1
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Laigre E, Bonnet H, Beauvineau C, Lavergne T, Verga D, Defrancq E, Dejeu J, Teulade-Fichou MP. Systematic Evaluation of Benchmark G4 Probes and G4 Clinical Drugs using three Biophysical Methods: A Guideline to Evaluate Rapidly G4-Binding Affinity. Chembiochem 2024; 25:e202400210. [PMID: 38619969 DOI: 10.1002/cbic.202400210] [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: 04/08/2024] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 04/17/2024]
Abstract
G-quadruplex DNA structures (G4) are proven to interfere with most genetic and epigenetic processes. Small molecules binding these structures (G4 ligands) are invaluable tools to probe G4-biology and address G4-druggability in various diseases (cancer, viral infections). However, the large number of reported G4 ligands (>1000) could lead to confusion while selecting one for a given application. Herein we conducted a systematic affinity ranking of 11 popular G4 ligands vs 5 classical G4 sequences using FRET-melting, G4-FID assays and SPR. Interestingly SPR data globally align with the rankings obtained from the two semi-quantitative assays despite discrepancies due to limits and characteristics of each assay. In the whole, PhenDC3 emerges as the most potent binder irrespective of the G4 sequence. Immediately below PDS, PDC-360A, BRACO19, TMPyP4 and RHPS4 feature strong to medium binding again with poor G4 topology discrimination. More strikingly, the G4 drugs Quarfloxin, CX5461 and c-PDS exhibit weak affinity with all G4s studied. Finally, NMM and Cu-ttpy showed heterogeneous behaviors due, in part, to their physicochemical particularities poorly compatible with screening conditions. The remarkable properties of PhenDC3 led us to propose its use for benchmarking FRET-melting and G4-FID assays for rapid G4-affinity evaluation of newly developed ligands.
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Affiliation(s)
- E Laigre
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, F-91405, Orsay, France
- CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405, Orsay, France
| | - H Bonnet
- DCM, UMR 5250, Univ. Grenoble Alpes, CNRS, 570 Rue de la Chimie, 38000, Grenoble, France
| | - C Beauvineau
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, F-91405, Orsay, France
- CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405, Orsay, France
| | - T Lavergne
- DCM, UMR 5250, Univ. Grenoble Alpes, CNRS, 570 Rue de la Chimie, 38000, Grenoble, France
| | - D Verga
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, F-91405, Orsay, France
- CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405, Orsay, France
| | - E Defrancq
- DCM, UMR 5250, Univ. Grenoble Alpes, CNRS, 570 Rue de la Chimie, 38000, Grenoble, France
| | - J Dejeu
- DCM, UMR 5250, Univ. Grenoble Alpes, CNRS, 570 Rue de la Chimie, 38000, Grenoble, France
- SUPMICROTECH, Université Franche-Comté, CNRS, Institut FEMTO-ST, 25000, Besançon, France
| | - M-P Teulade-Fichou
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, F-91405, Orsay, France
- CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405, Orsay, France
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2
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Farag M, Mouawad L. Comprehensive analysis of intramolecular G-quadruplex structures: furthering the understanding of their formalism. Nucleic Acids Res 2024; 52:3522-3546. [PMID: 38512075 DOI: 10.1093/nar/gkae182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 02/16/2024] [Accepted: 03/01/2024] [Indexed: 03/22/2024] Open
Abstract
G-quadruplexes (G4) are helical structures found in guanine-rich DNA or RNA sequences. Generally, their formalism is based on a few dozen structures, which can produce some inconsistencies or incompleteness. Using the website ASC-G4, we analyzed the structures of 333 intramolecular G4s, of all types, which allowed us to clarify some key concepts and present new information. To each of the eight distinguishable topologies corresponds a groove-width signature and a predominant glycosidic configuration (gc) pattern governed by the directions of the strands. The relative orientations of the stacking guanines within the strands, which we quantified and related to their vertical gc successions, determine the twist and tilt of the helices. The latter impact the minimum groove widths, which represent the space available for lateral ligand binding. The G4 four helices have similar twists, even when these twists are irregular, meaning that they have various angles along the strands. Despite its importance, the vertical gc succession has no strict one-to-one relationship with the topology, which explains the discrepancy between some topologies and their corresponding circular dichroism spectra. This study allowed us to introduce the new concept of platypus G4s, which are structures with properties corresponding to several topologies.
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Affiliation(s)
- Marc Farag
- Chemistry and Modeling for the Biology of Cancer, CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, Université Paris-Saclay, CS 90030, 91401 ORSAYCedex, France
| | - Liliane Mouawad
- Chemistry and Modeling for the Biology of Cancer, CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, Université Paris-Saclay, CS 90030, 91401 ORSAYCedex, France
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3
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Kundu N, Sharma T, Kaur S, Mahto AK, Prasad Dewangan R, Shankaraswamy J, Saxena S. Significant destabilization of human telomeric G-quadruplex upon peptide binding: dramatic effect of flanking bases. J Biomol Struct Dyn 2023; 41:7119-7127. [PMID: 36038986 DOI: 10.1080/07391102.2022.2116602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 08/16/2022] [Indexed: 10/14/2022]
Abstract
Human telomere is composed of highly repeated hexanucleotide sequence TTAGGG and a 3' single-stranded DNA tail. Many telomere G4 topologies characterized at atomic level by X-ray crystallography and NMR studies. Until now, various small ligands developed to interact with G-quadruplex mainly to stabilize the structure and least is known for its destabilization. In this study, we provide the first evidence of human telomeric G4 destabilization upon peptide binding in dilute and cell-mimicking molecular crowing conditions due to the changes in flanking bases of human telomeric sequences. Hence, our findings will open the new ways to target diseases related with increasing the efficiency of DNA replication, transcription or duplex reannealing.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Nikita Kundu
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - Taniya Sharma
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - Sarvpreet Kaur
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - Aman Kumar Mahto
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, India
| | - Rikeshwer Prasad Dewangan
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, India
| | - J Shankaraswamy
- Department of Fruit Science, College of Horticulture, Mojerla, Sri Konda Laxman Telangana State Horticultural University, Hyderabad, India
| | - Sarika Saxena
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
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4
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Roy S, Muniyappa K, Bhattacharya S. Deciphering the Binding Insights of Novel Disubstituted Anthraquinone Derivatives with G-Quadruplex DNA to Exhibit Selective Cancer Cell Cytotoxicity. ChemMedChem 2022; 17:e202200436. [PMID: 36161519 DOI: 10.1002/cmdc.202200436] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/22/2022] [Indexed: 01/14/2023]
Abstract
Anthraquinone-based compounds are well-known as duplex DNA as well as G-quadruplex DNA binders. Implications of various anthraquinone derivatives for specific recognition of G-quadruplex DNA over duplex DNA is a 'challenging' research work that requires adequate experience with molecular design. To address this important issue, we designed and synthesized ten new 2,6-disubstituted anthraquinone-based derivatives with different functionalized piperazinyl side-chains. Among these, particular compounds with certain distant groups have shown selective and significant binding affinities toward the c-MYC and c-KIT G-quadruplex DNA over the duplex DNA, as noticed from various biophysical experiments. The structural difference of quadruplex and duplex DNA was utilized to probe these derivatives for the end-stacking mode of binding with G-quadruplex DNA. The ability of the ligands to halt DNA synthesis by stabilizing G-quadruplex structures is one of the crucial points to further apply them for quadruplex-mediated anti-cancer therapeutics. Interestingly, these ligands trigger apoptosis to exhibit selective cytotoxicity toward cancer cells over normal cells. This was further evidenced by ligand-induced cell cycle arrest as well as cellular apoptotic morphological changes. These blood-compatible ligands provided detailed structure-activity relationship approaches for the molecular design of anthraquinone-based G-quadruplex binders.
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Affiliation(s)
- Soma Roy
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, 560012, India.,School of Applied & Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata, 700032, India
| | - Kalappa Muniyappa
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Santanu Bhattacharya
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, 560012, India.,School of Applied & Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata, 700032, India
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5
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Ghosh A, Trajkovski M, Teulade‐Fichou M, Gabelica V, Plavec J. Phen-DC 3 Induces Refolding of Human Telomeric DNA into a Chair-Type Antiparallel G-Quadruplex through Ligand Intercalation. Angew Chem Int Ed Engl 2022; 61:e202207384. [PMID: 35993443 PMCID: PMC9826182 DOI: 10.1002/anie.202207384] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Indexed: 01/11/2023]
Abstract
Human telomeric G-quadruplex DNA structures are attractive anticancer drug targets, but the target's polymorphism complicates the drug design: different ligands prefer different folds, and very few complexes have been solved at high resolution. Here we report that Phen-DC3 , one of the most prominent G-quadruplex ligands in terms of high binding affinity and selectivity, causes dTAGGG(TTAGGG)3 to completely change its fold in KCl solution from a hybrid-1 to an antiparallel chair-type structure, wherein the ligand intercalates between a two-quartet unit and a pseudo-quartet, thereby ejecting one potassium ion. This unprecedented high-resolution NMR structure shows for the first time a true ligand intercalation into an intramolecular G-quadruplex.
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Affiliation(s)
- Anirban Ghosh
- CNRS, INSERM, ARNA, UMR 5320, U1212, IECBUniversité de Bordeaux33600PessacFrance
| | - Marko Trajkovski
- Slovenian NMR CentreNational Institute of ChemistryHajdrihova 191000LjubljanaSlovenia
| | | | - Valérie Gabelica
- CNRS, INSERM, ARNA, UMR 5320, U1212, IECBUniversité de Bordeaux33600PessacFrance
| | - Janez Plavec
- Slovenian NMR CentreNational Institute of ChemistryHajdrihova 191000LjubljanaSlovenia,Faculty of Chemistry and Chemical TechnologyUniversity of Ljubljana1000LjubljanaSlovenia,EN-FIST, Centre of Excellence1000LjubljanaSlovenia
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6
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Ghosh A, Trajkovski M, Teulade-Fichou MP, Gabelica V, Plavec J. Phen‐DC3 Induces Refolding of Human Telomeric DNA into a Chair‐type Antiparallel G‐quadruplex through Ligand Intercalation. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202207384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Anirban Ghosh
- IECB: Institut Europeen de Chimie et Biologie ARNA FRANCE
| | - Marko Trajkovski
- National Institute of Chemistry Slovenia: Kemijski institut Slovenian NMR centre SLOVENIA
| | | | | | - Janez Plavec
- National Institute of Chemistry NMR centre Hajdrihova 19 SI-1001 Ljubljana SLOVENIA
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7
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Non-G Base Tetrads. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27165287. [PMID: 36014524 PMCID: PMC9414646 DOI: 10.3390/molecules27165287] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/03/2022] [Accepted: 08/11/2022] [Indexed: 11/17/2022]
Abstract
Tetrads (or quartets) are arrangements of four nucleobases commonly involved in the stability of four-stranded nucleic acids structures. Four-stranded or quadruplex structures have attracted enormous attention in the last few years, being the most extensively studied guanine quadruplex (G-quadruplex). Consequently, the G-tetrad is the most common and well-known tetrad. However, this is not the only possible arrangement of four nucleobases. A number of tetrads formed by the different nucleobases have been observed in experimental structures. In most cases, these tetrads occur in the context of G-quadruplex structures, either inserted between G-quartets, or as capping elements at the sides of the G-quadruplex core. In other cases, however, non-G tetrads are found in more unusual four stranded structures, such as i-motifs, or different types of peculiar fold-back structures. In this report, we review the diversity of these non-canonical tetrads, and the structural context in which they have been found.
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8
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Liu LY, Ma TZ, Zeng YL, Liu W, Mao ZW. Structural Basis of Pyridostatin and Its Derivatives Specifically Binding to G-Quadruplexes. J Am Chem Soc 2022; 144:11878-11887. [PMID: 35749293 DOI: 10.1021/jacs.2c04775] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The nucleic acid G-quadruplex (G4) has emerged as a promising therapeutic target for a variety of diseases such as cancer and neurodegenerative disease. Among small-molecule G4-binders, pyridostatin (PDS) and its derivatives (e.g., PyPDS) exhibit high specificity to G4s, but the structural basis for their specific recognition of G4s remains unknown. Here, we presented two solution structures of PyPDS and PDS with a quadruplex-duplex hybrid. The structures indicate that the rigid aromatic rings of PyPDS/PDS linked by flexible amide bonds match adaptively with G-tetrad planes, enhancing π-π stacking and achieving specific recognition of G4s. The aliphatic amine side chains of PyPDS/PDS adjust conformation to interact with the phosphate backbone via hydrogen bonding and electrostatic interactions, increasing affinity for G4s. Moreover, the N-H of PyPDS/PDS amide bonds interacts with two O6s of G-tetrad guanines via hydrogen bonding, achieving a further increase in affinity for G4s, which is different from most G4 ligands. Our findings reveal from structural perspectives that the rational assembly of rigid and flexible structural units in a ligand can synergistically improve the selectivity and affinity for G4s through spatial selective and adaptive matching.
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Affiliation(s)
- Liu-Yi Liu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, P. R. China
| | - Tian-Zhu Ma
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, P. R. China
| | - You-Liang Zeng
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, P. R. China
| | - Wenting Liu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, P. R. China
| | - Zong-Wan Mao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, P. R. China
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9
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Mendes E, Aljnadi IM, Bahls B, Victor BL, Paulo A. Major Achievements in the Design of Quadruplex-Interactive Small Molecules. Pharmaceuticals (Basel) 2022; 15:ph15030300. [PMID: 35337098 PMCID: PMC8953082 DOI: 10.3390/ph15030300] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 12/17/2022] Open
Abstract
Organic small molecules that can recognize and bind to G-quadruplex and i-Motif nucleic acids have great potential as selective drugs or as tools in drug target discovery programs, or even in the development of nanodevices for medical diagnosis. Hundreds of quadruplex-interactive small molecules have been reported, and the challenges in their design vary with the intended application. Herein, we survey the major achievements on the therapeutic potential of such quadruplex ligands, their mode of binding, effects upon interaction with quadruplexes, and consider the opportunities and challenges for their exploitation in drug discovery.
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Affiliation(s)
- Eduarda Mendes
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal; (E.M.); (I.M.A.); (B.B.)
| | - Israa M. Aljnadi
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal; (E.M.); (I.M.A.); (B.B.)
- Faculty of Sciences, BioISI, Biosystems and Integrative Sciences Institute, Universidade de Lisboa, 1749-016 Lisbon, Portugal;
| | - Bárbara Bahls
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal; (E.M.); (I.M.A.); (B.B.)
- Faculty of Sciences, BioISI, Biosystems and Integrative Sciences Institute, Universidade de Lisboa, 1749-016 Lisbon, Portugal;
| | - Bruno L. Victor
- Faculty of Sciences, BioISI, Biosystems and Integrative Sciences Institute, Universidade de Lisboa, 1749-016 Lisbon, Portugal;
| | - Alexandra Paulo
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal; (E.M.); (I.M.A.); (B.B.)
- Correspondence:
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10
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Vianney YM, Weisz K. Indoloquinoline Ligands Favor Intercalation at Quadruplex-Duplex Interfaces. Chemistry 2021; 28:e202103718. [PMID: 34905232 PMCID: PMC9303235 DOI: 10.1002/chem.202103718] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Indexed: 11/30/2022]
Abstract
Quadruplex‐duplex (Q‐D) junctions are increasingly considered promising targets for medicinal and technological applications. Here, a Q‐D hybrid with a hairpin‐type snapback loop coaxially stacked onto the quadruplex 3’‐outer tetrad was designed and employed as a target structure for the indoloquinoline ligand SYUIQ‐5. NMR spectral analysis demonstrated high‐affinity binding of the ligand at the quadruplex‐duplex interface with association constants determined by isothermal titration calorimetry of about 107 M−1 and large exothermicities ΔH° of −14 kcal/mol in a 120 mM K+ buffer at 40 °C. Determination of the ligand‐bound hybrid structure revealed intercalation of SYUIQ‐5 between 3’‐outer tetrad and the neighboring CG base pair, maximizing π–π stacking as well as electrostatic interactions with guanine carbonyl groups in close vicinity to the positively charged protonated quinoline nitrogen of the tetracyclic indoloquinoline. Exhibiting considerable flexibility, the SYUIQ‐5 sidechain resides in the duplex minor groove. Based on comparative binding studies with the non‐substituted N5‐methylated indoloquinoline cryptolepine, the sidechain is suggested to confer additional affinity and to fix the alignment of the intercalated indoloquinoline aromatic core. However, selectivity for the Q‐D junction mostly relies on the geometry and charge distribution of the indoloquinoline ring system. The presented results are expected to provide valuable guidelines for the design of ligands specifically targeting Q‐D interfaces.
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Affiliation(s)
- Yoanes Maria Vianney
- Universität Greifswald Mathematisch-Naturwissenschaftliche Fakultät: Universitat Greifswald Mathematisch-Naturwissenschaftliche Fakultat, Institut für Biochemie, Felix-Hausdorff-Str. 4, 17489, Greifswald, GERMANY
| | - Klaus Weisz
- Universität Greifswald, Institut für Biochemie, Felix-Hausdorff-Str. 4, 17487, Greifswald, GERMANY
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11
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Liu L, Wang K, Liu W, Zeng Y, Hou M, Yang J, Mao Z. Spatial Matching Selectivity and Solution Structure of Organic–Metal Hybrid to Quadruplex–Duplex Hybrid. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202106256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Liu‐Yi Liu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry School of Chemistry, State Key Laboratory of Oncology in South China Sun Yat-Sen University Guangzhou 510275 P. R. China
| | - Kang‐Nan Wang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry School of Chemistry, State Key Laboratory of Oncology in South China Sun Yat-Sen University Guangzhou 510275 P. R. China
| | - Wenting Liu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry School of Chemistry, State Key Laboratory of Oncology in South China Sun Yat-Sen University Guangzhou 510275 P. R. China
| | - You‐Liang Zeng
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry School of Chemistry, State Key Laboratory of Oncology in South China Sun Yat-Sen University Guangzhou 510275 P. R. China
| | - Ming‐Xuan Hou
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry School of Chemistry, State Key Laboratory of Oncology in South China Sun Yat-Sen University Guangzhou 510275 P. R. China
| | - Jing Yang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry School of Chemistry, State Key Laboratory of Oncology in South China Sun Yat-Sen University Guangzhou 510275 P. R. China
| | - Zong‐Wan Mao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry School of Chemistry, State Key Laboratory of Oncology in South China Sun Yat-Sen University Guangzhou 510275 P. R. China
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12
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Liu LY, Wang KN, Liu W, Zeng YL, Hou MX, Yang J, Mao ZW. Spatial Matching Selectivity and Solution Structure of Organic-Metal Hybrid to Quadruplex-Duplex Hybrid. Angew Chem Int Ed Engl 2021; 60:20833-20839. [PMID: 34288320 DOI: 10.1002/anie.202106256] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 06/27/2021] [Indexed: 12/16/2022]
Abstract
The sequence-dependent DNA secondary structures possess structure polymorphism. To date, studies on regulated ligands mainly focus on individual DNA secondary topologies, while lack focus on quadruplex-duplex hybrids (QDHs). Here, we design an organic-metal hybrid ligand L1 Pt(dien), which matches and selectively binds one type of QDHs with lateral duplex stem-loop (QLDH) with high affinity, while shows poor affinity for other QDHs and individual G4 or duplex DNA. The solution structure of QLDH MYT1L-L1 Pt(dien) complex was determined by NMR. The structure reveals that L1 Pt(dien) presents a chair-type conformation, whose large aromatic "chair surface" intercalates into the G-quadruplex-duplex interface via π-π stacking and "backrest" platinum unit interacts with duplex region through hydrogen bonding and electrostatic interactions, showing a highly matched lock-key binding mode. Our work provided guidance for spatial matching design of selectively targeting ligands to QDH structures.
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Affiliation(s)
- Liu-Yi Liu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, State Key Laboratory of Oncology in South China, Sun Yat-Sen University, Guangzhou, 510275, P. R. China
| | - Kang-Nan Wang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, State Key Laboratory of Oncology in South China, Sun Yat-Sen University, Guangzhou, 510275, P. R. China
| | - Wenting Liu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, State Key Laboratory of Oncology in South China, Sun Yat-Sen University, Guangzhou, 510275, P. R. China
| | - You-Liang Zeng
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, State Key Laboratory of Oncology in South China, Sun Yat-Sen University, Guangzhou, 510275, P. R. China
| | - Ming-Xuan Hou
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, State Key Laboratory of Oncology in South China, Sun Yat-Sen University, Guangzhou, 510275, P. R. China
| | - Jing Yang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, State Key Laboratory of Oncology in South China, Sun Yat-Sen University, Guangzhou, 510275, P. R. China
| | - Zong-Wan Mao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, State Key Laboratory of Oncology in South China, Sun Yat-Sen University, Guangzhou, 510275, P. R. China
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13
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Aznauryan M, Noer SL, Pedersen CW, Mergny JL, Teulade-Fichou MP, Birkedal V. Ligand Binding to Dynamically Populated G-Quadruplex DNA. Chembiochem 2021; 22:1811-1817. [PMID: 33450114 DOI: 10.1002/cbic.202000792] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/11/2021] [Indexed: 12/14/2022]
Abstract
Several small-molecule ligands specifically bind and stabilize G-quadruplex (G4) nucleic acid structures, which are considered to be promising therapeutic targets. G4s are polymorphic structures of varying stability, and their formation is dynamic. Here, we investigate the mechanisms of ligand binding to dynamically populated human telomere G4 DNA by using the bisquinolinium based ligand Phen-DC3 and a combination of single-molecule FRET microscopy, ensemble FRET and CD spectroscopies. Different cations are used to tune G4 polymorphism and folding dynamics. We find that ligand binding occurs to pre-folded G4 structures and that Phen-DC3 also induces G4 formation in unfolded single strands. Following ligand binding to dynamically populated G4s, the DNA undergoes pronounced conformational redistributions that do not involve direct ligand-induced G4 conformational interconversion. On the contrary, the redistribution is driven by ligand-induced G4 folding and trapping of dynamically populated short-lived conformation states. Thus, ligand-induced stabilization does not necessarily require the initial presence of stably folded G4s.
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Affiliation(s)
- Mikayel Aznauryan
- Department of Chemistry and iNANO center, Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus, Denmark.,Present address: Univ. Bordeaux, INSERM, CNRS ARNA, U1212, UMR 5320, IECB, 33600, Pessac, France
| | - Sofie Louise Noer
- Department of Chemistry and iNANO center, Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus, Denmark
| | - Camilla W Pedersen
- Department of Chemistry and iNANO center, Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus, Denmark
| | - Jean-Louis Mergny
- Laboratoire d'Optique et Biosciences (LOB), CNRS UMR7645, INSERM U1182, Ecole Polytechnique, 91128, Palaiseau Cedex, France.,Institute of Biophysics of the CAS, 61265, Brno, Czech Republic
| | - Marie-Paule Teulade-Fichou
- CMBC Laboratory (Chemistry and Modelling for the Biology of Cancer), Institut Curie, Research Center Orsay, CNRS UMR9187, INSERM U1196, Paris-Saclay University, Bât. 110, 91405, Orsay, France
| | - Victoria Birkedal
- Department of Chemistry and iNANO center, Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus, Denmark
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14
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Vianney YM, Preckwinkel P, Mohr S, Weisz K. Quadruplex-Duplex Junction: A High-Affinity Binding Site for Indoloquinoline Ligands. Chemistry 2020; 26:16910-16922. [PMID: 32975874 PMCID: PMC7756412 DOI: 10.1002/chem.202003540] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/21/2020] [Indexed: 12/23/2022]
Abstract
A parallel quadruplex derived from the Myc promoter sequence was extended by a stem-loop duplex at either its 5'- or 3'-terminus to mimic a quadruplex-duplex (Q-D) junction as a potential genomic target. High-resolution structures of the hybrids demonstrate continuous stacking of the duplex on the quadruplex core without significant perturbations. An indoloquinoline ligand carrying an aminoalkyl side chain was shown to bind the Q-D hybrids with a very high affinity in the order Ka ≈107 m-1 irrespective of the duplex location at the quadruplex 3'- or 5'-end. NMR chemical shift perturbations identified the tetrad face of the Q-D junction as specific binding site for the ligand. However, calorimetric analyses revealed significant differences in the thermodynamic profiles upon binding to hybrids with either a duplex extension at the quadruplex 3'- or 5'-terminus. A large enthalpic gain and considerable hydrophobic effects are accompanied by the binding of one ligand to the 3'-Q-D junction, whereas non-hydrophobic entropic contributions favor binding with formation of a 2:1 ligand-quadruplex complex in case of the 5'-Q-D hybrid.
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Affiliation(s)
- Yoanes Maria Vianney
- Institute of Biochemistry, Universität Greifswald, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
| | - Pit Preckwinkel
- Institute of Biochemistry, Universität Greifswald, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
| | - Swantje Mohr
- Institute of Biochemistry, Universität Greifswald, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
| | - Klaus Weisz
- Institute of Biochemistry, Universität Greifswald, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
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15
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Kotar A, Kocman V, Plavec J. Intercalation of a Heterocyclic Ligand between Quartets in a G-Rich Tetrahelical Structure. Chemistry 2020; 26:814-817. [PMID: 31750579 PMCID: PMC7004031 DOI: 10.1002/chem.201904923] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 11/20/2019] [Indexed: 11/20/2022]
Abstract
YES G‐rich oligonucleotide VK2 folds into an AGCGA‐quadruplex tetrahelical structure distinct and significantly different from G‐quadruplexes, even though it contains four G3 tracts. Herein, a bis‐quinolinium ligand 360A with high affinity for G‐quadruplex structures and selective telomerase inhibition is shown to strongly bind to VK2. Upon binding, 360A does not induce a conformational switch from VK2 to an expected G‐quadruplex. In contrast, NMR structural study revealed formation of a well‐defined VK2–360A complex with a 1:1 binding stoichiometry, in which 360A intercalates between GAGA‐ and GCGC‐quartets in the central cavity of VK2. This is the first high‐resolution structure of a G‐quadruplex ligand intercalating into a G‐rich tetrahelical fold. This unique mode of ligand binding into tetrahelical DNA architecture offers insights into the stabilization of an AGCGA‐quadruplex by a heterocyclic ligand and provides guidelines for rational design of novel VK2 binding molecules with selectivity for different DNA secondary structures.
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Affiliation(s)
- Anita Kotar
- National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia
| | - Vojč Kocman
- National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia
| | - Janez Plavec
- National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia.,Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, Ljubljana, Slovenia.,EN-FIST Center of Excellence, Trg Osvobodilne fronte 13, 1000, Ljubljana, Slovenia
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