1
|
Lin SM, Huang HT, Fang PJ, Chang CF, Satange R, Chang CK, Chou SH, Neidle S, Hou MH. Structural basis of water-mediated cis Watson-Crick/Hoogsteen base-pair formation in non-CpG methylation. Nucleic Acids Res 2024:gkae594. [PMID: 38989613 DOI: 10.1093/nar/gkae594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 05/30/2024] [Accepted: 06/28/2024] [Indexed: 07/12/2024] Open
Abstract
Non-CpG methylation is associated with several cellular processes, especially neuronal development and cancer, while its effect on DNA structure remains unclear. We have determined the crystal structures of DNA duplexes containing -CGCCG- regions as CCG repeat motifs that comprise a non-CpG site with or without cytosine methylation. Crystal structure analyses have revealed that the mC:G base-pair can simultaneously form two alternative conformations arising from non-CpG methylation, including a unique water-mediated cis Watson-Crick/Hoogsteen, (w)cWH, and Watson-Crick (WC) geometries, with partial occupancies of 0.1 and 0.9, respectively. NMR studies showed that an alternative conformation of methylated mC:G base-pair at non-CpG step exhibits characteristics of cWH with a syn-guanosine conformation in solution. DNA duplexes complexed with the DNA binding drug echinomycin result in increased occupancy of the (w)cWH geometry in the methylated base-pair (from 0.1 to 0.3). Our structural results demonstrated that cytosine methylation at a non-CpG step leads to an anti→syntransition of its complementary guanosine residue toward the (w)cWH geometry as a partial population of WC, in both drug-bound and naked mC:G base pairs. This particular geometry is specific to non-CpG methylated dinucleotide sites in B-form DNA. Overall, the current study provides new insights into DNA conformation during epigenetic regulation.
Collapse
Affiliation(s)
- Shan-Meng Lin
- Graduate Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan
| | - Hsiang-Ti Huang
- Graduate Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan
| | - Pei-Ju Fang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Chi-Fon Chang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Roshan Satange
- Graduate Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan
| | - Chung-Ke Chang
- Taiwan Biobank, Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Shan-Ho Chou
- Institute of Biochemistry, National Chung Hsing University, Taichung 402, Taiwan
| | - Stephen Neidle
- School of Pharmacy, University College London, London WC1N 1AX, UK
| | - Ming-Hon Hou
- Graduate Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan
- Doctoral Program in Medical Biotechnology, National Chung Hsing University, Taichung 402, Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 402, Taiwan
- Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan
- Biotechnology Center, National Chung Hsing University, Taichung 402, Taiwan
| |
Collapse
|
2
|
Ngo KH, Liew CW, Heddi B, Phan AT. Structural Basis for Parallel G-Quadruplex Recognition by an Ankyrin Protein. J Am Chem Soc 2024; 146:13709-13713. [PMID: 38738955 DOI: 10.1021/jacs.4c01971] [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: 05/14/2024]
Abstract
G-Quadruplex (G4) structures formed by guanine-rich DNA and RNA sequences are implicated in various biological processes. Understanding the mechanisms by which proteins recognize G4 structures is crucial for elucidating their functional roles. Here we present the X-ray crystal structure of an ankyrin protein bound to a parallel G4 structure. Our findings reveal a new specific recognition mode in which a bundle of α-helices and loops of the ankyrin form a flat surface to stack on the G-tetrad core. The protein employs a combination of hydrogen bonds and hydrophobic contacts to interact with the G4, and electrostatic interaction is used to enhance the binding affinity. This binding mechanism provides valuable insights into understanding G4 recognition by proteins.
Collapse
Affiliation(s)
- Khac Huy Ngo
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Chong Wai Liew
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore 636921, Singapore
| | - Brahim Heddi
- Laboratoire de Biologie et Pharmacologie Appliquée (LBPA), UMR8113 CNRS, ENS Paris-Saclay, Gif-sur-Yvette 91190, France
| | - 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
| |
Collapse
|
3
|
Aderinto SO, John T, Onawole A, Galleh RP, Thomas JA. Iridium(III)-based minor groove binding complexes as DNA photocleavage agents. Dalton Trans 2024; 53:7282-7291. [PMID: 38466178 DOI: 10.1039/d4dt00171k] [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: 03/12/2024]
Abstract
Transition metal complexes containing the qtpy ligand (2':4,4'':4',4'''-quaterpyridyl) are known to be DNA intercalators or minor groove binders. In this study, new tricationic iridium(III) complexes of qtpy are reported. Both [Ir(bpy)2(qtpy)]3+1 and [Ir(phen)2(qtpy)]3+2 display good water solubility as chloride salts. The complexes possess high-energy excited states, which are quenched in the presence of duplex DNA and even by the mononucleotides guanosine monophosphate and adenosine monophosphate. Further studies reveal that although the complexes bind to quadruplex DNA, they display a preference for duplex structures, which are bound with an order of magnitude higher affinities than their isostructural dicationic RuII-analogues. Detailed molecular dynamics simulations confirm that the complexes are groove binders through the insertion of, predominantly, the qtpy ligand into the minor groove. Photoirradiation of 1 in the presence of plasmid DNA confirms that this class of complexes can function as synthetic photonucleases by cleaving DNA.
Collapse
Affiliation(s)
- Stephen O Aderinto
- Department of Chemistry, University of Sheffield, Sheffield, S3 7HF, UK.
| | - Torsten John
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Abdulmujeeb Onawole
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia
| | | | - Jim A Thomas
- Department of Chemistry, University of Sheffield, Sheffield, S3 7HF, UK.
| |
Collapse
|
4
|
Prieto Otoya TD, McQuaid KT, Hennessy J, Menounou G, Gibney A, Paterson NG, Cardin DJ, Kellett A, Cardin CJ. Probing a Major DNA Weakness: Resolving the Groove and Sequence Selectivity of the Diimine Complex Λ-[Ru(phen) 2 phi] 2. Angew Chem Int Ed Engl 2024; 63:e202318863. [PMID: 38271265 DOI: 10.1002/anie.202318863] [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: 12/07/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 01/27/2024]
Abstract
The grooves of DNA provide recognition sites for many nucleic acid binding proteins and anticancer drugs such as the covalently binding cisplatin. Here we report a crystal structure showing, for the first time, groove selectivity by an intercalating ruthenium complex. The complex Λ-[Ru(phen)2 phi]2+ , where phi=9,10-phenanthrenediimine, is bound to the DNA decamer duplex d(CCGGTACCGG)2 . The structure shows that the metal complex is symmetrically bound in the major groove at the central TA/TA step, and asymmetrically bound in the minor groove at the adjacent GG/CC steps. A third type of binding links the strands, in which each terminal cytosine base stacks with one phen ligand. The overall binding stoichiometry is four Ru complexes per duplex. Complementary biophysical measurements confirm the binding preference for the Λ-enantiomer and show a high affinity for TA/TA steps and, more generally, TA-rich sequences. A striking enantiospecific elevation of melting temperatures is found for oligonucleotides which include the TATA box sequence.
Collapse
Affiliation(s)
| | - Kane T McQuaid
- Department of Chemistry, University of Reading, Whiteknights, Reading, RG6 6AD, UK
| | - Joseph Hennessy
- SSPC, the Science Foundation Ireland Research Centre for Pharmaceuticals, School of Chemical Sciences, Dublin City University, Glasnevin, Dublin, 9, Ireland Email
| | - Georgia Menounou
- SSPC, the Science Foundation Ireland Research Centre for Pharmaceuticals, School of Chemical Sciences, Dublin City University, Glasnevin, Dublin, 9, Ireland Email
| | - Alex Gibney
- SSPC, the Science Foundation Ireland Research Centre for Pharmaceuticals, School of Chemical Sciences, Dublin City University, Glasnevin, Dublin, 9, Ireland Email
| | - Neil G Paterson
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK
| | - David J Cardin
- Department of Chemistry, University of Reading, Whiteknights, Reading, RG6 6AD, UK
| | - Andrew Kellett
- SSPC, the Science Foundation Ireland Research Centre for Pharmaceuticals, School of Chemical Sciences, Dublin City University, Glasnevin, Dublin, 9, Ireland Email
| | - Christine J Cardin
- Department of Chemistry, University of Reading, Whiteknights, Reading, RG6 6AD, UK
| |
Collapse
|
5
|
Tran VT, Turek-Herman J, Ferreira M, Martin KN, Beseiso D, Williams BR, Rosu F, Gabelica V, Burgmayer SJN, Yatsunyk LA. Interactions of ruthenium(II) polypyridyl complexes with human telomeric DNA. J Inorg Biochem 2023; 249:112388. [PMID: 37837940 PMCID: PMC10668861 DOI: 10.1016/j.jinorgbio.2023.112388] [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: 05/12/2023] [Revised: 09/12/2023] [Accepted: 09/24/2023] [Indexed: 10/16/2023]
Abstract
Eight [Ru(bpy)2L]2+ and three [Ru(phen)2L]2+complexes (where bpy = 2,2'-bipyridine and phen = 1,10-phenanthroline are ancillary ligands, and L = a polypyridyl experimental ligand) were investigated for their G-quadruplex binding abilities. Fluorescence resonance energy transfer melting assays were used to screen these complexes for their ability to selectively stabilize human telomeric DNA variant, Tel22. The best G-quadruplex stabilizers were further characterized for their binding properties (binding constant and stoichiometry) using UV-vis, fluorescence spectroscopy, and mass spectrometry. The ligands' ability to alter the structure of Tel22 was determined via circular dichroism and PAGE studies. We identified me2allox as the experimental ligand capable of conferring excellent stabilizing ability and good selectivity to polypyridyl Ru(II) complexes. Replacing bpy by phen did not significantly impact interactions with Tel22, suggesting that binding involves mostly the experimental ligand. However, using a particular ancillary ligand can help fine-tune G-quadruplex-binding properties of Ru(II) complexes. Finally, the fluorescence "light switch" behavior of all Ru(II) complexes in the presence of Tel22 G-quadruplex was explored. All Ru(II) complexes displayed "light switch" properties, especially [Ru(bpy)2(diamino)]2+, [Ru(bpy)2(dppz)]2+, and [Ru(bpy)2(aap)]2+. Current work sheds light on how Ru(II) polypyridyl complexes interact with human telomeric DNA with possible application in cancer therapy or G-quadruplex sensing.
Collapse
Affiliation(s)
- Vienna T Tran
- Department of Chemistry and Biochemistry, Swarthmore College, 500 College Ave., Swarthmore, PA, USA.
| | - Joshua Turek-Herman
- Department of Chemistry and Biochemistry, Swarthmore College, 500 College Ave., Swarthmore, PA, USA.
| | - Michelle Ferreira
- Department of Chemistry and Biochemistry, Swarthmore College, 500 College Ave., Swarthmore, PA, USA.
| | - Kailey N Martin
- Department of Chemistry and Biochemistry, Swarthmore College, 500 College Ave., Swarthmore, PA, USA.
| | - Dana Beseiso
- Department of Chemistry and Biochemistry, Swarthmore College, 500 College Ave., Swarthmore, PA, USA.
| | | | - Frederic Rosu
- Univ. Bordeaux, CNRS, INSERM, IECB, UAR3033, US01, F-33600 Pessac, France.
| | - Valérie Gabelica
- Univ. Bordeaux, CNRS, INSERM, IECB, UAR3033, US01, F-33600 Pessac, France; Univ. Bordeaux, CNRS, INSERM, ARNA, UMR5320, U1212, IECB, F-33600 Pessac, France.
| | | | - Liliya A Yatsunyk
- Department of Chemistry and Biochemistry, Swarthmore College, 500 College Ave., Swarthmore, PA, USA.
| |
Collapse
|
6
|
Stitch M, Avagliano D, Graczyk D, Clark IP, González L, Towrie M, Quinn SJ. Good Vibrations Report on the DNA Quadruplex Binding of an Excited State Amplified Ruthenium Polypyridyl IR Probe. J Am Chem Soc 2023; 145:21344-21360. [PMID: 37736878 PMCID: PMC10557146 DOI: 10.1021/jacs.3c06099] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Indexed: 09/23/2023]
Abstract
The nitrile containing Ru(II)polypyridyl complex [Ru(phen)2(11,12-dCN-dppz)]2+ (1) is shown to act as a sensitive infrared probe of G-quadruplex (G4) structures. UV-visible absorption spectroscopy reveals enantiomer sensitive binding for the hybrid htel(K) and antiparallel htel(Na) G4s formed by the human telomer sequence d[AG3(TTAG3)3]. Time-resolved infrared (TRIR) of 1 upon 400 nm excitation indicates dominant interactions with the guanine bases in the case of Λ-1/htel(K), Δ-1/htel(K), and Λ-1/htel(Na) binding, whereas Δ-1/htel(Na) binding is associated with interactions with thymine and adenine bases in the loop. The intense nitrile transient at 2232 cm-1 undergoes a linear shift to lower frequency as the solution hydrogen bonding environment decreases in DMSO/water mixtures. This shift is used as a sensitive reporter of the nitrile environment within the binding pocket. The lifetime of 1 in D2O (ca. 100 ps) is found to increase upon DNA binding, and monitoring of the nitrile and ligand transients as well as the diagnostic DNA bleach bands shows that this increase is related to greater protection from the solvent environment. Molecular dynamics simulations together with binding energy calculations identify the most favorable binding site for each system, which are in excellent agreement with the observed TRIR solution study. This study shows the power of combining the environmental sensitivity of an infrared (IR) probe in its excited state with the TRIR DNA "site effect" to gain important information about the binding site of photoactive agents and points to the potential of such amplified IR probes as sensitive reporters of biological environments.
Collapse
Affiliation(s)
- Mark Stitch
- School
of Chemistry, University College Dublin, Dublin, D04 V1W8, Ireland
| | - Davide Avagliano
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währingerstr. 19, 1090 Vienna, Austria
- Department
of Chemistry, Chemical Physics Theory Group, University of Toronto, 80 St. George St., Toronto, Ontario M5S 3H6, Canada
| | - Daniel Graczyk
- School
of Chemistry, University College Dublin, Dublin, D04 V1W8, Ireland
| | - Ian P. Clark
- Central
Laser Facility, STFC Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0QX, U.K.
| | - Leticia González
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währingerstr. 19, 1090 Vienna, Austria
- Vienna
Research Platform on Accelerating Photoreaction Discovery, University of Vienna, Währingerstr. 19, 1090 Vienna, Austria
| | - Michael Towrie
- Central
Laser Facility, STFC Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0QX, U.K.
| | - Susan J Quinn
- School
of Chemistry, University College Dublin, Dublin, D04 V1W8, Ireland
| |
Collapse
|
7
|
Ju P, Zhu YY, Jiang TT, Gao G, Wang SL, Jiang XW, Xu YT, Zhai XF, Zhou H, Zhao WW. DNA intercalation makes possible superior-gain organic photoelectrochemical transistor detection. Biosens Bioelectron 2023; 237:115543. [PMID: 37499378 DOI: 10.1016/j.bios.2023.115543] [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: 05/31/2023] [Revised: 07/06/2023] [Accepted: 07/20/2023] [Indexed: 07/29/2023]
Abstract
DNA intercalation has increasingly been studied for various scenario implementations due to the diverse functions of DNA/intercalators. Nascent organic photoelectrochemical transistor (OPECT) biosensing taking place in organic electronics and photoelectrochemical bioanalysis represents a promising technological frontier in the arena. In this work, we first devise DNA intercalation-enabled OPECT for miRNA detection with a superior gain up to 17100. Intercalation of [Ru(bpy)2dppz]2+ within the miRNA-initiated hybrid chain reaction (HCR)-derived duplex DNA is realized for producing anodic photocurrent upon light stimulation, causing the corresponding target-dependent alternation in gate voltage (VG) and hence the modulated channel current (IDS) of poly (3,4-ethylenedioxythiophene) doped with poly (styrene sulfonate) (PEDOT:PSS) under specific drain voltage (VDS) for quantitative miRNA-21 analysis, which shows a wide linear relationship and a low detection limit of 5.5 × 10-15 mol L-1. This study features the DNA intercalation-enabled organic electronics with superior gain and is envisaged to attract more attention to explore DNA adducts for innovative bioelectronics and biosensing, given the diverse DNA binders with multiple functions.
Collapse
Affiliation(s)
- Peng Ju
- Key Laboratory of Marine Eco-Environmental Science and Technology, Marine Bioresource and Environment Research Center, First Institute of Oceanography, Ministry of Natural Resources, No. 6 Xianxialing Road, Qingdao, 266061, China; Shandong Key Laboratory of Marine Ecological Environment and Disaster Prevention and Mitigation, Qingdao, 266061, China; College of Safety and Environmental Engineering, Shandong University of Science and Technology, Qingdao, 266590, PR China
| | - Yu-Yue Zhu
- Key Laboratory of Marine Eco-Environmental Science and Technology, Marine Bioresource and Environment Research Center, First Institute of Oceanography, Ministry of Natural Resources, No. 6 Xianxialing Road, Qingdao, 266061, China; State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China; College of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China
| | - Tian-Tong Jiang
- Key Laboratory of Marine Eco-Environmental Science and Technology, Marine Bioresource and Environment Research Center, First Institute of Oceanography, Ministry of Natural Resources, No. 6 Xianxialing Road, Qingdao, 266061, China
| | - Ge Gao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China; Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China
| | - Shi-Liang Wang
- Key Laboratory of Marine Eco-Environmental Science and Technology, Marine Bioresource and Environment Research Center, First Institute of Oceanography, Ministry of Natural Resources, No. 6 Xianxialing Road, Qingdao, 266061, China; College of Safety and Environmental Engineering, Shandong University of Science and Technology, Qingdao, 266590, PR China
| | - Xing-Wu Jiang
- Key Laboratory of Marine Eco-Environmental Science and Technology, Marine Bioresource and Environment Research Center, First Institute of Oceanography, Ministry of Natural Resources, No. 6 Xianxialing Road, Qingdao, 266061, China; State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China; Shandong Key Laboratory of Marine Ecological Environment and Disaster Prevention and Mitigation, Qingdao, 266061, China
| | - Yi-Tong Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Xiao-Fan Zhai
- CAS Key Laboratory of Marine Environmental Corrosion and Bio-fouling, Institute of Oceanology, Chinese Academy of Sciences, No. 7 Nanhai Road, Qingdao, 266071, China.
| | - Hong Zhou
- Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China.
| | - Wei-Wei Zhao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China.
| |
Collapse
|
8
|
Das S, Takahashi S, Ohyama T, Bhowmik S, Sugimoto N. Theranostic approach to specifically targeting the interloop region of BCL2 i-motif DNA by crystal violet. Sci Rep 2023; 13:14338. [PMID: 37658102 PMCID: PMC10474294 DOI: 10.1038/s41598-023-39407-9] [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: 05/17/2023] [Accepted: 07/25/2023] [Indexed: 09/03/2023] Open
Abstract
Ligands that recognise specific i-motif DNAs are helpful in cancer diagnostics and therapeutics, as i-motif formation can cause cancer. Although the loop regions of i-motifs are promising targets for ligands, the interaction between a ligand and the loop regions based on sequence information remains unexplored. Herein, we investigated the loop regions of various i-motif DNAs to determine whether these regions specifically interact with fluorescent ligands. Crystal violet (CV), a triphenylmethane dye, exhibited strong fluorescence with the i-motif derived from the promoter region of the human BCL2 gene in a sequence- and structure-specific manner. Our systematic sequence analysis indicated that CV was bound to the site formed by the first and third loops through inter-loop interactions between the guanine bases present in these loops. As the structural stability of the BCL2 i-motif was unaffected by CV, the local stabilisation of the loops by CV could inhibit the interaction of transcription factors with these loops, repressing the BCL2 expression of MCF-7 cells. Our finding suggests that the loops of the i-motif can act as a novel platform for the specific binding of small molecules; thus, they could be utilised for the theranostics of diseases associated with i-motif DNAs.
Collapse
Affiliation(s)
- Sinjan Das
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Kobe, 650-0047, Japan
| | - Shuntaro Takahashi
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Kobe, 650-0047, Japan
| | - Tatsuya Ohyama
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Kobe, 650-0047, Japan
| | - Sudipta Bhowmik
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, A.P.C Road, Kolkata, 700009, India
- Mahatma Gandhi Medical Advanced Research Institute (MGMARI), Sri Balaji Vidyapeeth (Deemed to be University), Pondy-Cuddalore Main Road, Pillayarkuppam, Pondicherry, 607402, India
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Kobe, 650-0047, Japan.
- Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-Minamimachi, Kobe, 650-0047, Japan.
| |
Collapse
|
9
|
Peterková K, Stitch M, Boota RZ, Scattergood PA, Elliott PIP, Towrie M, Podbevšek P, Plavec J, Quinn SJ. G-Quadruplex Binding of an NIR Emitting Osmium Polypyridyl Probe Revealed by Solution NMR and Time-Resolved Infrared Studies. Chemistry 2023; 29:e202203250. [PMID: 36398697 DOI: 10.1002/chem.202203250] [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: 10/18/2022] [Revised: 11/11/2022] [Accepted: 11/17/2022] [Indexed: 11/19/2022]
Abstract
G-quadruplexes are emerging targets in cancer research and understanding how diagnostic probes bind to DNA G-quadruplexes in solution is critical to the development of new molecular tools. In this study the binding of an enantiopure NIR emitting [Os(TAP)2 (dppz)]2+ complex to different G-quadruplex structures formed by human telomer (hTel) and cMYC sequences in solution is reported. The combination of NMR and time-resolved infrared spectroscopic techniques reveals the sensitivity of the emission response to subtle changes in the binding environment of the complex. Similar behaviour is also observed for the related complex [Os(TAP)2 (dppp2)]2+ upon quadruplex binding.
Collapse
Affiliation(s)
- Kateřina Peterková
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia
- National Centre for Biomolecular Research Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czechia
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, 1000, Ljubljana, Slovenia
| | - Mark Stitch
- School of Chemistry, University College Dublin, Dublin, 4, Ireland
| | - Rayhaan Z Boota
- Department of Chemical Sciences, School of Applied Sciences University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK
| | - Paul A Scattergood
- Department of Chemical Sciences, School of Applied Sciences University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK
| | - Paul I P Elliott
- Department of Chemical Sciences, School of Applied Sciences University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK
| | - Michael Towrie
- Rutherford Appleton Laboratory, STFC, Harwell Campus, OX11 0FA, UK
| | - Peter Podbevšek
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia
| | - Janez Plavec
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, 1000, Ljubljana, Slovenia
- EN-FIST Centre of Excellence Trg OF 13, 1000, Ljubljana, Slovenia
| | - Susan J Quinn
- School of Chemistry, University College Dublin, Dublin, 4, Ireland
| |
Collapse
|
10
|
Chen C, Lv H, Xu H, Zhu D, Shen C. Cyclometalated Ru(II)-NHC complexes with phenanthroline ligands induce apoptosis mediated by mitochondria and endoplasmic reticulum stress in cancer cells. Dalton Trans 2023; 52:1671-1679. [PMID: 36648504 DOI: 10.1039/d2dt03405k] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The exploration of ruthenium complexes as anticancer drugs has been the focus of intense investigation. In this study, we synthesized and characterized four C,N-cyclometalated ruthenium(II) complexes (Ru1-Ru4) coordinated with pyridine-functionalized N-heterocyclic carbene (NHC) and auxiliary ligands (e.g., acetonitrile, 1,10-phenanthroline, 3,4,7,8-tetramethyl-1,10-phenanthroline, and 4,7-diphenyl-1,10-phenanthroline). X-ray diffraction analysis showed that all of the four cycloruthenated complexes are hexa-coordinated in a typical octahedral geometry. In vitro cytotoxic studies revealed that cyclometalated Ru-NHC complexes Ru3 and Ru4 had stronger anticancer activity than their corresponding Ru-NHC precursor Ru1 and the clinically used cisplatin. For HeLa cells, Ru3 and Ru4 exhibited potent cytotoxicity with the IC50 value of 4.31 ± 0.42 μM and 3.14 ± 0.23 μM, respectively, which was approximately three times lower than that of cisplatin. More interestingly, Ru3 and Ru4 not only effectively inhibited the proliferation of HeLa cells, but also exhibited potential anti-migration activity. In the scratch wound healing assay, Ru3 and Ru4 treatment significantly reduced the wound healing rate of HUVEC cells. Mechanistic studies showed that Ru3 and Ru4 caused a dual action mode of mitochondrial membrane depolarization and endoplasmic reticulum stress and finally induced apoptosis of HeLa cells.
Collapse
Affiliation(s)
- Chao Chen
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, College of Biology and Environmental Engineering, Zhejiang Shuren University, Hangzhou 310015, China. .,College of Life Sciences, Huzhou University, Huzhou, 313000, PR China
| | - He Lv
- College of Life Sciences, Huzhou University, Huzhou, 313000, PR China
| | - Hao Xu
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, College of Biology and Environmental Engineering, Zhejiang Shuren University, Hangzhou 310015, China.
| | - Dancheng Zhu
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, College of Biology and Environmental Engineering, Zhejiang Shuren University, Hangzhou 310015, China.
| | - Chao Shen
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, College of Biology and Environmental Engineering, Zhejiang Shuren University, Hangzhou 310015, China.
| |
Collapse
|
11
|
Wang Z, Liu W, Li G, Wang J, Zhao B, Huang P, Mei W. Ruthenium(II) Complexes Coupled by Erianin via a Flexible Carbon Chain as a Potential Stabilizer of c-myc G-Quadruplex DNA. Molecules 2023; 28:molecules28041529. [PMID: 36838516 PMCID: PMC9958891 DOI: 10.3390/molecules28041529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/08/2023] Open
Abstract
Herein, two novel ruthenium(II) complexes coupled by erianin via a flexible carbon chain, [Ru(phen)2(L1-(CH2)4-erianin)](ClO4)2 (L1 = 2-(2-(tri-fluoromethyphenyl))-imidazo [4,5f][1-10]phenanthroline (1) and [Ru(phen)2(L2-(CH2)4-eria)](ClO4)2 (L2 = 2-(4-(tri-fluoromethyphenyl))-imidazo [4,5f][1,10]phenanthroline (2), have been synthesized and investigated as a potential G-quadruplex(G4) DNA stabilizer. Both complexes, especially 2, can bind to c-myc G4 DNA with high affinity by electronic spectra, and the binding constant calculated for 1 and 2 is about 15.1 and 2.05 × 107 M-1, respectively. This was further confirmed by the increase in fluorescence intensity for both complexes. Moreover, the positive band at 265 nm in the CD spectra of c-myc G4 DNA decreased treated with 2, indicating that 2 may bind to c-myc G4 DNA through extern groove binding mode. Furthermore, fluorescence resonance energy transfer (FRET) assay indicated that the melting point of c-myc G4 DNA treated with 1 and 2 increased 15.5 and 16.5 °C, respectively. Finally, molecular docking showed that 1 can bind to c-myc G4 DNA in the extern groove formed by base pairs G7-G9 and G22-A24, and 2 inserts into the small groove of c-myc G4 DNA formed by base pairs T19-A24. In summary, these ruthenium(II) complexes, especially 2, can be developed as potential c-myc G4 DNA stabilizers and will be exploited as potential anticancer agents in the future.
Collapse
Affiliation(s)
- Zhixiang Wang
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Wentao Liu
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Guohu Li
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Jiacheng Wang
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Bin Zhao
- Department of Southern Pharmacy, Guangdong Jiangmen Chinese Medical, Jiangmen 510047, China
- Correspondence: (B.Z.); (W.M.)
| | - Peishan Huang
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Wenjie Mei
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
- Guangdong Province Engineering Technology Centre for Molecular Probe and Bio-Medical Imaging, Guangzhou 510006, China
- Correspondence: (B.Z.); (W.M.)
| |
Collapse
|
12
|
Yuan C, Wang Z, Wang Z, Liu W, Li G, Meng J, Wu R, Wu Q, Wang J, Mei W. Novel Chiral Ru(II) Complexes as Potential c-myc G-quadruplex DNA Stabilizers Inducing DNA Damage to Suppress Triple-Negative Breast Cancer Progression. Int J Mol Sci 2022; 24:ijms24010203. [PMID: 36613647 PMCID: PMC9820592 DOI: 10.3390/ijms24010203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/13/2022] [Accepted: 12/15/2022] [Indexed: 12/25/2022] Open
Abstract
Currently, effective drugs for triple-negative breast cancer (TNBC) are lacking in clinics. c-myc is one of the core members during TNBC tumorigenesis, and G-rich sequences in the promoter region can form a G-quadruplex conformation, indicating that the c-myc inhibitor is a possible strategy to fight cancer. Herein, a series of chiral ruthenium(II) complexes ([Ru(bpy)2(DPPZ-R)](ClO4)2, Λ/Δ-1: R = -H, Λ/Δ-2: R = -Br, Λ/Δ-3: R = -C≡C(C6H4)NH2) were researched based on their interaction with c-myc G-quadruplex DNA. Λ-3 and Δ-3 show high affinity and stability to decrease their replication. Additional studies showed that Λ-3 and Δ-3 exhibit higher inhibition against different tumor cells than other molecules. Δ-3 decreases the viability of MDA-MB-231 cells with an IC50 of 25.51 μM, which is comparable with that of cisplatin, with an IC50 of 25.9 μM. Moreover, Δ-3 exhibits acceptable cytotoxic activity against MDA-MB-231 cells in a zebrafish xenograft breast cancer model. Further studies suggested that Δ-3 decreases the viability of MDA-MB-231 cells predominantly through DNA-damage-mediated apoptosis, which may be because Δ-3 can induce DNA damage. In summary, the results indicate that Ru(II) complexes containing alkinyl groups can be developed as c-myc G-quadruplex DNA binders to block TNBC progression.
Collapse
Affiliation(s)
- Chanling Yuan
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Zhixiang Wang
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Zongtao Wang
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Wentao Liu
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Guohu Li
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Jinlan Meng
- Department of Physiology, School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Ruzhen Wu
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Qiong Wu
- Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou 530316, China
- Guangdong Engineering Technology Research Centre of Molecular Probe and Biomedicine Imaging, Guangdong Pharmaceutical University, Guangzhou 510006, China
- Correspondence: (Q.W.); (W.M.)
| | - Jiacheng Wang
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Wenjie Mei
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
- Guangdong Engineering Technology Research Centre of Molecular Probe and Biomedicine Imaging, Guangdong Pharmaceutical University, Guangzhou 510006, China
- Correspondence: (Q.W.); (W.M.)
| |
Collapse
|
13
|
Peng P, Luo L, Wang Y. Synthesis and spectroscopic properties of osmium based polypyridyl compound, cis-Os II(phen) 2Cl 2, and its one-electron oxidation product [ cis-Os III(phen) 2Cl 2](PF 6). J COORD CHEM 2022. [DOI: 10.1080/00958972.2022.2157721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Pei Peng
- Hubei Key Laboratory of Drug Synthesis and Optimization, College of Chemical Engineering and Pharmacy, Jingchu University of Technology, Jingmen, Hubei, P. R. China
| | - Lei Luo
- Hubei Key Laboratory of Drug Synthesis and Optimization, College of Chemical Engineering and Pharmacy, Jingchu University of Technology, Jingmen, Hubei, P. R. China
| | - Yong Wang
- Hubei Key Laboratory of Drug Synthesis and Optimization, College of Chemical Engineering and Pharmacy, Jingchu University of Technology, Jingmen, Hubei, P. R. China
| |
Collapse
|
14
|
Li H, Wang P, Zhu C, Zhang W, Zhou M, Zhang S, Zhang C, Yun Y, Kang X, Pei Y, Zhu M. Triple-Helical Self-Assembly of Atomically Precise Nanoclusters. J Am Chem Soc 2022; 144:23205-23213. [DOI: 10.1021/jacs.2c11341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Hao Li
- Department of Chemistry and Centre for Atomic Engineering of Advanced Materials, Key Laboratory of Structure and Functional Regulation of Hybrid Materials of Ministry of Education, Institutes of Physical Science and Information Technology and Anhui Province Key Laboratory of Chemistry for Inorganic/Organic Hybrid Functionalized Materials, Anhui University, Hefei 230601, Anhui, China
| | - Pu Wang
- Department of Chemistry, Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, Xiangtan University, Xiangtan 411105, Hunan, P. R. China
| | - Chen Zhu
- Department of Chemistry and Centre for Atomic Engineering of Advanced Materials, Key Laboratory of Structure and Functional Regulation of Hybrid Materials of Ministry of Education, Institutes of Physical Science and Information Technology and Anhui Province Key Laboratory of Chemistry for Inorganic/Organic Hybrid Functionalized Materials, Anhui University, Hefei 230601, Anhui, China
| | - Wei Zhang
- Hefei National Research Center for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, Anhui, China
| | - Meng Zhou
- Hefei National Research Center for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, Anhui, China
| | - San Zhang
- National Laboratory of Solid State Microstructures, School of Physics, and Collaborative Innovation Center for Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Chunfeng Zhang
- National Laboratory of Solid State Microstructures, School of Physics, and Collaborative Innovation Center for Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Yapei Yun
- Department of Chemistry and Centre for Atomic Engineering of Advanced Materials, Key Laboratory of Structure and Functional Regulation of Hybrid Materials of Ministry of Education, Institutes of Physical Science and Information Technology and Anhui Province Key Laboratory of Chemistry for Inorganic/Organic Hybrid Functionalized Materials, Anhui University, Hefei 230601, Anhui, China
| | - Xi Kang
- Department of Chemistry and Centre for Atomic Engineering of Advanced Materials, Key Laboratory of Structure and Functional Regulation of Hybrid Materials of Ministry of Education, Institutes of Physical Science and Information Technology and Anhui Province Key Laboratory of Chemistry for Inorganic/Organic Hybrid Functionalized Materials, Anhui University, Hefei 230601, Anhui, China
| | - Yong Pei
- Department of Chemistry, Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, Xiangtan University, Xiangtan 411105, Hunan, P. R. China
| | - Manzhou Zhu
- Department of Chemistry and Centre for Atomic Engineering of Advanced Materials, Key Laboratory of Structure and Functional Regulation of Hybrid Materials of Ministry of Education, Institutes of Physical Science and Information Technology and Anhui Province Key Laboratory of Chemistry for Inorganic/Organic Hybrid Functionalized Materials, Anhui University, Hefei 230601, Anhui, China
| |
Collapse
|
15
|
Criscuolo A, Napolitano E, Riccardi C, Musumeci D, Platella C, Montesarchio D. Insights into the Small Molecule Targeting of Biologically Relevant G-Quadruplexes: An Overview of NMR and Crystal Structures. Pharmaceutics 2022; 14:pharmaceutics14112361. [PMID: 36365179 PMCID: PMC9696056 DOI: 10.3390/pharmaceutics14112361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/23/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022] Open
Abstract
G-quadruplexes turned out to be important targets for the development of novel targeted anticancer/antiviral therapies. More than 3000 G-quadruplex small-molecule ligands have been described, with most of them exerting anticancer/antiviral activity by inducing telomeric damage and/or altering oncogene or viral gene expression in cancer cells and viruses, respectively. For some ligands, in-depth NMR and/or crystallographic studies were performed, providing detailed knowledge on their interactions with diverse G-quadruplex targets. Here, the PDB-deposited NMR and crystal structures of the complexes between telomeric, oncogenic or viral G-quadruplexes and small-molecule ligands, of both organic and metal-organic nature, have been summarized and described based on the G-quadruplex target, from telomeric DNA and RNA G-quadruplexes to DNA oncogenic G-quadruplexes, and finally to RNA viral G-quadruplexes. An overview of the structural details of these complexes is here provided to guide the design of novel ligands targeting more efficiently and selectively cancer- and virus-related G-quadruplex structures.
Collapse
Affiliation(s)
- Andrea Criscuolo
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, 80126 Naples, Italy
| | - Ettore Napolitano
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, 80126 Naples, Italy
| | - Claudia Riccardi
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, 80126 Naples, Italy
| | - Domenica Musumeci
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, 80126 Naples, Italy
- Institute of Biostructures and Bioimages, CNR, 80134 Naples, Italy
| | - Chiara Platella
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, 80126 Naples, Italy
- Correspondence:
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, 80126 Naples, Italy
| |
Collapse
|
16
|
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.
Collapse
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
| |
Collapse
|
17
|
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
| |
Collapse
|
18
|
Biver T. Discriminating between Parallel, Anti-Parallel and Hybrid G-Quadruplexes: Mechanistic Details on Their Binding to Small Molecules. Molecules 2022; 27:molecules27134165. [PMID: 35807410 PMCID: PMC9268745 DOI: 10.3390/molecules27134165] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/22/2022] [Accepted: 06/27/2022] [Indexed: 12/04/2022] Open
Abstract
G-quadruplexes (G4) are now extensively recognised as a peculiar non-canonical DNA geometry that plays a prime importance role in processes of biological relevance whose number is increasing continuously. The same is true for the less-studied RNA G4 counterpart. G4s are stable structures; however, their geometrical parameters may be finely tuned not only by the presence of particular sequences of nucleotides but also by the salt content of the medium or by a small molecule that may act as a peculiar topology inducer. As far as the interest in G4s increases and our knowledge of these species deepens, researchers do not only verify the G4s binding by small molecules and the subsequent G4 stabilisation. The most innovative studies now aim to elucidate the mechanistic details of the interaction and the ability of a target species (drug) to bind only to a peculiar G4 geometry. In this focused review, we survey the advances in the studies of the binding of small molecules of medical interest to G4s, with particular attention to the ability of these species to bind differently (intercalation, lateral binding or sitting atop) to different G4 topologies (parallel, anti-parallel or hybrid structures). Some species, given the very high affinity with some peculiar G4 topology, can first bind to a less favourable geometry and then induce its conversion. This aspect is also considered.
Collapse
Affiliation(s)
- Tarita Biver
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| |
Collapse
|
19
|
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.
Collapse
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
| |
Collapse
|
20
|
Zhu BC, He J, Xia XY, Jiang J, Liu W, Liu LY, Liang BB, Yao HG, Ke Z, Xia W, Mao ZW. Solution structure of thrombin binding aptamer complex with a non-planar platinum(II) compound. Chem Sci 2022; 13:8371-8379. [PMID: 35919711 PMCID: PMC9297526 DOI: 10.1039/d2sc01196d] [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: 02/27/2022] [Accepted: 05/29/2022] [Indexed: 11/21/2022] Open
Abstract
Thrombin Binding Aptamer (TBA) is a monomolecular well-defined two G-tetrads antiparallel G-quadruplex DNA that inhibits the activity of human α-thrombin. In this report, we synthesized a quasi-cross-shaped platinum(II) compound (L'2LPt)...
Collapse
Affiliation(s)
- Bo-Chen Zhu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-sen University Guangzhou 510275 China
| | - Juan He
- School of Pharmaceutical and Chemical Engineering, Guangdong Pharmaceutical University Zhongshan 528458 China
| | - Xiao-Yu Xia
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-sen University Guangzhou 510275 China
| | - Jingxing Jiang
- School of Materials Science and Engineering, PCFM Lab, School of Chemistry, Sun Yat-sen University Guangzhou 510275 China
| | - Wenting Liu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-sen University Guangzhou 510275 China
| | - Liu-Yi Liu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-sen University Guangzhou 510275 China
| | - Bing-Bing Liang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-sen University Guangzhou 510275 China
| | - Hua-Gang Yao
- School of Pharmaceutical and Chemical Engineering, Guangdong Pharmaceutical University Zhongshan 528458 China
| | - Zhuofeng Ke
- School of Materials Science and Engineering, PCFM Lab, School of Chemistry, Sun Yat-sen University Guangzhou 510275 China
| | - Wei Xia
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-sen University Guangzhou 510275 China
| | - Zong-Wan Mao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-sen University Guangzhou 510275 China
| |
Collapse
|