology and Drug Evaluation, Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, School of Pharmacy, Yantai University, 30 Qingquan Road, Yantai 264005, China
| | - Anqi Yin
- Key Laboratory of Molecular Pharmacology and Drug Evaluation, Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, School of Pharmacy, Yantai University, 30 Qingquan Road, Yantai 264005, China
| | - Hongbo Wang
- Key Laboratory of Molecular Pharmacology and Drug Evaluation, Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, School of Pharmacy, Yantai University, 30 Qingquan Road, Yantai 264005, China
| | - Qikun Yin
- Key Laboratory of Molecular Pharmacology and Drug Evaluation, Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, School of Pharmacy, Yantai University, 30 Qingquan Road, Yantai 264005, China
- Bohai Rim Advanced Research Institute for Drug Discovery, 198 Binhai East Road, Yantai 264005, China
- Correspondence:
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6
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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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7
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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: 4] [Impact Index Per Article: 1.3] [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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8
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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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9
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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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10
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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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11
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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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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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Duskova K, Lamarche J, Amor S, Caron C, Queyriaux N, Gaschard M, Penouilh MJ, de Robillard G, Delmas D, Devillers CH, Granzhan A, Teulade-Fichou MP, Chavarot-Kerlidou M, Therrien B, Britton S, Monchaud D. Identification of Three-Way DNA Junction Ligands through Screening of Chemical Libraries and Validation by Complementary in Vitro Assays. J Med Chem 2019; 62:4456-4466. [PMID: 30942581 DOI: 10.1021/acs.jmedchem.8b01978] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The human genome is replete with repetitive DNA sequences that can fold into thermodynamically stable secondary structures such as hairpins and quadruplexes. Cellular enzymes exist to cope with these structures whose stable accumulation would result in DNA damage through interference with DNA transactions such as transcription and replication. Therefore, the chemical stabilization of secondary DNA structures offers an attractive way to foster DNA transaction-associated damages to trigger cell death in proliferating cancer cells. While much emphasis has been recently given to DNA quadruplexes, we focused here on three-way DNA junctions (TWJ) and report on a strategy to identify TWJ-targeting agents through a combination of in vitro techniques (TWJ-screen, polyacrylamide gel electrophoresis, fluorescence resonance energy transfer-melting, electrospray ionization mass spectrometry, dialysis equilibrium, and sulforhodamine B assays). We designed a complete workflow and screened 1200 compounds to identify promising TWJ ligands selected on stringent criteria in terms of TWJ-folding ability, affinity, and selectivity.
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Affiliation(s)
- Katerina Duskova
- Institut de Chimie Moléculaire (ICMUB), CNRS UMR6302, UBFC , 21078 Dijon , France
| | - Jérémy Lamarche
- Institut de Chimie Moléculaire (ICMUB), CNRS UMR6302, UBFC , 21078 Dijon , France
| | - Souheila Amor
- Lipids, Nutrition & Cancers (LNC), INSERM U1321, UBFC , 21000 Dijon , France
| | - Coralie Caron
- Institut Curie, PSL Research University, CNRS UMR9187, INSERM U1196 , 91405 Orsay , France.,Université Paris-Sud, Université Paris Saclay , 91405 Orsay , France
| | - Nicolas Queyriaux
- Laboratoire de Chimie et Biologie des Métaux , Université Grenoble Alpes, CNRS UMR5249, CEA , 38054 Grenoble , France
| | - Marie Gaschard
- Institut de Chimie , Université de Neuchâtel , CH-2000 Neuchatel , Switzerland
| | - Marie-José Penouilh
- Pôle Chimie Moléculaire (PACSMUB) , Faculté des Sciences Mirande, UBFC , 21078 Dijon , France
| | | | - Dominique Delmas
- Lipids, Nutrition & Cancers (LNC), INSERM U1321, UBFC , 21000 Dijon , France
| | - Charles H Devillers
- Institut de Chimie Moléculaire (ICMUB), CNRS UMR6302, UBFC , 21078 Dijon , France
| | - Anton Granzhan
- Institut Curie, PSL Research University, CNRS UMR9187, INSERM U1196 , 91405 Orsay , France.,Université Paris-Sud, Université Paris Saclay , 91405 Orsay , France
| | - Marie-Paule Teulade-Fichou
- Institut Curie, PSL Research University, CNRS UMR9187, INSERM U1196 , 91405 Orsay , France.,Université Paris-Sud, Université Paris Saclay , 91405 Orsay , France
| | - Murielle Chavarot-Kerlidou
- Laboratoire de Chimie et Biologie des Métaux , Université Grenoble Alpes, CNRS UMR5249, CEA , 38054 Grenoble , France
| | - Bruno Therrien
- Institut de Chimie , Université de Neuchâtel , CH-2000 Neuchatel , Switzerland
| | - Sébastien Britton
- Institut de Pharmacologie et de Biologie Structurale, IPBS, CNRS UMR5089, Université de Toulouse, UPS, équipe labellisée la Ligue Contre le Cancer , 31077 Toulouse , France
| | - David Monchaud
- Institut de Chimie Moléculaire (ICMUB), CNRS UMR6302, UBFC , 21078 Dijon , France
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