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Kumari A, Pandav K, Nath M, Barthwal R, Peddinti RK. Recognition of human telomeric G-quadruplex DNA by 1,5-disubstituted diethyl-amido anthraquinone derivative in different ion environments causing thermal stabilization and apoptosis. J Biomol Struct Dyn 2024:1-17. [PMID: 38174595 DOI: 10.1080/07391102.2023.2298733] [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: 10/09/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024]
Abstract
Ligand binding to G-quadruplex (G4) structures at human telomeric DNA ends promotes thermal stabilization, disrupting the interaction of the telomerase enzyme, which is found active in 80-85% of cancers and serves as a molecular marker. Anthraquinone compounds are well-known G-quadruplex (G4) binders that inhibit telomerase and induce apoptosis in cancer cells. Our current investigation is based on 1,5-bis[3-(diethylamino)propionamido]anthracene-9,10-dione, a derivative of anthraquinone and its binding characterization with two different human telomeric DNA structures, wHTel26 and HTel22, in the effect of K+ and Na+ by using an array of biophysical, calorimetry, molecular docking and cell viability assay techniques. Binding constants (Kb) in the range of ∼105-107 M-1 and stoichiometries of 1:1, 2:1 & 4:1 were obtained from the absorbance, fluorescence, and circular dichroism study. Remarkable hypochromism (55, 97%) and ∼17 nm shift in absorbance, fluorescence quenching (95, 97%), the unaltered value of fluorescence lifetime, restoration of Circular Dichroism bands, absence of ICD band, indicated the external groove binding/binding somewhere at loops. This is also evident in molecular docking results, the ligand binds to groove forming base (G4, G5, G24, T25) and in the vicinity to TTA loop (G14, G15, T17) bases of wHTel26 and HTel22, respectively. Thermal stabilization induced by ligand was found greater in Na+ ion (27.5 °C) than (19.1 °C) in K+ ion. Ligand caused cell toxicity in MCF-7 cancer cell lines with an IC50 value of ∼8.4 µM. The above findings suggest the ligand, 1,5-bis[3-(diethylamino)propionamido]anthracene-9,10-dione could be a potent anticancer drug candidate and has great therapeutic implications.Binding of disubstituted amido anthraquinone derivative, 1,5-bis[3-(diethylamino)propionamido]anthracene-9,10-dione to human telomere HTel22 antiparallel conformation induced thermal stabilization.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Anjana Kumari
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Kumud Pandav
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Mala Nath
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Ritu Barthwal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Rama Krishna Peddinti
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
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2
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Alexander A, Sumohan Pillai A, Sri Varalakshmi G, Ananthi N, Pal H, V. M. V. Enoch I, Sayed M. G-Quadruplex binding affinity variation on molecular encapsulation of ligands by porphyrin-tethered cyclodextrin. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2023.121233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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3
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Binding characterization of anthraquinone derivatives by stabilizing G-quadruplex DNA leads to an anticancerous activity. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 30:648-662. [PMID: 36514353 PMCID: PMC9720492 DOI: 10.1016/j.omtn.2022.11.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022]
Abstract
G-quadruplex is a non-canonical secondary structure identified in the telomeric region and the promoter of many oncogenes. Anthraquinone derivatives, a well-known inducer of telomere disruption in malignant cells and activate the apoptotic pathway. We used biophysical and biochemical studies to confirm the interaction of synthesized anthraquinone derivatives with the human telomeric G-quadruplex sequence. The binding affinity of N-2DEA and N-1DEA are K b = 4.8 × 106 M-1 and K b = 7.6 × 105 M-1, respectively, leading to hypochroism, fluorescence quenching with minor redshift and ellipticity variations indicating ligand binding in the external groove. We found that sodium ions induced stabilization more rather than potassium ions. Molecular docking of complex demonstrates a molecule's exterior binding to a quadruplex. The investigation of ROS activity indicated that the cell initiates mortality in response to the IC50 concentration. Cellular morphology, nuclear condensation, and fragmentation were altered in the treated cell, impairing cellular function. Finally, the transcriptional regulatory study paves the way for drug design as an anti-cancer agent because of the tremendous possibilities of changing substituent groups on anthraquinones to improve efficacy and selectivity for G-quartet DNA. Our research focused on how ligand binding to telomere sequences induces oxidative stress and inhibits the growth of malignant cells.
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Zhai LY, Liu JF, Zhao JJ, Su AM, Xi XG, Hou XM. Targeting the RNA G-Quadruplex and Protein Interactome for Antiviral Therapy. J Med Chem 2022; 65:10161-10182. [PMID: 35862260 DOI: 10.1021/acs.jmedchem.2c00649] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In recent years, G-quadruplexes (G4s), types of noncanonical four-stranded nucleic acid structures, have been identified in many viruses that threaten human health, such as HIV and Epstein-Barr virus. In this context, G4 ligands were designed to target the G4 structures, among which some have shown promising antiviral effects. In this Perspective, we first summarize the diversified roles of RNA G4s in different viruses. Next, we introduce small-molecule ligands developed as G4 modulators and highlight their applications in antiviral studies. In addition to G4s, we comprehensively review the medical intervention of G4-interacting proteins from both the virus (N protein, viral-encoded helicases, severe acute respiratory syndrome-unique domain, and Epstein-Barr nuclear antigen 1) and the host (heterogeneous nuclear ribonucleoproteins, RNA helicases, zinc-finger cellular nucelic acid-binding protein, and nucleolin) by inhibitors as an alternative way to disturb the normal functions of G4s. Finally, we discuss the challenges and opportunities in G4-based antiviral therapy.
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Affiliation(s)
- Li-Yan Zhai
- College of Life Sciences, Northwest A&F University, Xianyang, Shaanxi 712100, China
| | - Jing-Fan Liu
- College of Life Sciences, Northwest A&F University, Xianyang, Shaanxi 712100, China
| | - Jian-Jin Zhao
- College of Life Sciences, Northwest A&F University, Xianyang, Shaanxi 712100, China
| | - Ai-Min Su
- College of Life Sciences, Northwest A&F University, Xianyang, Shaanxi 712100, China
| | - Xu-Guang Xi
- College of Life Sciences, Northwest A&F University, Xianyang, Shaanxi 712100, China.,Laboratory of Biology and Applied Pharmacology, CNRS UMR 8113, IDA FR3242, ENS Paris-Saclay, Université Paris-Saclay, Gif-sur-Yvette 91190, France
| | - Xi-Miao Hou
- College of Life Sciences, Northwest A&F University, Xianyang, Shaanxi 712100, China
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5
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Ruthenium(II) Polypyridyl Complexes and Their Use as Probes and Photoreactive Agents for G-quadruplexes Labelling. Molecules 2022; 27:molecules27051541. [PMID: 35268640 PMCID: PMC8912042 DOI: 10.3390/molecules27051541] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/21/2022] [Accepted: 02/22/2022] [Indexed: 02/01/2023] Open
Abstract
Due to their optical and electrochemical properties, ruthenium(II) polypyridyl complexes have been used in a wide array of applications. Since the discovery of the light-switch ON effect of [Ru(bpy)2dppz]2+ when interacting with DNA, the design of new Ru(II) complexes as light-up probes for specific regions of DNA has been intensively explored. Amongst them, G-quadruplexes (G4s) are of particular interest. These structures formed by guanine-rich parts of DNA and RNA may be associated with a wide range of biological events. However, locating them and understanding their implications in biological pathways has proven challenging. Elegant approaches to tackle this challenge relies on the use of photoprobes capable of marking, reversibly or irreversibly, these G4s. Indeed, Ru(II) complexes containing ancillary π-deficient TAP ligands can create a covalently linked adduct with G4s after a photoinduced electron transfer from a guanine residue to the excited complex. Through careful design of the ligands, high selectivity of interaction with G4 structures can be achieved. This allows the creation of specific Ru(II) light-up probes and photoreactive agents for G4 labelling, which is at the core of this review composed of an introduction dedicated to a brief description of G-quadruplex structures and two main sections. The first one will provide a general picture of ligands and metal complexes interacting with G4s. The second one will focus on an exhaustive and comprehensive overview of the interactions and (photo)reactions of Ru(II) complexes with G4s.
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Hu XX, Wang SQ, Gan SQ, Liu L, Zhong MQ, Jia MH, Jiang F, Xu Y, Xiao CD, Shen XC. A Small Ligand That Selectively Binds to the G-quadruplex at the Human Vascular Endothelial Growth Factor Internal Ribosomal Entry Site and Represses the Translation. Front Chem 2021; 9:781198. [PMID: 34858949 PMCID: PMC8630693 DOI: 10.3389/fchem.2021.781198] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 10/19/2021] [Indexed: 11/13/2022] Open
Abstract
G-quadruplexes are believed to have important biological functions, so many small molecules have been screened or developed for targeting G-quadruplexes. However, it is still a major challenge to find molecules that recognize specific G-quadruplexes. Here, by using a combination of surface plasmon resonance, electrospray ionization mass spectrometry, circular dichroism, Western blot, luciferase assay, and reverse transcriptase stop assay, we observed a small molecule, namely, oxymatrine (OMT) that could selectively bind to the RNA G-quadruplex in 5′-untranslated regions (UTRs) of human vascular endothelial growth factor (hVEGF), but could not bind to other G-quadruplexes. OMT could selectively repress the translation of VEGF in cervical cancer cells. Furthermore, it could recognize VEGF RNA G-quadruplexes in special conformations. The results indicate that OMT may serve as a potentially special tool for studying the VEGF RNA G-quadruplex in cells and as a valuable scaffold for the design of ligands that recognize different G-quadruplexes.
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Affiliation(s)
- Xiao-Xia Hu
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, China.,Department of Physiology, College of Basic Medical Sciences, Guizhou Medical University, Guiyang, China
| | - Sheng-Quan Wang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, China
| | - Shi-Quan Gan
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, China
| | - Lei Liu
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, China
| | - Ming-Qing Zhong
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, China
| | - Meng-Hao Jia
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, China
| | - Fei Jiang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, China
| | - Yan Xu
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Chao-Da Xiao
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, China.,The Key Laboratory of Optimal Utilization of Natural Medicine Resources, Guizhou Medical University, Guiyang, China
| | - Xiang-Chun Shen
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, China.,The Key Laboratory of Optimal Utilization of Natural Medicine Resources, Guizhou Medical University, Guiyang, China
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Ribaudo G, Ongaro A, Oselladore E, Memo M, Gianoncelli A. Combining Electrospray Mass Spectrometry (ESI-MS) and Computational Techniques in the Assessment of G-Quadruplex Ligands: A Hybrid Approach to Optimize Hit Discovery. J Med Chem 2021; 64:13174-13190. [PMID: 34510895 PMCID: PMC8474113 DOI: 10.1021/acs.jmedchem.1c00962] [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] [Indexed: 12/05/2022]
Abstract
![]()
Guanine-rich sequences
forming G-quadruplexes (GQs) are present
in several genomes, ranging from viral to human. Given their peculiar
localization, the induction of GQ formation or GQ stabilization with
small molecules represents a strategy for interfering with crucial
biological functions. Investigating the recognition event at the molecular
level, with the aim of fully understanding the triggered pharmacological
effects, is challenging. Native electrospray ionization mass spectrometry
(ESI-MS) is being optimized to study these noncovalent assemblies.
Quantitative parameters retrieved from ESI-MS studies, such as binding
affinity, the equilibrium binding constant, and sequence selectivity,
will be overviewed. Computational experiments supporting the ESI-MS
investigation and boosting its efficiency in the search for GQ ligands
will also be discussed with practical examples. The combination of
ESI-MS and in silico techniques in a hybrid high-throughput-screening
workflow represents a valuable tool for the medicinal chemist, providing
data on the quantitative and structural aspects of ligand–GQ
interactions.
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Affiliation(s)
- Giovanni Ribaudo
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Alberto Ongaro
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Erika Oselladore
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Maurizio Memo
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Alessandra Gianoncelli
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy
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Tateishi-Karimata H, Banerjee D, Ohyama T, Matsumoto S, Miyoshi D, Nakano SI, Sugimoto N. Hydroxyl groups in cosolutes regulate the G-quadruplex topology of telomeric DNA. Biochem Biophys Res Commun 2020; 525:S0006-291X(20)30313-2. [PMID: 32081425 DOI: 10.1016/j.bbrc.2020.02.045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 02/08/2020] [Indexed: 01/12/2023]
Abstract
Telomeric G-quadruplex topology has the ability to regulate telomerase activity, which counteracts the shortening of telomere with successive cell divisions, thereby causing genomic longevity. However, the detailed mechanism of G-quadruplexes topologies formed by telomeric sequences requires further investigation. In this study, we quantitatively investigated the effect of cosolutes, particularly the varying number of hydroxyl groups, on the structural transition between hybrid type and parallel G-quadruplexes formed by telomeric DNA sequences. Cosolutes with one or no hydroxyl groups in the vicinal position more efficiently induced the transition to parallel G-quadruplex from hybrid G-quadruplex than those with more hydroxyl groups. We also examined the effect of cosolute structures on the hydration of G-quadruplex formation; the results indicated that cosolutes with fewer hydroxyl groups lead to the release of greater amount of water during G-quadruplex formation. Molecular dynamics results showed that the parallel G-quadruplex was more dehydrated than the hybrid type G-quadruplex. Generally, a dehydrated structure is favored under crowding condition. Thus, depending on the surrounding cosolutes, the G-quadruplex topology can be controlled by the G-quadruplex hydration state.
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Affiliation(s)
| | - Dipanwita Banerjee
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, Japan
| | - Tatsuya Ohyama
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, Japan
| | - Saki Matsumoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, Japan
| | - Daisuke Miyoshi
- Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Japan
| | - Shu-Ich Nakano
- Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Japan
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, Japan; Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Japan.
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10
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Tripathi S, Barthwal R. NMR based structure reveals groove binding of mitoxantrone to two sites of [d-(TTAGGGT)]4 having human telomeric DNA sequence leading to thermal stabilization of G-quadruplex. Int J Biol Macromol 2018; 111:326-341. [DOI: 10.1016/j.ijbiomac.2017.12.134] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Revised: 12/18/2017] [Accepted: 12/27/2017] [Indexed: 01/03/2023]
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Zhang R, Cheng M, Zhang LM, Zhu LN, Kong DM. Asymmetric Cationic Porphyrin as a New G-Quadruplex Probe with Wash-Free Cancer-Targeted Imaging Ability Under Acidic Microenvironments. ACS APPLIED MATERIALS & INTERFACES 2018; 10:13350-13360. [PMID: 29619818 DOI: 10.1021/acsami.8b01901] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Porphyrins are promising candidates for nucleic acid G-quadruplex-specific optical recognition. We previously demonstrated that G-quadruplex recognition specificity of porphyrins could be improved by introducing bulky side arm substituents, but the enhanced protonation tendency limits their applications in some cases, such as under acidic conditions. Here, we demonstrated that the protonation tendency of porphyrin derivatives could be efficiently overcome by increasing molecular asymmetry. To validate this, an asymmetric, water-soluble, cationic porphyrin FA-TMPipEOPP (5-{4-[2-[[(2 E)-3-[3-methoxy-4-[2-(1-methyl-1-piperidinyl)ethoxy]phenyl]-1-oxo-2-propenyl]oxy]ethoxy]phenyl},10,15,20-tri{4-[2-(1-methyl-1-piperidinyl)ethoxy]-phenyl}porphyrin) was synthesized by introducing a ferulic acid (FA) unit at one side arm, and its structure was well-characterized. Unlike its symmetric counterpart TMPipEOPP that has a tendency to protonate under acidic conditions, FA-TMPipEOPP remained in the unprotonated monomeric form under the pH range of 2.0-8.0. Correspondingly, FA-TMPipEOPP showed better G-quadruplex recognition specificity than TMPipEOPP and thus might be used as a specific optical probe for colorimetric and fluorescent recognition of G-quadruplexes under acidic conditions. The feasibility was demonstrated by two proof-of-concept studies: probing structural competition between G-quadruplexes and duplexes and label-free and wash-free cancer cell-targeted bioimaging under an acidic tumor microenvironment. As G-quadruplex optical probes, FA-TMPipEOPP works well under acidic conditions, whereas TMPipEOPP works well under neutral conditions. This finding provides useful information for G-quadruplex probe research. That is, porphyrin-based G-quadruplex probes suitable for different pH conditions might be obtained by adjusting the molecular symmetry.
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Affiliation(s)
- Ran Zhang
- Department of Chemistry, School of Science , Tianjin University , Tianjin 300072 , P R China
- Collaborative Innovation Center of Chemical Science and Engineering , Tianjin 30072 , P R China
| | - Meng Cheng
- Department of Chemistry, School of Science , Tianjin University , Tianjin 300072 , P R China
- Collaborative Innovation Center of Chemical Science and Engineering , Tianjin 30072 , P R China
| | - Li-Ming Zhang
- Department of Chemistry, School of Science , Tianjin University , Tianjin 300072 , P R China
- Collaborative Innovation Center of Chemical Science and Engineering , Tianjin 30072 , P R China
| | - Li-Na Zhu
- Department of Chemistry, School of Science , Tianjin University , Tianjin 300072 , P R China
- Collaborative Innovation Center of Chemical Science and Engineering , Tianjin 30072 , P R China
| | - De-Ming Kong
- Collaborative Innovation Center of Chemical Science and Engineering , Tianjin 30072 , P R China
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry , Nankai University , Tianjin 300071 , P R China
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Sillapapongwarakorn S, Yanarojana S, Pinthong D, Thithapandha A, Ungwitayatorn J, Supavilai P. Molecular docking based screening of triterpenoids as potential G-quadruplex stabilizing ligands with anti-cancer activity. Bioinformation 2017; 13:284-292. [PMID: 29081607 PMCID: PMC5651221 DOI: 10.6026/97320630013284] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 08/30/2017] [Accepted: 09/02/2017] [Indexed: 01/13/2023] Open
Abstract
Triterpenoids isolated from Ganoderma lucidum (GLTs) exhibit a broad spectrum of anti-cancer properties, including anti-proliferative, anti-metastatic and anti-angiogenic activities. Current research studies revealed the role by GLTs in inducing apoptosis and suppression of telomerase activity of cancer cells with much lower toxicity to healthy cells. Compounds selectively binding and stabilizing G-quadruplex structures could inhibit the telomerase or downregulate the oncogenes and may act as anti-cancer agents. Targeting human telomeric G-quadruplex DNA could be one of the mechanisms by which these GLTs exert anti-cancer activity. In this study, 208 GLTs were screened for ligands with high binding affinity and selectively to stabilize the pG4DNA by using the docking tool AutoDock4. The results showed that ganoderic acid A and ganoderic acid Df exhibit high binding affinity and selectively bind to the lateral groove of pG4DNA. Based on our findings, we suggest that the triterpenoid represents a new class of G-quadruplex groove binding ligands and thus act as potential anti-cancer agents.
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Affiliation(s)
| | - Somchai Yanarojana
- Department of Pharmacology, Faculty of Science, Mahidol University, 272 Rama 6 Road, Bangkok 10400, Thailand
| | - Darawan Pinthong
- Department of Pharmacology, Faculty of Science, Mahidol University, 272 Rama 6 Road, Bangkok 10400, Thailand
| | - Amnuay Thithapandha
- Department of Pharmacology, Faculty of Science, Mahidol University, 272 Rama 6 Road, Bangkok 10400, Thailand
| | - Jiraporn Ungwitayatorn
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Mahidol University, 447 Sri-Ayudhaya Road, Bangkok 10400, Thailand
| | - Porntip Supavilai
- Department of Pharmacology, Faculty of Science, Mahidol University, 272 Rama 6 Road, Bangkok 10400, Thailand
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Zhao A, Howson SE, Zhao C, Ren J, Scott P, Wang C, Qu X. Chiral metallohelices enantioselectively target hybrid human telomeric G-quadruplex DNA. Nucleic Acids Res 2017; 45:5026-5035. [PMID: 28398500 PMCID: PMC5435910 DOI: 10.1093/nar/gkx244] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 03/30/2017] [Indexed: 02/05/2023] Open
Abstract
The design and synthesis of metal complexes that can specifically target DNA secondary structure has attracted considerable attention. Chiral metallosupramolecular complexes (e.g. helicates) in particular display unique DNA-binding behavior, however until recently few examples which are both water-compatible and enantiomerically pure have been reported. Herein we report that one metallohelix enantiomer Δ1a, available from a diastereoselective synthesis with no need for resolution, can enantioselectively stabilize human telomeric hybrid G-quadruplex and strongly inhibit telomerase activity with IC50 of 600 nM. In contrast, no such a preference is observed for the mirror image complex Λ1a. More intriguingly, neither of the two enantiomers binds specifically to human telomeric antiparallel G-quadruplex. To the best of our knowledge, this is the first example of one pair of enantiomers with contrasting selectivity for human telomeric hybrid G-quadruplex. Further studies show that Δ1a can discriminate human telomeric G-quadruplex from other telomeric G-quadruplexes.
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Affiliation(s)
- Andong Zhao
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
- University of Chinese Academy of Science, Beijing 100039, China
| | - Suzanne E. Howson
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Chuanqi Zhao
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
- To whom correspondence should be addressed. Tel: +86 431 8526 2656; Fax: +86 431 8526 2656; . Correspondence may also be addressed to Chuanqi Zhao. Tel: +86 431 8526 2656; Fax: +86 431 8526 2656;
| | - Jinsong Ren
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Peter Scott
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Chunyu Wang
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, 2699 Qianjin Avenue, Changchun 130012, China
| | - Xiaogang Qu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
- To whom correspondence should be addressed. Tel: +86 431 8526 2656; Fax: +86 431 8526 2656; . Correspondence may also be addressed to Chuanqi Zhao. Tel: +86 431 8526 2656; Fax: +86 431 8526 2656;
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Carvalho J, Nottelet P, Mergny JL, Queiroz JA, Salgado GF, Cruz C. Study of the interaction between indole-based compounds and biologically relevant G-quadruplexes. Biochimie 2017; 135:186-195. [DOI: 10.1016/j.biochi.2017.02.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 01/21/2017] [Accepted: 02/13/2017] [Indexed: 10/20/2022]
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Dolinnaya NG, Ogloblina AM, Yakubovskaya MG. Structure, Properties, and Biological Relevance of the DNA and RNA G-Quadruplexes: Overview 50 Years after Their Discovery. BIOCHEMISTRY (MOSCOW) 2017; 81:1602-1649. [PMID: 28260487 PMCID: PMC7087716 DOI: 10.1134/s0006297916130034] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
G-quadruplexes (G4s), which are known to have important roles in regulation of key biological processes in both normal and pathological cells, are the most actively studied non-canonical structures of nucleic acids. In this review, we summarize the results of studies published in recent years that change significantly scientific views on various aspects of our understanding of quadruplexes. Modern notions on the polymorphism of DNA quadruplexes, on factors affecting thermodynamics and kinetics of G4 folding–unfolding, on structural organization of multiquadruplex systems, and on conformational features of RNA G4s and hybrid DNA–RNA G4s are discussed. Here we report the data on location of G4 sequence motifs in the genomes of eukaryotes, bacteria, and viruses, characterize G4-specific small-molecule ligands and proteins, as well as the mechanisms of their interactions with quadruplexes. New information on the structure and stability of G4s in telomeric DNA and oncogene promoters is discussed as well as proof being provided on the occurrence of G-quadruplexes in cells. Prominence is given to novel experimental techniques (single molecule manipulations, optical and magnetic tweezers, original chemical approaches, G4 detection in situ, in-cell NMR spectroscopy) that facilitate breakthroughs in the investigation of the structure and functions of G-quadruplexes.
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Affiliation(s)
- N G Dolinnaya
- Lomonosov Moscow State University, Department of Chemistry, Moscow, 119991, Russia.
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Padmapriya K, Barthwal R. NMR based structural studies decipher stacking of the alkaloid coralyne to terminal guanines at two different sites in parallel G-quadruplex DNA, [d(TTGGGGT)]4 and [d(TTAGGGT)]4. Biochim Biophys Acta Gen Subj 2017; 1861:37-48. [DOI: 10.1016/j.bbagen.2016.11.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 10/13/2016] [Accepted: 11/08/2016] [Indexed: 01/15/2023]
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Pradeep TP, Barthwal R. A 4:1 stoichiometric binding and stabilization of mitoxantrone-parallel stranded G-quadruplex complex established by spectroscopy techniques. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2016; 162:106-114. [DOI: 10.1016/j.jphotobiol.2016.06.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Revised: 06/10/2016] [Accepted: 06/11/2016] [Indexed: 12/30/2022]
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Pradeep TP, Barthwal R. NMR structure of dual site binding of mitoxantrone dimer to opposite grooves of parallel stranded G-quadruplex [d-(TTGGGGT)]4. Biochimie 2016; 128-129:59-69. [DOI: 10.1016/j.biochi.2016.07.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 07/11/2016] [Indexed: 12/27/2022]
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Recent advances in targeting the telomeric G-quadruplex DNA sequence with small molecules as a strategy for anticancer therapies. Future Med Chem 2016; 8:1259-90. [PMID: 27442231 DOI: 10.4155/fmc-2015-0017] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Human telomeric DNA (hTelo), present at the ends of chromosomes to protect their integrity during cell division, comprises tandem repeats of the sequence d(TTAGGG) which is known to form a G-quadruplex secondary structure. This unique structural formation of DNA is distinct from the well-known helical structure that most genomic DNA is thought to adopt, and has recently gained prominence as a molecular target for new types of anticancer agents. In particular, compounds that can stabilize the intramolecular G-quadruplex formed within the human telomeric DNA sequence can inhibit the activity of the enzyme telomerase which is known to be upregulated in tumor cells and is a major contributor to their immortality. This provides the basis for the discovery and development of small molecules with the potential for selective toxicity toward tumor cells. This review summarizes the various families of small molecules reported in the literature that have telomeric quadruplex stabilizing properties, and assesses the potential for compounds of this type to be developed as novel anticancer therapies. A future perspective is also presented, emphasizing the need for researchers to adopt approaches that will allow the discovery of molecules with more drug-like properties in order to improve the chances of lead molecules reaching the clinic in the next decade.
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Tripathi S, Pradeep TP, Barthwal R. Molecular Recognition of Parallel DNA Quadruplex d(TTAGGGT)4by Mitoxantrone: Binding with 1:2 Stoichiometry Leading to Thermal Stabilization and Telomerase Inhibition. Chembiochem 2016; 17:554-60. [DOI: 10.1002/cbic.201500588] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Indexed: 01/28/2023]
Affiliation(s)
- Sweta Tripathi
- Department of Biotechnology; Indian Institute of Technology Roorkee; Roorkee 247667 India
| | | | - Ritu Barthwal
- Department of Biotechnology; Indian Institute of Technology Roorkee; Roorkee 247667 India
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Mandal P, Bhattacharya M, Chowdhury J. Targeting G-quadruplex DNA and B-DNA with a natural alkaloid: a comparative spectroscopic study. RSC Adv 2016. [DOI: 10.1039/c6ra22776g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Different modes of binding of natural alkaloid harmine with G-quadruplex DNA and B-DNA: key roles in molecular recognition.
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Affiliation(s)
- Paulami Mandal
- Department of Biochemistry
- University of Calcutta
- Kolkata-700019
- India
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Pradeep TP, Tripathi S, Barthwal R. Molecular recognition of parallel quadruplex [d-(TTGGGGT)]4 by mitoxantrone: binding with 1 : 4 stoichiometry leads to telomerase inhibition. RSC Adv 2016. [DOI: 10.1039/c6ra05266e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
NMR and CD studies show that anti-cancer drug mitoxantrone (MTX) binds to parallel G-quadruplex DNA [d-(TTGGGGT)4] as stacked dimer at grooves leading to increase in thermal stabilization of DNA by ~25 °C and inhibits telomerase with IC50 = 2 μM.
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Affiliation(s)
| | - Sweta Tripathi
- Department of Biotechnology
- Indian Institute of Technology Roorkee
- Roorkee 247667
- India
| | - Ritu Barthwal
- Department of Biotechnology
- Indian Institute of Technology Roorkee
- Roorkee 247667
- India
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Duskova K, Sierra S, Arias-Pérez MS, Gude L. Human telomeric G-quadruplex DNA interactions of N-phenanthroline glycosylamine copper(II) complexes. Bioorg Med Chem 2015; 24:33-41. [PMID: 26678174 DOI: 10.1016/j.bmc.2015.11.037] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 11/24/2015] [Accepted: 11/26/2015] [Indexed: 01/12/2023]
Abstract
We report in this article the interactions of five N-(1,10-phenanthrolin-5-yl)-β-glycopyranosylamine copper(II) complexes with G-quadruplex DNA. Specifically, the interactions of these compounds with a human telomeric oligonucleotide have been assessed by fluorescence-based assays (FRET melting and G4-FID), circular dichroism and competitive equilibrium dialysis experiments. The metal complexes bind and stabilize G-quadruplex DNA structures with apparent association constants in the order of 10(4)-10(5)M(-1) and the affinity observed is dependent on the ionic conditions utilized and the specific nature of the carbohydrate moiety tethered to the 1,10-phenanthroline system. The compounds showed only a slight preference to bind G-quadruplex DNA over duplex DNA when the quadruplex DNA was folded in sodium ionic conditions. However, the binding affinity and selectivity, although modest, were notably increased when the G-quadruplex DNA was folded in the presence of potassium metal ions. Moreover, the study points towards a significant contribution of groove and/or loop binding in the recognition mode of quadruplex structures by these non-classical quadruplex ligands. The results reported herein highlight the potential and the versatility of carbohydrate bis-phenanthroline metal-complex conjugates to recognize G-quadruplex DNA structures.
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Affiliation(s)
- Katerina Duskova
- Departamento de Química Orgánica y Química Inorgánica, Universidad de Alcalá, 28805 Alcalá de Henares (Madrid), Spain
| | - Sara Sierra
- Departamento de Química Orgánica y Química Inorgánica, Universidad de Alcalá, 28805 Alcalá de Henares (Madrid), Spain
| | - María-Selma Arias-Pérez
- Departamento de Química Orgánica y Química Inorgánica, Universidad de Alcalá, 28805 Alcalá de Henares (Madrid), Spain
| | - Lourdes Gude
- Departamento de Química Orgánica y Química Inorgánica, Universidad de Alcalá, 28805 Alcalá de Henares (Madrid), Spain.
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Rizeq N, Georgiades SN. Linear and Branched Pyridyl-Oxazole Oligomers: Synthesis and Circular Dichroism Detectable Effect on c-Myc G-Quadruplex Helicity. European J Org Chem 2015. [DOI: 10.1002/ejoc.201501269] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Non-Flat Bisbenzylisoquinoline Alkaloid Fangchinoline As a Class of Potent G-Quadruplex Stabilizer with Anti-cancer Activity. CHINESE J CHEM 2015. [DOI: 10.1002/cjoc.201400841] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Hou JQ, Chen SB, Zan LP, Ou TM, Tan JH, Luyt LG, Huang ZS. Identification of a selective G-quadruplex DNA binder using a multistep virtual screening approach. Chem Commun (Camb) 2015; 51:198-201. [DOI: 10.1039/c4cc06951j] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A selective G-quadruplex binder was identified using a multistep virtual screening approach by simultaneously taking into account G-quadruplex and duplex DNA.
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Affiliation(s)
- Jin-Qiang Hou
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou 510006
- China
- London Regional Cancer Program
| | - Shuo-Bin Chen
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou 510006
- China
| | - Li-Peng Zan
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou 510006
- China
| | - Tian-Miao Ou
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou 510006
- China
| | - Jia-Heng Tan
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou 510006
- China
| | - Leonard G. Luyt
- London Regional Cancer Program
- Ontario N6A 4L6
- Canada
- Depts. Oncology, Chemistry, Medical Imaging
- The University of Western Ontario
| | - Zhi-Shu Huang
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou 510006
- China
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Targeting G-quadruplex nucleic acids with heterocyclic alkaloids and their derivatives. Eur J Med Chem 2014; 97:538-51. [PMID: 25466923 DOI: 10.1016/j.ejmech.2014.11.021] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Revised: 11/05/2014] [Accepted: 11/11/2014] [Indexed: 01/25/2023]
Abstract
G-Quadruplex nucleic acids or G-quadruplexes (G4s) are four-stranded DNA or RNA secondary structures that are formed in guanine-rich sequences. They are widely distributed in functional regions of the human genome, such as telomeres, ribosomal DNA (rDNA), transcription start sites, promoter regions and untranslated regions of mRNA, suggesting that G-quadruplex structures may play a pivotal role in the control of a variety of cellular processes. G-Quadruplexes are viewed as valid therapeutic targets in human cancer diseases. Small molecules, from naturally occurring to synthetic, are exploited to specifically target G-quadruplexes and have proven to be a new class of anticancer agents. Notably, alkaloids are an important source of G-quadruplex ligands and have significant bioactivities in anticancer therapy. In this review, the authors provide a brief, up-to-date summary of heterocyclic alkaloids and their derivatives targeting G-quadruplexes.
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Di Leva FS, Novellino E, Cavalli A, Parrinello M, Limongelli V. Mechanistic insight into ligand binding to G-quadruplex DNA. Nucleic Acids Res 2014; 42:5447-55. [PMID: 24753420 PMCID: PMC4027208 DOI: 10.1093/nar/gku247] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2013] [Revised: 03/10/2014] [Accepted: 03/13/2014] [Indexed: 12/12/2022] Open
Abstract
Specific guanine-rich regions in human genome can form higher-order DNA structures called G-quadruplexes, which regulate many relevant biological processes. For instance, the formation of G-quadruplex at telomeres can alter cellular functions, inducing apoptosis. Thus, developing small molecules that are able to bind and stabilize the telomeric G-quadruplexes represents an attractive strategy for antitumor therapy. An example is 3-(benzo[d]thiazol-2-yl)-7-hydroxy-8-((4-(2-hydroxyethyl)piperazin-1-yl)methyl)-2H-chromen-2-one (compound 1: ), recently identified as potent ligand of the G-quadruplex [d(TGGGGT)]4 with promising in vitro antitumor activity. The experimental observations are suggestive of a complex binding mechanism that, despite efforts, has defied full characterization. Here, we provide through metadynamics simulations a comprehensive understanding of the binding mechanism of 1: to the G-quadruplex [d(TGGGGT)]4. In our calculations, the ligand explores all the available binding sites on the DNA structure and the free-energy landscape of the whole binding process is computed. We have thus disclosed a peculiar hopping binding mechanism whereas 1: is able to bind both to the groove and to the 3' end of the G-quadruplex. Our results fully explain the available experimental data, rendering our approach of great value for further ligand/DNA studies.
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Affiliation(s)
- Francesco Saverio Di Leva
- Department of Drug Discovery and Development, Istituto Italiano di Tecnologia, via Morego, 30, I-16163 Genoa, Italy
| | - Ettore Novellino
- Department of Pharmacy, University of Naples "Federico II", via D. Montesano, 49, I-80131 Naples, Italy
| | - Andrea Cavalli
- Department of Drug Discovery and Development, Istituto Italiano di Tecnologia, via Morego, 30, I-16163 Genoa, Italy Department of Pharmacy and Biotechnology, Alma Mater Studiorum, University of Bologna, via Belmeloro, 6, I-40126 Bologna, Italy
| | - Michele Parrinello
- Department of Chemistry and Applied Biosciences, ETH Zurich, and Facoltà di Informatica, Istituto di Scienze Computazionali, Università della Svizzera Italiana, via G. Buffi, 13, CH-6900 Lugano, Switzerland
| | - Vittorio Limongelli
- Department of Pharmacy, University of Naples "Federico II", via D. Montesano, 49, I-80131 Naples, Italy
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Zhang S, Wu Y, Zhang W. G-Quadruplex Structures and Their Interaction Diversity with Ligands. ChemMedChem 2014; 9:899-911. [DOI: 10.1002/cmdc.201300566] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Indexed: 12/22/2022]
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Maji B, Bhattacharya S. Advances in the molecular design of potential anticancer agents via targeting of human telomeric DNA. Chem Commun (Camb) 2014; 50:6422-38. [DOI: 10.1039/c4cc00611a] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Telomerase is an attractive drug target to develop new generation drugs against cancer.
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Affiliation(s)
- Basudeb Maji
- Department of Organic Chemistry
- Indian Institute of Science
- Bangalore-560012, India
| | - Santanu Bhattacharya
- Department of Organic Chemistry
- Indian Institute of Science
- Bangalore-560012, India
- Chemical Biology Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research
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Gai W, Yang Q, Xiang J, Sun H, Shang Q, Li Q, Jiang W, Guan A, Zhang H, Tang Y, Xu G. Roles of flanking sequences in the binding between unimolecular parallel-stranded G-quadruplexes and ligands. ACTA ACUST UNITED AC 2013. [DOI: 10.1007/s11434-012-5639-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Alcaro S, Musetti C, Distinto S, Casatti M, Zagotto G, Artese A, Parrotta L, Moraca F, Costa G, Ortuso F, Maccioni E, Sissi C. Identification and characterization of new DNA G-quadruplex binders selected by a combination of ligand and structure-based virtual screening approaches. J Med Chem 2013; 56:843-55. [PMID: 23294188 DOI: 10.1021/jm3013486] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Nowadays, it has been demonstrated that DNA G-quadruplex arrangements are involved in cellular aging and cancer, thus boosting the discovery of selective binders for these DNA secondary structures. By taking advantage of available structural and biological information on these structures, we performed a high throughput in silico screening of commercially available molecules databases by merging ligand- and structure-based approaches by means of docking experiments. Compounds selected by the virtual screening procedure were then tested for their ability to interact with the human telomeric G-quadruplex folding by circular dichroism, fluorescence spectroscopy, and photodynamic techniques. Interestingly, our screening succeeded in retrieving a new promising scaffold for G-quadruplex binders characterized by a psoralen moiety.
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Affiliation(s)
- Stefano Alcaro
- Dipartimento di Scienze della Salute, Università di Catanzaro, Campus "Salvatore Venuta", Viale Europa, 88100 Catanzaro, Italy
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Ma L, Song F, Liu Z, Liu S. Study on noncovalent complexes of alkaloids with DNA duplex using electrospray ionization mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2013; 27:51-58. [PMID: 23239316 DOI: 10.1002/rcm.6424] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Revised: 09/27/2012] [Accepted: 09/29/2012] [Indexed: 06/01/2023]
Abstract
RATIONALE DNA is an important molecular target in modern medicine research. Some DNA-binding ligands have been used to treat numerous diseases. Therefore, understanding the interactions of different ligands with DNA and looking for new DNA agents are necessary to develop new drugs. METHODS Electrospray ionization mass spectrometry (ESI-MS) in the negative ion mode was used to screen the noncovalent complexes between 11 alkaloids with double helix oligonucleotides at molar ratios 1:1 to 1:4. The relative binding affinities based on the fraction of bound DNA and sequence selectivities of alkaloids towards the duplex were also investigated by ESI-MS. Moreover, tandem mass spectrometry of 5-charged complex ions was used to try to determine DNA-binding modes. RESULTS Six alkaloids showed complexation with the selected DNA duplex, i.e., berberine, coptisine, peimine, aconitine, oxysophoridine and cytisine. They showed their binding affinities with d(AACTCCCGGCACAC/GTGTGCCGGGAGTT) in the order of berberine > coptisine > peimine > aconitine, oxysophoridine > cytosine; additional experiments involving collision energy proved this result. Sequence selectivities were not apparent for coptisine, peimine, aconitine and oxysophoridine with four DNA duplexes. The complexes containing berberine and coptisine underwent the predominant loss of the G base. However, for complexes containing the other four alkaloids, they dissociated via the loss of neutral drug. The results confirmed that they may have different binding modes. CONCLUSIONS According to experiment data and structural information, the binding mode of individual drugs with DNA was speculated. It was noted that the bindings of alkaloids peimine, aconitine and oxysophoridine with DNA are discovered firstly. This may give a clue to design duplex-binding ligands and be helpful for understanding biological activities of these alkaloids.
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Affiliation(s)
- Lei Ma
- Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun Center of Mass Spectrometry, Changchun, 130022, PR China
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Li Q, Xiang JF, Yang QF, Sun HX, Guan AJ, Tang YL. G4LDB: a database for discovering and studying G-quadruplex ligands. Nucleic Acids Res 2012; 41:D1115-23. [PMID: 23161677 PMCID: PMC3531060 DOI: 10.1093/nar/gks1101] [Citation(s) in RCA: 111] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The G-quadruplex ligands database (G4LDB, http://www.g4ldb.org) provides a unique collection of reported G-quadruplex ligands to streamline ligand/drug discovery targeting G-quadruplexes. G-quadruplexes are guanine-rich nucleic acid sequences in human telomeres and gene promoter regions. There is a growing recognition for their profound roles in a wide spectrum of diseases, such as cancer, diabetes and cardiovascular disease. Ligands that affect the structure and activity of G-quadruplexes can shed light on the search for G-quadruplex-targeting drugs. Therefore, we built the G4LDB to (i) compile a data set covering various physical properties and 3D structure of G-quadruplex ligands; (ii) provide Web-based tools for G-quadruplex ligand design; and (iii) to facilitate the discovery of novel therapeutic and diagnostic agents targeting G-quadruplexes. G4LDB currently contains >800 G-quadruplex ligands with ∼4000 activity records, which, to our knowledge, is the most extensive collection of its kind. It offers a user friendly interface that can meet a variety of data inquiries from researchers. For example, ligands can be searched for by name, molecular properties, structures, ligand activities and so on. Building on the reported data, the database also provides an online ligand design module that can predict ligand binding affinity in real time.
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Affiliation(s)
- Qian Li
- Beijing National Laboratory for Molecular Sciences (BNLMS), Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, PR China
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Cosconati S, Rizzo A, Trotta R, Pagano B, Iachettini S, De Tito S, Lauri I, Fotticchia I, Giustiniano M, Marinelli L, Giancola C, Novellino E, Biroccio A, Randazzo A. Shooting for selective druglike G-quadruplex binders: evidence for telomeric DNA damage and tumor cell death. J Med Chem 2012; 55:9785-92. [PMID: 23057850 DOI: 10.1021/jm301019w] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Targeting of DNA secondary structures, such as G-quadruplexes, is now considered an appealing opportunity for drug intervention in anticancer therapy. So far, efforts made in the discovery of chemotypes able to target G-quadruplexes mainly succeeded in the identification of a number of polyaromatic compounds featuring end-stacking binding properties. Against this general trend, we were persuaded that the G-quadruplex grooves can recognize molecular entities with better drug-like and selectivity properties. From this idea, a set of small molecules was identified and the structural features responsible for G-quadruplex recognition were delineated. These compounds were demonstrated to have enhanced affinity and selectivity for the G-quadruplex over the duplex structure. Their ability to induce selective DNA damage at telomeric level and to induction of apoptosis and senescence on tumor cells is herein experimentally proven.
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Affiliation(s)
- Sandro Cosconati
- Dipartimento di Scienze Ambientali, Seconda Università di Napoli , 81100 Caserta, Italy
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Ji X, Sun H, Zhou H, Xiang J, Tang Y, Zhao C. The interaction of telomeric DNA and C-myc22 G-quadruplex with 11 natural alkaloids. Nucleic Acid Ther 2012; 22:127-36. [PMID: 22480315 DOI: 10.1089/nat.2012.0342] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Telomeric DNA and C-myc22 are DNA G-quadruplex (G4)-forming sequences associated with tumorigenesis. Ligands that can facilitate the formation and increase the stabilization of G4 can halt tumor cell proliferation and have been regarded as potential anti-cancer drugs. In the present study, we have investigated the interaction of 11 natural alkaloids with G4 formed by telomeric DNA and C-myc22 sequences. Our results indicated that sanguinarine (San), palmatine (Pal), and berberine (Beb) of the first series (S1) can induce the formation of G4 as well as increase the stabilization ability. Daurisoline (S2-1), O-methyldauricine (S2-2), O-diacetyldaurisoline (S2-3), daurinoline (S2-4), dauricinoline (S2-5), N,N'-dimethyldauricine iodide (S2-6), and N,N'-dimethyldaurisoline iodide (S2-7) of the second series (S2) showed similar stabilization ability. We found that unsaturated ring C, N(+) positively charged centers, and conjugated aromatic rings are key factors to increase the stabilization ability of S1, and we gave some advice on structure modification to S2 through structure-activity study. Besides, we found San and Pal to be cell cycle blocker in G(1). San was speculated to bind to G4 through intercalation or end stacking.
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Affiliation(s)
- Xiaohui Ji
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, Beijing Key Laboratory of Gene Engineering Drugs and Biological Technology College of Life Science, Beijing Normal University, Beijing, People's Republic of China
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Molecular dynamic and quantum mechanics study of drug recognition for the extremity of DNA G-quadruplex groove. Med Chem Res 2011. [DOI: 10.1007/s00044-011-9927-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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Li J, Jin X, Hu L, Wang J, Su Z. Identification of nonplanar small molecule for G-quadruplex grooves: Molecular docking and molecular dynamic study. Bioorg Med Chem Lett 2011; 21:6969-72. [DOI: 10.1016/j.bmcl.2011.09.125] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2011] [Revised: 09/14/2011] [Accepted: 09/29/2011] [Indexed: 12/26/2022]
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39
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Largy E, Hamon F, Rosu F, Gabelica V, De Pauw E, Guédin A, Mergny JL, Teulade-Fichou MP. Tridentate N-Donor Palladium(II) Complexes as Efficient Coordinating Quadruplex DNA Binders. Chemistry 2011; 17:13274-83. [DOI: 10.1002/chem.201102300] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Indexed: 11/05/2022]
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40
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Guan AJ, Zhang EX, Xiang JF, Li Q, Yang QF, Li L, Tang YL, Wang MX. Effects of loops and nucleotides in G-quadruplexes on their interaction with an azacalixarene, methylazacalix[6]pyridine. J Phys Chem B 2011; 115:12584-90. [PMID: 21923138 DOI: 10.1021/jp204154m] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A novel trend in G-quadruplex ligand design is to build a binder that is able to not only discriminate G-quadruplex from duplex-DNA, but also among various G-quadruplex structures. Methylazacalix[6]pyridine (MACP6), a new type of azacalixarene with flexible conformation, exhibits induced circular dichroism signals when interacted with most of G-quadruplexes. The intensities of the induced signals are strongly dependent on the topology of G-quadruplexes. Further evidence has shown that these signals can be ascribed to the preferred binding of MACP6 to the loops of G-quadruplexes, which rely on the nature of nucleotides in the loops.
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Affiliation(s)
- Ai-Jiao Guan
- Beijing National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Chinese Academy of Sciences, Beijing, P R China
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41
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Direct screening of G-quadruplex ligands from Kalopanax septemlobus (Thunb.) Koidz extract by high performance liquid chromatography. J Chromatogr A 2011; 1218:6433-8. [DOI: 10.1016/j.chroma.2011.07.028] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2011] [Revised: 07/05/2011] [Accepted: 07/11/2011] [Indexed: 01/13/2023]
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42
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Hamon F, Largy E, Guédin-Beaurepaire A, Rouchon-Dagois M, Sidibe A, Monchaud D, Mergny JL, Riou JF, Nguyen CH, Teulade-Fichou MP. An Acyclic Oligoheteroaryle That Discriminates Strongly between Diverse G-Quadruplex Topologies. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201103422] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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43
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Hamon F, Largy E, Guédin-Beaurepaire A, Rouchon-Dagois M, Sidibe A, Monchaud D, Mergny JL, Riou JF, Nguyen CH, Teulade-Fichou MP. An Acyclic Oligoheteroaryle That Discriminates Strongly between Diverse G-Quadruplex Topologies. Angew Chem Int Ed Engl 2011; 50:8745-9. [DOI: 10.1002/anie.201103422] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2011] [Indexed: 11/09/2022]
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44
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Ma DL, Chan DSH, Lee P, Kwan MHT, Leung CH. Molecular modeling of drug–DNA interactions: Virtual screening to structure-based design. Biochimie 2011; 93:1252-66. [PMID: 21514356 DOI: 10.1016/j.biochi.2011.04.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Accepted: 04/01/2011] [Indexed: 12/11/2022]
Affiliation(s)
- Dik-Lung Ma
- Department of Chemistry, Hong Kong Baptist University, Hong Kong, China.
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45
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Shang Q, Xiang JF, Zhang XF, Sun HX, Li L, Tang YL. Fishing potential antitumor agents from natural plant extracts pool by dialysis and G-quadruplex recognition. Talanta 2011; 85:820-3. [DOI: 10.1016/j.talanta.2011.04.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2011] [Revised: 03/30/2011] [Accepted: 04/05/2011] [Indexed: 12/13/2022]
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46
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Chen SB, Tan JH, Ou TM, Huang SL, An LK, Luo HB, Li D, Gu LQ, Huang ZS. Pharmacophore-based discovery of triaryl-substituted imidazole as new telomeric G-quadruplex ligand. Bioorg Med Chem Lett 2011; 21:1004-9. [DOI: 10.1016/j.bmcl.2010.12.019] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2010] [Revised: 11/23/2010] [Accepted: 12/07/2010] [Indexed: 10/18/2022]
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47
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Yang Q, Xiang JF, Yang S, Li Q, Zhou Q, Guan A, Li L, Zhang Y, Zhang X, Zhang H, Tang Y, Xu G. Verification of Intramolecular Hybrid/Parallel G-Quadruplex Structure under Physiological Conditions Using Novel Cyanine Dye H-Aggregates: Both in Solution and on Au Film. Anal Chem 2010; 82:9135-7. [DOI: 10.1021/ac1017716] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Qianfan Yang
- Beijing National Laboratory for Molecular Sciences (BNLMS), Center for Molecular Sciences, State Key Laboratory for Structural Chemistry for Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences (ICCAS), Beijing, 100190, P. R. China, and Graduate University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Jun-Feng Xiang
- Beijing National Laboratory for Molecular Sciences (BNLMS), Center for Molecular Sciences, State Key Laboratory for Structural Chemistry for Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences (ICCAS), Beijing, 100190, P. R. China, and Graduate University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Shu Yang
- Beijing National Laboratory for Molecular Sciences (BNLMS), Center for Molecular Sciences, State Key Laboratory for Structural Chemistry for Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences (ICCAS), Beijing, 100190, P. R. China, and Graduate University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Qian Li
- Beijing National Laboratory for Molecular Sciences (BNLMS), Center for Molecular Sciences, State Key Laboratory for Structural Chemistry for Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences (ICCAS), Beijing, 100190, P. R. China, and Graduate University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Qiuju Zhou
- Beijing National Laboratory for Molecular Sciences (BNLMS), Center for Molecular Sciences, State Key Laboratory for Structural Chemistry for Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences (ICCAS), Beijing, 100190, P. R. China, and Graduate University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Aijiao Guan
- Beijing National Laboratory for Molecular Sciences (BNLMS), Center for Molecular Sciences, State Key Laboratory for Structural Chemistry for Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences (ICCAS), Beijing, 100190, P. R. China, and Graduate University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Lin Li
- Beijing National Laboratory for Molecular Sciences (BNLMS), Center for Molecular Sciences, State Key Laboratory for Structural Chemistry for Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences (ICCAS), Beijing, 100190, P. R. China, and Graduate University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Yanxia Zhang
- Beijing National Laboratory for Molecular Sciences (BNLMS), Center for Molecular Sciences, State Key Laboratory for Structural Chemistry for Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences (ICCAS), Beijing, 100190, P. R. China, and Graduate University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Xiufeng Zhang
- Beijing National Laboratory for Molecular Sciences (BNLMS), Center for Molecular Sciences, State Key Laboratory for Structural Chemistry for Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences (ICCAS), Beijing, 100190, P. R. China, and Graduate University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Hong Zhang
- Beijing National Laboratory for Molecular Sciences (BNLMS), Center for Molecular Sciences, State Key Laboratory for Structural Chemistry for Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences (ICCAS), Beijing, 100190, P. R. China, and Graduate University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Yalin Tang
- Beijing National Laboratory for Molecular Sciences (BNLMS), Center for Molecular Sciences, State Key Laboratory for Structural Chemistry for Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences (ICCAS), Beijing, 100190, P. R. China, and Graduate University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Guangzhi Xu
- Beijing National Laboratory for Molecular Sciences (BNLMS), Center for Molecular Sciences, State Key Laboratory for Structural Chemistry for Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences (ICCAS), Beijing, 100190, P. R. China, and Graduate University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
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48
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Yang Q, Xiang J, Yang S, Zhou Q, Li Q, Guan A, Zhang X, Zhang H, Tang Y, Xu G. Recognizing Hybrid/Mixed G-quadruplex in Human Telomeres by Using a Cyanine Dye Supramolecule with Confocal Laser Scanning Microscopy. CHINESE J CHEM 2010. [DOI: 10.1002/cjoc.201090196] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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49
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Arora A, Kumar N, Agarwal T, Maiti S. Retraction: Human telomeric G-quadruplex: targeting with small molecules. FEBS J 2009; 277:1345. [DOI: 10.1111/j.1742-4658.2009.07461.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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50
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Yang Q, Xiang J, Yang S, Li Q, Zhou Q, Guan A, Zhang X, Zhang H, Tang Y, Xu G. Verification of specific G-quadruplex structure by using a novel cyanine dye supramolecular assembly: II. The binding characterization with specific intramolecular G-quadruplex and the recognizing mechanism. Nucleic Acids Res 2009; 38:1022-33. [PMID: 19933263 PMCID: PMC2817466 DOI: 10.1093/nar/gkp1045] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The supramolecular assembly of a novel cyanine dye, 3,3′-di(3-sulfopropyl)-4,5,4′,5′-dibenzo-9-ethyl-thiacarbocyanine triethylammonium salt (ETC) was designed to verify specific intramolecular G-quadruplexes from duplex and single-strand DNAs. Spectral results have shown that ETC presented two major distinct signatures with specific intramolecular G-quadruplexes in vitro: (i) dramatic changes in the absorption spectra (including disappearance of absorption peak around 660 nm and appearance of independent new peak around 584 nm); (ii) ∼70 times enhancement of fluorescence signal at 600 nm. Furthermore, based on 1H-nuclear magnetic resonance and circular dichroism results, the preferring binding of ETC to specific intramolecular G-quadruplexes probably result from end-stacking, and the loop structure nearby also plays an important role.
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Affiliation(s)
- Qianfan Yang
- Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, People's Republic of China
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