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Ma TZ, Liu LY, Zeng YL, Ding K, Zhang H, Liu W, Cao Q, Xia W, Xiong X, Wu C, Mao ZW. G-quadruplex-guided cisplatin triggers multiple pathways in targeted chemotherapy and immunotherapy. Chem Sci 2024; 15:9756-9774. [PMID: 38939132 PMCID: PMC11206235 DOI: 10.1039/d4sc00643g] [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: 01/27/2024] [Accepted: 05/09/2024] [Indexed: 06/29/2024] Open
Abstract
G-quadruplexes (G4s) are atypical nucleic acid structures involved in basic human biological processes and are regulated by small molecules. To date, pyridostatin and its derivatives [e.g., PyPDS (4-(2-aminoethoxy)-N 2,N 6-bis(4-(2-(pyrrolidin-1-yl) ethoxy) quinolin-2-yl) pyridine-2,6-dicarboxamide)] are the most widely used G4-binding small molecules and considered to have the best G4 specificity, which provides a new option for the development of cisplatin-binding DNA. By combining PyPDS with cisplatin and its analogs, we synthesize three platinum complexes, named PyPDSplatins. We found that cisplatin with PyPDS (CP) exhibits stronger specificity for covalent binding to G4 domains even in the presence of large amounts of dsDNA compared with PyPDS either extracellularly or intracellularly. Multiomics analysis reveals that CP can effectively regulate G4 functions, directly damage G4 structures, activate multiple antitumor signaling pathways, including the typical cGAS-STING pathway and AIM2-ASC pathway, trigger a strong immune response and lead to potent antitumor effects. These findings reflect that cisplatin-conjugated specific G4 targeting groups have antitumor mechanisms different from those of classic cisplatin and provide new strategies for the antitumor immunity of metals.
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Affiliation(s)
- Tian-Zhu Ma
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, IGCME, GBRCE for Functional Molecular Engineering, Sun Yat-Sen University Guangzhou 510275 P. R. China
| | - Liu-Yi Liu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, IGCME, GBRCE for Functional Molecular Engineering, Sun Yat-Sen University Guangzhou 510275 P. R. China
| | - You-Liang Zeng
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, IGCME, GBRCE for Functional Molecular Engineering, Sun Yat-Sen University Guangzhou 510275 P. R. China
| | - Ke Ding
- The Second Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine Hangzhou 311121 P. R. China
| | - Hang Zhang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, IGCME, GBRCE for Functional Molecular Engineering, Sun Yat-Sen University Guangzhou 510275 P. R. China
| | - Wenting Liu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, IGCME, GBRCE for Functional Molecular Engineering, Sun Yat-Sen University Guangzhou 510275 P. R. China
| | - Qian Cao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, IGCME, GBRCE for Functional Molecular Engineering, Sun Yat-Sen University Guangzhou 510275 P. R. China
| | - Wei Xia
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, IGCME, GBRCE for Functional Molecular Engineering, Sun Yat-Sen University Guangzhou 510275 P. R. China
| | - Xushen Xiong
- The Second Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine Hangzhou 311121 P. R. China
| | - Chao Wu
- Department of Neurology, The First Affiliated Hospital, Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases, National Key Clinical Department and Key Discipline of Neurology, Sun Yat-sen University Guangzhou 510080 P. R. China
| | - Zong-Wan Mao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, IGCME, GBRCE for Functional Molecular Engineering, Sun Yat-Sen University Guangzhou 510275 P. R. China
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2
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Simisi Clovis N, Alam P, Kumar Chand A, Sardana D, Firoz Khan M, Sen S. Molecular Crowders Modulate Ligand Binding Affinity to G-Quadruplex DNA by Decelerating Ligand Association. J Photochem Photobiol A Chem 2022. [DOI: 10.1016/j.jphotochem.2022.114432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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3
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Clovis NS, Sen S. G-Tetrad-Selective Ligand Binding Kinetics in G-Quadruplex DNA Probed with Fluorescence Correlation Spectroscopy. J Phys Chem B 2022; 126:6007-6015. [PMID: 35939531 DOI: 10.1021/acs.jpcb.2c04181] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Probing the kinetics of ligand binding to biomolecules is of paramount interest in biology and pharmacology. Measurements of such kinetic processes provide information on the rate-determining steps that control the binding affinity of ligands to biomolecules, thereby predicting the mechanism of the molecular interaction. In this context, ligand binding to G-quadruplex DNA (GqDNA) structures has attracted tremendous attention primarily because of their use in possible anticancer therapy. Although a large number of G-quadruplex-specific ligands have been proposed, probing the kinetics of G-tetrad-selective binding of (multiple) ligands within a G-quadruplex DNA (GqDNA) structure remains challenging. Most of the earlier studies focused on the thermodynamics of ligand binding; however, the kinetics of ligand association and dissociation with GqDNA, particularly binding of multiple ligands within a GqDNA structure, have not been explored. Here, we propose a simple fluorescence correlation spectroscopy-based method that measures the G-tetrad-selective association and dissociation rates of ligands within a GqDNA structure by correlating the fluorescence fluctuations of a site-specific (5' or 3' end-labeled) fluorophore (Cy3) in GqDNA due to quenching of Cy3 fluorescence, induced by the ligand binding to the G-tetrads. We show that well-known GqDNA ligands, BRACO19, TMPyP4, Hoechst 33258, and Hoechst 33342, have G-tetrad-selective association and dissociation rates, which suggest site-dependent variation of free energy barriers for binding/unbinding of the ligands with GqDNA. We also show that the measured kinetic rates depend not only on the G-tetrad site (5' vs 3' end) but also on the ligand and GqDNA structures.
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Affiliation(s)
- Ndege Simisi Clovis
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Sobhan Sen
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
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Xiong K, Ouyang C, Liu J, Karges J, Lin X, Chen X, Chen Y, Wan J, Ji L, Chao H. Chiral RuII‐PtII Complexes Inducing Telomere Dysfunction against Cisplatin‐Resistant Cancer Cells. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202204866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Kai Xiong
- Sun Yat-Sen University School of Chemistry CHINA
| | - Cheng Ouyang
- Sun Yat-Sen University School of Chemistry CHINA
| | - Jiaqi Liu
- Central China Normal University College of Chemistry CHINA
| | | | - Xinlin Lin
- Sun Yat-Sen University School of Chemistry CHINA
| | - Xiang Chen
- Sun Yat-Sen University School of Chemistry CHINA
| | - Yu Chen
- Sun Yat-Sen University School of Chemistry CHINA
| | - Jian Wan
- Central China Normal University College of Chemistry CHINA
| | - Liangnian Ji
- Sun Yat-Sen University School of Chemistry CHINA
| | - Hui Chao
- Sun Yat-Sen University Chemistry Xingang Xilu 135# 510275 Guangzhou CHINA
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5
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Xiong K, Ouyang C, Liu J, Karges J, Lin X, Chen X, Chen Y, Wan J, Ji L, Chao H. Chiral Ru II -Pt II Complexes Inducing Telomere Dysfunction against Cisplatin-Resistant Cancer Cells. Angew Chem Int Ed Engl 2022; 61:e202204866. [PMID: 35736788 DOI: 10.1002/anie.202204866] [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: 04/02/2022] [Indexed: 11/06/2022]
Abstract
The application of G-quadruplex stabilizers presents a promising anticancer strategy. However, the molecular crowding conditions within cells diminish the potency of current G-quadruplex stabilizers. Herein, chiral RuII -PtII dinuclear complexes were developed as highly potent G-quadruplex stabilizers even under challenging molecular crowding conditions. The compounds were encapsulated with biotin-functionalized DNA cages to enhance sub-cellular localization and provide cancer selectivity. The nanoparticles were able to efficiently inhibit the endogenous activities of telomerase in cisplatin-resistant cancer cells and cause cell death by apoptosis. The nanomaterials demonstrated high antitumor activity towards cisplatin-resistant tumor cells as well as tumor-bearing mice. To the best of our knowledge, this study presents the first example of a RuII -PtII dinuclear complex as a G-quadruplex stabilizer with an anti-cancer effect towards drug-resistant tumors inside an animal model.
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Affiliation(s)
- Kai Xiong
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Guangdong Provincial Key Laboratory of Digestive Cancer Research, The Seventh Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510006, P. R. China
| | - Cheng Ouyang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Guangdong Provincial Key Laboratory of Digestive Cancer Research, The Seventh Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510006, P. R. China
| | - Jiaqi Liu
- College of Chemistry, Central China Normal University, Wuhan, 430079, P. R. China
| | - Johannes Karges
- Department of Chemistry and, Biochemistry University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Xinlin Lin
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Guangdong Provincial Key Laboratory of Digestive Cancer Research, The Seventh Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510006, P. R. China
| | - Xiang Chen
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Guangdong Provincial Key Laboratory of Digestive Cancer Research, The Seventh Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510006, P. R. China
| | - Yu Chen
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Guangdong Provincial Key Laboratory of Digestive Cancer Research, The Seventh Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510006, P. R. China
| | - Jian Wan
- College of Chemistry, Central China Normal University, Wuhan, 430079, P. R. China
| | - Liangnian Ji
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Guangdong Provincial Key Laboratory of Digestive Cancer Research, The Seventh Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510006, P. R. China
| | - Hui Chao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Guangdong Provincial Key Laboratory of Digestive Cancer Research, The Seventh Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510006, P. R. China.,MOE Key Laboratory of Theoretical Organic Chemistry and Functional Molecule, School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, 400201, P. R. China
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6
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Cheng XR, Wang F, Liu CY, Li J, Shan C, Wang K, Wang Y, Li PF, Li XM. Sensitive naked-eye detection of telomerase activity based on exponential amplification reaction and lateral flow assay. Anal Bioanal Chem 2022; 414:6139-6147. [PMID: 35715586 DOI: 10.1007/s00216-022-04179-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/09/2022] [Accepted: 06/13/2022] [Indexed: 11/27/2022]
Abstract
Telomerase is a promising diagnostic and prognostic biomarker for cancers. Sensitive, simple, and reliable telomerase activity detection is vital for cancer diagnosis. Herein, we developed an ultrasensitive visualized assay for telomerase activity that combined the exponential amplification reaction (EXPAR) and lateral flow assay for easy and quick signal readout, which we termed as a lateral flow readout-EXPAR (LFR-EXPAR) assay. In the LFR-EXPAR assay, telomerase elongation products initiate the exponential amplification reaction, the generated trigger hybridizes with the reporter to form the recognition site of the nicking enzyme, and the nicking enzyme cuts the reporter strand. The degradation of the reporter can be detected with a universal lateral flow dipstick and read out with the naked eye. After conducting a series of proof-of-concept investigations, the LFR-EXPAR assay was found to achieve a sensitivity comparable to that of a TRAP (telomere repeat amplification protocol) assay. The LFR-EXPAR assay can be used to realize ultrasensitive and point-of-care detection of telomerase without requiring specialized instruments, holding great promise for early cancer diagnosis.
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Affiliation(s)
- Xue-Ru Cheng
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 1 Ningde Road, Qingdao, 266073, China
| | - Fei Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 1 Ningde Road, Qingdao, 266073, China
| | - Cui-Yun Liu
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 1 Ningde Road, Qingdao, 266073, China
| | - Jing Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 1 Ningde Road, Qingdao, 266073, China
| | - Chan Shan
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 1 Ningde Road, Qingdao, 266073, China
| | - Kun Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 1 Ningde Road, Qingdao, 266073, China
| | - Yin Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 1 Ningde Road, Qingdao, 266073, China.
| | - Pei-Feng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 1 Ningde Road, Qingdao, 266073, China.
| | - Xin-Min Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 1 Ningde Road, Qingdao, 266073, China.
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Yadav K, Sardana D, Shweta H, Clovis NS, Sen S. Molecular Picture of the Effect of Cosolvent Crowding on Ligand Binding and Dispersed Solvation Dynamics in G-Quadruplex DNA. J Phys Chem B 2022; 126:1668-1681. [PMID: 35170968 DOI: 10.1021/acs.jpcb.1c09349] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Understanding molecular interactions and dynamics of proteins and DNA in a cell-like crowded environment is crucial for predicting their functions within the cell. Noncanonical G-quadruplex DNA (GqDNA) structures adopt various topologies that were shown to be strongly affected by molecular crowding. However, it is unknown how such crowding affects the solvation dynamics in GqDNA. Here, we study the effect of cosolvent (acetonitrile) crowding on ligand (DAPI) solvation dynamics within human telomeric antiparallel GqDNA through direct comparison of time-resolved fluorescence Stokes shift (TRFSS) experiments and molecular dynamics (MD) simulations results. We show that ligand binding affinity to GqDNA is drastically affected by acetonitrile (ACN). Solvation dynamics probed by DAPI in GqDNA groove show dispersed dynamics from ∼100 fs to 10 ns in the absence and presence of 20% and 40% (v/v) ACN. The nature of dynamics remain similar in buffer and 20% ACN, although in 40% ACN, distinct dynamics is observed in <100 ps. MD simulations performed on GqDNA/DAPI complex reveal preferential solvation of ligand by ACN, particularly in 40% ACN. Simulated solvation time-correlation functions calculated from MD trajectories compare very well to the overall solvation dynamics of DAPI in GqDNA, observed in experiments. Linear response decomposition of simulated solvation correlation functions unfolds the origin of dispersed dynamics, showing that the slower dynamics is dominated by DNA-motion in the presence of ACN (and also by the ACN dynamics at higher concentration). However, water-DNA coupled motion controls the slow dynamics in the absence of ACN. Our data, thus, unravel a detailed molecular picture showing that though ACN crowding affect ligand binding affinity to GqDNA significantly, the overall dispersed solvation dynamics in GqDNA remain similar in the absence and the presence of 20% ACN, albeit with a small effect on the dynamics in the presence of 40% ACN due to preferential solvation of ligand by ACN.
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Affiliation(s)
- Kavita Yadav
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Deepika Sardana
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Him Shweta
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Ndege Simisi Clovis
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Sobhan Sen
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
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8
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Rastogi H, Chowdhury PK. Understanding enzyme behavior in a crowded scenario through modulation in activity, conformation and dynamics. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2021; 1869:140699. [PMID: 34298166 DOI: 10.1016/j.bbapap.2021.140699] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/08/2021] [Accepted: 07/19/2021] [Indexed: 01/25/2023]
Abstract
Macromolecular crowding, inside the physiological interior, modulates the energy landscape of biological macromolecules in multiple ways. Amongst these, enzymes occupy a special place and hence understanding the function of the same in the crowded interior is of utmost importance. In this study, we have investigated the manner in which the multidomain enzyme, AK3L1 (PDB ID: 1ZD8), an isoform of adenylate kinase, has its features affected in presence of commonly used crowders (PEG 8, Dextran 40, Dextran 70, and Ficoll 70). Michaelis Menten plots reveal that the crowders in general enhance the activity of the enzyme, with the Km and Vmax values showing significant variations. Ficoll 70, induced the maximum activity for AK3L1 at 100 g/L, beyond which the activity reduced. Ensemble FRET studies were performed to provide insights into the relative domain (LID and CORE) displacements in presence of the crowders. Solvation studies reveal that the protein matrix surrounding the probe CPM (7-diethylamino-3-(4-maleimido-phenyl)-4-methylcoumarin) gets restricted in presence of the crowders, with Ficoll 70 providing the maximum rigidity, the same being linked to the decrease in the activity of the enzyme. Through our multipronged approach, we have observed a distinct correlation between domain displacement, enzyme activity and associated dynamics. Thus, keeping in mind the complex nature of enzyme activity and the surrounding bath of dense soup that the biological entity remains immersed in, indeed more such approaches need to be undertaken to have a better grasp of the "enzymes in the crowd".
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Affiliation(s)
- Harshita Rastogi
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Pramit K Chowdhury
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.
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9
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Popielec A, Ostrowska N, Wojciechowska M, Feig M, Trylska J. Crowded environment affects the activity and inhibition of the NS3/4A protease. Biochimie 2020; 176:169-180. [DOI: 10.1016/j.biochi.2020.07.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 07/17/2020] [Accepted: 07/17/2020] [Indexed: 12/18/2022]
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10
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Li M, Liu Z, Ren J, Qu X. Molecular crowding effects on the biochemical properties of amyloid β-heme, Aβ-Cu and Aβ-heme-Cu complexes. Chem Sci 2020; 11:7479-7486. [PMID: 34123030 PMCID: PMC8159413 DOI: 10.1039/d0sc01020k] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Heme as a cofactor has been proposed to bind with β-amyloid peptide (Aβ) and the formed Aβ-heme complex exhibits enhanced peroxidase-like activity. So far, in vitro studies on the interactions between heme, Cu and Aβ have been exclusively performed in dilute solution. However, the intracellular environment is highly crowded with biomolecules. Therefore, exploring how Aβ-heme-Cu complexes behave under molecular crowding conditions is critical for understanding the mechanism of Aβ neurotoxicity in vivo. Herein, we selected PEG-200 as a crowding agent to mimic the crowded cytoplasmic environment for addressing the contributions of crowded physiological environments to the biochemical properties of Aβ-heme, Aβ-Cu and Aβ-heme-Cu complexes. Surprisingly, experimental studies and theoretical calculations revealed that molecular crowding weakened the stabilization of the Aβ-heme complex and decreased its peroxidase activity. Our data attributed this consequence to the decreased binding affinity of heme to Aβ as a result of the alterations in water activity and Aβ conformation. Our findings highlight the significance of hydration effects on the interaction of Aβ-heme and Aβ-Cu and their peroxidase activities. Molecular crowding inside cells may potentially impose a positive effect on Aβ-Cu but a negative effect on the interaction of Aβ with heme. This indicates that Aβ40-Cu but not Aβ40-heme may play more important roles in the oxidative damage in the etiology of AD. Therefore, this work provides a new clue for understanding the oxidative damage occurring in AD.
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Affiliation(s)
- Meng Li
- Laboratory of Chemical Biology, Division of Biological Inorganic Chemistry, State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun Jilin 130022 P. R. China +86-431-85262656.,College of Pharmaceutical Sciences, Hebei Medical University Shijiazhuang 050017 P. R. China
| | - Zhenqi Liu
- Laboratory of Chemical Biology, Division of Biological Inorganic Chemistry, State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun Jilin 130022 P. R. China +86-431-85262656.,University of Science and Technology of China Hefei Anhui 230026 P. R. China
| | - Jinsong Ren
- Laboratory of Chemical Biology, Division of Biological Inorganic Chemistry, State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun Jilin 130022 P. R. China +86-431-85262656.,University of Science and Technology of China Hefei Anhui 230026 P. R. China
| | - Xiaogang Qu
- Laboratory of Chemical Biology, Division of Biological Inorganic Chemistry, State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun Jilin 130022 P. R. China +86-431-85262656.,University of Science and Technology of China Hefei Anhui 230026 P. R. China
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Nearest-neighbor parameters for predicting DNA duplex stability in diverse molecular crowding conditions. Proc Natl Acad Sci U S A 2020; 117:14194-14201. [PMID: 32522884 DOI: 10.1073/pnas.1920886117] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The intracellular environment is crowded and heterogeneous. Although the thermodynamic stability of nucleic acid duplexes is predictable in dilute solutions, methods of predicting such stability under specific intracellular conditions are not yet available. We recently showed that the nearest-neighbor model for self-complementary DNA is valid under molecular crowding condition of 40% polyethylene glycol with an average molecular weight of 200 (PEG 200) in 100 mM NaCl. Here, we determined nearest-neighbor parameters for DNA duplex formation under the same crowding condition to predict the thermodynamics of DNA duplexes in the intracellular environment. Preferential hydration of the nucleotides was found to be the key factor for nearest-neighbor parameters in the crowding condition. The determined parameters were shown to predict the thermodynamic parameters (∆H°, ∆S°, and ∆G°37) and melting temperatures (T m) of the DNA duplexes in the crowding condition with significant accuracy. Moreover, we proposed a general method for predicting the stability of short DNA duplexes in different cosolutes based on the relationship between duplex stability and the water activity of the cosolute solution. The method described herein would be valuable for investigating biological processes that occur under specific intracellular crowded conditions and for the application of DNA-based biotechnologies in crowded environments.
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12
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Kinetics, conformation, stability, and targeting of G-quadruplexes from a physiological perspective. Biochem Biophys Res Commun 2020; 531:84-87. [PMID: 32331835 DOI: 10.1016/j.bbrc.2020.04.047] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 04/13/2020] [Indexed: 02/05/2023]
Abstract
The particular enrichment of G-quadruplex-forming sequences near transcription start sites signifies the involvement of G-quadruplexes in the regulation of transcription. The characterization of G-quadruplex formation, which holds the key to understand the function it plays in physiological and pathological processes, is mostly performed under simplified in vitro experimental conditions. Formation of G-quadruplexes in cells, however, occurs in an environment far different from the ones in which the in vitro studies on G-quadruplexes are normally carried out. Therefore, the characteristics of G-quadruplex structures obtained under the in vitro conditions may not faithfully reveal how the G-quadruplexes would behave in a physiologically relevant situation. In this mini-review, we attempt to briefly summarize the differences in a few important characteristics, including kinetics, conformation, and stability of G-quadruplex formation observed under the two conditions to illustrate how the intracellular environment might affect the behavior of G-quadruplexes largely based on the previous work carried out in the authors' laboratory. We also propose that unstable G-quadruplex variants may be better drug target candidates to improve selectivity and potency.
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Ma C, Chan RCT, Chan CTL, Wong AKW, Kwok WM. Real-time Monitoring Excitation Dynamics of Human Telomeric Guanine Quadruplexes: Effect of Folding Topology, Metal Cation, and Confinement by Nanocavity Water Pool. J Phys Chem Lett 2019; 10:7577-7585. [PMID: 31769690 DOI: 10.1021/acs.jpclett.9b02932] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Guanine(G)-rich human telomeric (HT) DNA repeats, crucial to maintenance of genome stability, readily form G-quadruplexes (GQs) with various folding topologies. Research on excitation dynamics of HT-GQs is, however, scarce. Herein, we report a femtosecond time-resolved fluorescence coupled with transient absorption investigation on HT-GQ with the basket-type structure in Na+ solution. The result unveils an unusual multichannel nonradiative mechanism dominated by states with varying character of charge transfer lasting ten and hundreds of picoseconds, accounting altogether for an overwhelming ∼85% of the overall deactivation involving proton transfer. Our comparative study shows that encapsulating the GQ in nanocavity water pool or changing it into hydrid-type topologies with the presence of K+ ions alter differently energies and lifetimes of these states, yet without affecting the nature of the electronic excitation involved. The finding of this work underscores a leading role of structural rigidity in regulating the interplay with the microenvironment of photoexcited monomolecularly folded HT-GQs.
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Affiliation(s)
- Chensheng Ma
- College of Chemistry and Environmental Engineering , Shenzhen University , Shenzhen , Guangdong P. R. China
| | - Ruth C-T Chan
- College of Chemistry and Environmental Engineering , Shenzhen University , Shenzhen , Guangdong P. R. China
| | - Chris T-L Chan
- College of Chemistry and Environmental Engineering , Shenzhen University , Shenzhen , Guangdong P. R. China
| | - Allen K-W Wong
- Department of Applied Biology and Chemical Technology , The Hong Kong Polytechnic University , Hung Hom, Kowloon , Hong Kong , P. R. China
| | - Wai-Ming Kwok
- Department of Applied Biology and Chemical Technology , The Hong Kong Polytechnic University , Hung Hom, Kowloon , Hong Kong , P. R. China
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14
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Perez CP, Elmore DE, Radhakrishnan ML. Computationally Modeling Electrostatic Binding Energetics in a Crowded, Dynamic Environment: Physical Insights from a Peptide–DNA System. J Phys Chem B 2019; 123:10718-10734. [DOI: 10.1021/acs.jpcb.9b09478] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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15
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Lee YH, Chen YY, Yeh YL, Wang YJ, Chen RJ. Stilbene Compounds Inhibit Tumor Growth by the Induction of Cellular Senescence and the Inhibition of Telomerase Activity. Int J Mol Sci 2019; 20:ijms20112716. [PMID: 31159515 PMCID: PMC6600253 DOI: 10.3390/ijms20112716] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 05/30/2019] [Accepted: 05/31/2019] [Indexed: 12/17/2022] Open
Abstract
Cellular senescence is a state of cell cycle arrest characterized by a distinct morphology, gene expression pattern, and secretory phenotype. It can be triggered by multiple mechanisms, including those involved in telomere shortening, the accumulation of DNA damage, epigenetic pathways, and the senescence-associated secretory phenotype (SASP), and so on. In current cancer therapy, cellular senescence has emerged as a potent tumor suppression mechanism that restrains proliferation in cells at risk for malignant transformation. Therefore, compounds that stimulate the growth inhibition effects of senescence while limiting its detrimental effects are believed to have great clinical potential. In this review article, we first review the current knowledge of the pro- and antitumorigeneic functions of senescence and summarize the key roles of telomerase in the regulation of senescence in tumors. Second, we review the current literature regarding the anticancer effects of stilbene compounds that are mediated by the targeting of telomerase and cell senescence. Finally, we provide future perspectives on the clinical utilization of stilbene compounds, especially resveratrol and pterostilbene, as novel cancer therapeutic remedies. We conclude and propose that stilbene compounds may induce senescence and may potentially be used as the therapeutic or adjuvant agents for cancers with high telomerase activity.
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Affiliation(s)
- Yu-Hsuan Lee
- Department of Food Safety/Hygiene and Risk Management, College of Medicine, National Cheng Kung University, Tainan 70428, Taiwan.
| | - Yu-Ying Chen
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan 70428, Taiwan.
| | - Ya-Ling Yeh
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan 70428, Taiwan.
| | - Ying-Jan Wang
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan 70428, Taiwan.
- Department of Medical Research, China Medical University Hospital, China Medical University, Taichung 40402, Taiwan.
| | - Rong-Jane Chen
- Department of Food Safety/Hygiene and Risk Management, College of Medicine, National Cheng Kung University, Tainan 70428, Taiwan.
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16
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Di Fonzo S, Bottari C, Brady JW, Tavagnacco L, Caterino M, Petraccone L, Amato J, Giancola C, Cesàro A. Crowding and conformation interplay on human DNA G-quadruplex by ultraviolet resonant Raman scattering. Phys Chem Chem Phys 2019; 21:2093-2101. [DOI: 10.1039/c8cp04728f] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The G-quadruplex-forming telomeric sequence (TTAGGG)4TT was investigated by polarized Ultraviolet Resonance Raman Scattering (UVRR) at 266 nm.
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Affiliation(s)
- Silvia Di Fonzo
- Elettra-Sincrotrone Trieste S. C. p. A
- Science Park
- Trieste
- Italy
| | - Cettina Bottari
- Elettra-Sincrotrone Trieste S. C. p. A
- Science Park
- Trieste
- Italy
- Department of Physics
| | - John W. Brady
- Department of Food Science
- Cornell University
- Ithaca
- USA
| | - Letizia Tavagnacco
- Department of Chemical and Pharmaceutical Sciences
- University of Trieste
- Trieste
- Italy
| | - Marco Caterino
- Department of Pharmacy
- University of Naples Federico II
- Naples
- Italy
| | - Luigi Petraccone
- Department of Chemical Sciences
- University of Naples Federico II
- Naples
- Italy
| | - Jussara Amato
- Department of Pharmacy
- University of Naples Federico II
- Naples
- Italy
| | | | - Attilio Cesàro
- Elettra-Sincrotrone Trieste S. C. p. A
- Science Park
- Trieste
- Italy
- Department of Chemical and Pharmaceutical Sciences
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17
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Manna S, Sarkar D, Srivatsan SG. A Dual-App Nucleoside Probe Provides Structural Insights into the Human Telomeric Overhang in Live Cells. J Am Chem Soc 2018; 140:12622-12633. [PMID: 30192541 PMCID: PMC6348103 DOI: 10.1021/jacs.8b08436] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Understanding the topology adopted by individual G-quadruplex (GQ)-forming sequences in vivo and targeting a specific GQ motif among others in the genome will have a profound impact on GQ-directed therapeutic strategies. However, this remains a major challenge as most of the tools poorly distinguish different GQ conformations and are not suitable for both cell-free and in-cell analysis. Here, we describe an innovative probe design to investigate GQ conformations and recognition in both cell-free and native cellular environments by using a conformation-sensitive dual-app nucleoside analogue probe. The nucleoside probe, derived by conjugating fluorobenzofuran at the 5-position of 2'-deoxyuridine, is composed of a microenvironment-sensitive fluorophore and an in-cell NMR compatible 19F label. This noninvasive nucleoside, incorporated into the human telomeric DNA oligonucleotide repeat, serves as a common probe to distinguish different GQ topologies and quantify topology-specific binding of ligands by fluorescence and NMR techniques. Importantly, unique signatures displayed by the 19F-labeled nucleoside for different GQs enabled a systematic study in Xenopus laevis oocytes to provide new structural insights into the GQ topologies adopted by human telomeric overhang in cells, which so far has remained unclear. Studies using synthetic cell models, immunostaining on fixed cells, and crystallization conditions suggest that parallel GQ is the preferred conformation of telomeric DNA repeat. However, our findings using the dual-app probe clearly indicate that multiple structures including hybrid-type parallel-antiparallel and parallel GQs are formed in the cellular environment. Taken together, our findings open new experimental strategies to investigate topology, recognition, and therapeutic potential of individual GQ-forming motifs in a biologically relevant context.
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Affiliation(s)
- Sudeshna Manna
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
| | - Debayan Sarkar
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
| | - Seergazhi G. Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
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18
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Rubio‐Magnieto J, Kajouj S, Di Meo F, Fossépré M, Trouillas P, Norman P, Linares M, Moucheron C, Surin M. Binding Modes and Selectivity of Ruthenium Complexes to Human Telomeric DNA G‐Quadruplexes. Chemistry 2018; 24:15577-15588. [DOI: 10.1002/chem.201802147] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 07/12/2018] [Indexed: 02/05/2023]
Affiliation(s)
- Jenifer Rubio‐Magnieto
- Laboratory for Chemistry of Novel Materials Center for Innovation in Materials and Polymers University of Mons-UMONS 20 Place du Parc 7000 Mons Belgium
- Current address: Bioinspired Supramolecular Chemistry and Materials group Departament de Química Inorgànica i Orgànica Universitat Jaume I Avda Sos Baynat s/n E-12071 Castelló Spain
| | - Sofia Kajouj
- Chimie Organique et Photochimie CP160/08 Université libre de Bruxelles 50 avenue F. D. Roosevelt 1050 Bruxelles Belgium
| | - Florent Di Meo
- INSERM U1248 IPPRITT University of Limoges School of Pharmacy 2 rue du Dr. Marcland 87025 Limoges France
| | - Mathieu Fossépré
- Laboratory for Chemistry of Novel Materials Center for Innovation in Materials and Polymers University of Mons-UMONS 20 Place du Parc 7000 Mons Belgium
| | - Patrick Trouillas
- INSERM U1248 IPPRITT University of Limoges School of Pharmacy 2 rue du Dr. Marcland 87025 Limoges France
- RCPTM Palacký University Faculty of Sciences Šlechtitelů 27 78371 Olomouc Czech Republic
| | - Patrick Norman
- Department of Theoretical Chemistry and Biology School of Engineering Sciences in Chemistry Biotechnology and Health KTH Royal Institute of Technology SE-106 91 Stockholm Sweden
| | - Mathieu Linares
- Department of Theoretical Chemistry and Biology School of Engineering Sciences in Chemistry Biotechnology and Health KTH Royal Institute of Technology SE-106 91 Stockholm Sweden
- Swedish e-Science Research Centre (SeRC) KTH Royal Institute of Technology 104 50 Stockholm Sweden
| | - Cécile Moucheron
- Chimie Organique et Photochimie CP160/08 Université libre de Bruxelles 50 avenue F. D. Roosevelt 1050 Bruxelles Belgium
| | - Mathieu Surin
- Laboratory for Chemistry of Novel Materials Center for Innovation in Materials and Polymers University of Mons-UMONS 20 Place du Parc 7000 Mons Belgium
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19
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Manna S, Srivatsan SG. Fluorescence-based tools to probe G-quadruplexes in cell-free and cellular environments. RSC Adv 2018; 8:25673-25694. [PMID: 30210793 PMCID: PMC6130854 DOI: 10.1039/c8ra03708f] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 07/08/2018] [Indexed: 12/26/2022] Open
Abstract
Biophysical and biochemical investigations provide compelling evidence connecting the four-stranded G-quadruplex (GQ) structure with its role in regulating multiple cellular processes. Hence, modulating the function of GQs by using small molecule binders is being actively pursued as a strategy to develop new chemotherapeutic agents. However, sequence diversity and structural polymorphism of GQs have posed immense challenges in terms of understanding what conformation a G-rich sequence adopts inside the cell and how to specifically target a GQ motif amidst several other GQ-forming sequences. In this context, here we review recent developments in the applications of biophysical tools that use fluorescence readout to probe the GQ structure and recognition in cell-free and cellular environments. First, we provide a detailed discussion on the utility of covalently labeled environment-sensitive fluorescent nucleoside analogs in assessing the subtle difference in GQ structures and their ligand binding abilities. Furthermore, a detailed discussion on structure-specific antibodies and small molecule probes used to visualize and confirm the existence of DNA and RNA GQs in cells is provided. We also highlight the open challenges in the study of tetraplexes (GQ and i-motif structures) and how addressing these challenges by developing new tools and techniques will have a profound impact on tetraplex-directed therapeutic strategies.
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Affiliation(s)
- Sudeshna Manna
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), PuneDr. Homi Bhabha RoadPune 411008India
| | - Seergazhi G. Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), PuneDr. Homi Bhabha RoadPune 411008India
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20
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Abstract
Guanine-rich nucleic acid sequences able to form four-stranded structures (G-quadruplexes, G4) play key cellular regulatory roles and are considered as promising drug targets for anticancer therapy. On the basis of the organization of their structural elements, G4 ligands can be divided into three major families: one, fused heteroaromatic polycyclic systems; two, macrocycles; three, modular aromatic compounds. The design of modular G4 ligands emerged as the answer to achieve not only more drug-like compounds but also more selective ligands by targeting the diversity of the G4 loops and grooves. The rationale behind the design of a very comprehensive set of ligands, with particular focus on the structural features required for binding to G4, is discussed and combined with the corresponding biochemical/biological data to highlight key structure-G4 interaction relationships. Analysis of the data suggests that the shape of the ligand is the major factor behind the G4 stabilizing effect of the ligands. The information here critically reviewed will certainly contribute to the development of new and better G4 ligands with application either as therapeutics or probes.
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Affiliation(s)
- Ana Rita Duarte
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Enrico Cadoni
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Ana S Ressurreição
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Rui Moreira
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Alexandra Paulo
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
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21
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Che T, Chen SB, Tu JL, Wang B, Wang YQ, Zhang Y, Wang J, Wang ZQ, Zhang ZP, Ou TM, Zhao Y, Tan JH, Huang ZS. Discovery of Novel Schizocommunin Derivatives as Telomeric G-Quadruplex Ligands That Trigger Telomere Dysfunction and the Deoxyribonucleic Acid (DNA) Damage Response. J Med Chem 2018; 61:3436-3453. [PMID: 29618208 DOI: 10.1021/acs.jmedchem.7b01615] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Telomeric G-quadruplex targeting and telomere maintenance interference are emerging as attractive strategies for anticancer therapies. Here, a novel molecular scaffold is explored for telomeric G-quadruplex targeting. A series of novel schizocommunin derivatives was designed and synthesized as potential telomeric G-quadruplex ligands. The interaction of telomeric G-quadruplex DNA with the derivatives was explored by biophysical assay. The cytotoxicity of the derivatives toward cancer cell lines was evaluated by the methyl thiazolyl tetrazolium (MTT) assay. Among the derivatives, compound 16 showed great stabilization ability toward telomeric G-quadruplex DNA and good cytotoxicity toward cancer cell lines. Further cellular experiments indicated that 16 could induce the formation of telomeric G-quadruplex in cells, triggering a DNA damage response at the telomere and causing telomere dysfunction. These effects ultimately provoked p53-mediated cell cycle arrest and apoptosis, and suppressed tumor growth in a mouse xenograft model. Our work provides a novel scaffold for the development of telomeric G-quadruplex ligands.
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Affiliation(s)
- Tong Che
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences , Sun Yat-sen University , Guangzhou 510006 , People's Republic of China
| | - Shuo-Bin Chen
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences , Sun Yat-sen University , Guangzhou 510006 , People's Republic of China
| | - Jia-Li Tu
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences , Sun Yat-sen University , Guangzhou 510006 , People's Republic of China
| | - Bo Wang
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences , Sun Yat-sen University , Guangzhou 510006 , People's Republic of China
| | - Yu-Qing Wang
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences , Sun Yat-sen University , Guangzhou 510006 , People's Republic of China
| | - Yan Zhang
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences , Sun Yat-sen University , Guangzhou 510006 , People's Republic of China
| | - Jing Wang
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences , Sun Yat-sen University , Guangzhou 510006 , People's Republic of China
| | - Zeng-Qing Wang
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences , Sun Yat-sen University , Guangzhou 510006 , People's Republic of China
| | - Ze-Peng Zhang
- School of Life Sciences , Sun Yat-sen University , Guangzhou 510006 , People's Republic of China
| | - Tian-Miao Ou
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences , Sun Yat-sen University , Guangzhou 510006 , People's Republic of China
| | - Yong Zhao
- School of Life Sciences , Sun Yat-sen University , Guangzhou 510006 , People's Republic of China
| | - Jia-Heng Tan
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences , Sun Yat-sen University , Guangzhou 510006 , People's Republic of China
| | - Zhi-Shu Huang
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences , Sun Yat-sen University , Guangzhou 510006 , People's Republic of China
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22
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Zheng KW, He YD, Liu HH, Li XM, Hao YH, Tan Z. Superhelicity Constrains a Localized and R-Loop-Dependent Formation of G-Quadruplexes at the Upstream Region of Transcription. ACS Chem Biol 2017; 12:2609-2618. [PMID: 28846373 DOI: 10.1021/acschembio.7b00435] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Transcription induces formation of intramolecular G-quadruplex structures at the upstream region of a DNA duplex by an upward transmission of negative supercoiling through the DNA. Currently the regulation of such G-quadruplex formation remains unclear. Using plasmid as a model, we demonstrate that while it is the dynamic negative supercoiling generated by a moving RNA polymerase that triggers a formation of a G-quadruplex, the constitutional superhelicity determines the potential and range of the formation of a G-quadruplex by constraining the propagation of the negative supercoiling. G-quadruplex formation is maximal in negatively supercoiled and nearly abolished in relaxed plasmids while being moderate in nicked and linear ones. The formation of a G-quadruplex strongly correlates with the presence of an R-loop. Preventing R-loop formation virtually abolished G-quadruplex formation even in the negatively supercoiled plasmid. Enzymatic action and protein binding that manipulate supercoiling or its propagation all impact the formation of G-quadruplexes. Because chromosomes and plasmids in cells in their natural form are maintained in a supercoiled state, our findings reveal a physical basis that justifies the formation and regulation of G-quadruplexes in vivo. The structural features involved in G-quadruplex formation may all serve as potential targets in clinical and therapeutic applications.
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Affiliation(s)
- Ke-wei Zheng
- State
Key Laboratory of Membrane Biology, Institute of Zoology, ‡University of Chinese
Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Yi-de He
- State
Key Laboratory of Membrane Biology, Institute of Zoology, ‡University of Chinese
Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Hong-he Liu
- State
Key Laboratory of Membrane Biology, Institute of Zoology, ‡University of Chinese
Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Xin-min Li
- State
Key Laboratory of Membrane Biology, Institute of Zoology, ‡University of Chinese
Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Yu-hua Hao
- State
Key Laboratory of Membrane Biology, Institute of Zoology, ‡University of Chinese
Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Zheng Tan
- State
Key Laboratory of Membrane Biology, Institute of Zoology, ‡University of Chinese
Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
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23
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Manna S, Panse CH, Sontakke VA, Sangamesh S, Srivatsan SG. Probing Human Telomeric DNA and RNA Topology and Ligand Binding in a Cellular Model by Using Responsive Fluorescent Nucleoside Probes. Chembiochem 2017; 18:1604-1615. [PMID: 28569423 PMCID: PMC5724660 DOI: 10.1002/cbic.201700283] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Indexed: 01/03/2023]
Abstract
The development of biophysical systems that enable an understanding of the structure and ligand-binding properties of G-quadruplex (GQ)-forming nucleic acid sequences in cells or models that mimic the cellular environment would be highly beneficial in advancing GQ-directed therapeutic strategies. Herein, the establishment of a biophysical platform to investigate the structure and recognition properties of human telomeric (H-Telo) DNA and RNA repeats in a cell-like confined environment by using conformation-sensitive fluorescent nucleoside probes and a widely used cellular model, bis(2-ethylhexyl) sodium sulfosuccinate reverse micelles (RMs), is described. The 2'-deoxy and ribonucleoside probes, composed of a 5-benzofuran uracil base analogue, faithfully report the aqueous micellar core through changes in their fluorescence properties. The nucleoside probes incorporated into different loops of H-Telo DNA and RNA oligonucleotide repeats are minimally perturbing and photophysically signal the formation of respective GQ structures in both aqueous buffer and RMs. Furthermore, these sensors enable a direct comparison of the binding affinity of a ligand to H-Telo DNA and RNA GQ structures in the bulk and confined environment of RMs. These results demonstrate that this combination of a GQ nucleoside probe and easy-to-handle RMs could provide new opportunities to study and devise screening-compatible assays in a cell-like environment to discover GQ binders of clinical potential.
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Affiliation(s)
- Sudeshna Manna
- Department of ChemistryIndian Institute of Science Education and Research (IISER)Dr. Homi Bhabha RoadPune411008India
| | - Cornelia H. Panse
- Department of ChemistryIndian Institute of Science Education and Research (IISER)Dr. Homi Bhabha RoadPune411008India
| | - Vyankat A. Sontakke
- Department of ChemistryIndian Institute of Science Education and Research (IISER)Dr. Homi Bhabha RoadPune411008India
| | - Sarangamath Sangamesh
- Department of ChemistryIndian Institute of Science Education and Research (IISER)Dr. Homi Bhabha RoadPune411008India
| | - Seergazhi G. Srivatsan
- Department of ChemistryIndian Institute of Science Education and Research (IISER)Dr. Homi Bhabha RoadPune411008India
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24
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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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25
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Targeting human telomeric and c-myc G-quadruplexes with alkynylplatinum(II) terpyridine complexes under molecular crowding conditions. J Inorg Biochem 2016; 166:126-134. [PMID: 27852004 DOI: 10.1016/j.jinorgbio.2016.11.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Revised: 11/05/2016] [Accepted: 11/08/2016] [Indexed: 12/27/2022]
Abstract
The interactions between alkynylplatinum(II) terpyridine complexes 1-3 and the G-quadruplex DNA, including c-myc and telomeric quadruplex DNA, are investigated both in dilute solution and under molecular crowding conditions. The UV-vis absorption spectroscopy, circular dichroism and molecular docking studies suggest that 1-3 associate with telomeric and c-myc G-quadruplexes via groove binding, and electrostatic interactions. Experimental studies indicate that under molecular crowding conditions (in the presence of 40wt% PEG 200), 1-2 show weak affinity for c-myc, while 3 still displays high affinity and selectivity for c-myc. On the other hand, 1-3 act as efficient and selective ligand for telomeric quadruplex DNA under molecular crowding conditions. The complex 3 exhibits excellent cytotoxicity against A549, K562 and SGC-7901, with IC50 values that are 35.0-fold, 10.0-fold, and 12.1-fold lower than the values of cisplatin under the same conditions, respectively.
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26
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Singh MK, Shweta H, Sen S. Dispersed dynamics of solvation in G-quadruplex DNA: comparison of dynamic Stokes shifts of probes in parallel and antiparallel quadruplex structures. Methods Appl Fluoresc 2016; 4:034009. [PMID: 28355155 DOI: 10.1088/2050-6120/4/3/034009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
G-quadruplex DNA (GqDNA) structures play an important role in many specific cellular functions and are promising anti-tumor targets for small molecules (ligands). Here, we measured the dynamic Stokes shift of a ligand (Hoechst) bound to parallel c-Myc (mPu22) GqDNA over five decades of time from 100 fs to 10 ns, and compared it with the previously reported dynamics of DAPI bound to antiparallel human telomeric (hTelo22) GqDNA (Pal et al 2015 J. Phys. Chem. Lett. 6 1754). Stokes shift data from fluorescence up-conversion and time-correlated single photon counting experiments was combined to cover the broad dynamic range. The results show that the solvation dynamics of Hoechst in parallel mPu22 GqDNA follow a power law relaxation, added to fast 2 ps exponential relaxation, from 100 fs to 10 ns, with only a subtle difference of power law exponents in the two ligand-GqDNA systems (0.06 in Hoechst-mPu22 compared to 0.16 in DAPI-hTelo22). We measured steady-state fluorescence spectra and time-resolved anisotropy decays which confirm the tight binding of Hoechst to parallel mPu22 with a binding constant of ~1 × 105 M-1. The molecular docking of Hoechst in parallel GqDNA followed by a 50 ns molecular dynamics (MD) simulation on a Hoechst-GqDNA complex reveals that Hoechst binds to one of the outer G-tetrads by end-stacking near G13 and G4, which is different from the binding site of DAPI inside a groove of antiparallel hTelo22 GqDNA. Reconciling previous experimental and simulation results, we assign the 2 ps component to the hydration dynamics of only weakly perturbed water near mPu22 and the power law relaxation to the coupled motion of water and DNA (i.e. DNA backbone, unpaired bases and loops connecting G-tetrads) which come near the Hoechst inside parallel GqDNA.
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Affiliation(s)
- Moirangthem Kiran Singh
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
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27
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Lin S, Long H, Zhou J, Yuan G. Study of G-quadruplexes in the STAT3 gene using electrospray ionization mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30 Suppl 1:173-178. [PMID: 27539434 DOI: 10.1002/rcm.7640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
RATIONALE As a key signal transducer and transcription activator, STAT3 plays a very important role in many cell processes. We found that there were many G-rich sequences existing in the STAT3 gene including its promoter, intron, exon and 3'-flanking regions. These G-rich tracts can form G-quadruplexes under near physiological conditions. In this research, we systemically studied the G-quadruplexes in the STAT3 gene at a whole gene scale for the first time. METHODS In this research, the formation of G-quadruplexes in the STAT3 gene was probed by electrospray ionization mass spectrometry (ESI-MS) and circular dichroism (CD). Their structures were constructed and refined by a molecular modeling method. We also used ESI-MS to study the recognition of the G-quadruplexes in the promoter of the STAT3 gene by flexible molecules which do not have a planar core like the other common quadruplex ligands. RESULTS The results based on ESI-MS suggested that the G-quadruplexes in the promoter of the STAT3 gene formed and were further recognized by some small molecules. CONCLUSION Our research proved that the G-rich sequences in the STAT3 gene could form G-quadruplexes under near physiological conditions. This provides a promising target to study the regulation of cell signal transduction in vivo and drug design that aims to target STAT3 G-quadruplexes. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Sen Lin
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
- Beijing National Day School, Beijing, 100871, China
| | - Haitao Long
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Jiang Zhou
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Gu Yuan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
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Wang SK, Su HF, Gu YC, Lin SL, Tan JH, Huang ZS, Ou TM. Complicated behavior of G-quadruplexes and evaluating G-quadruplexes' ligands in various systems mimicking cellular circumstance. Biochem Biophys Rep 2015; 5:439-447. [PMID: 28955851 PMCID: PMC5600415 DOI: 10.1016/j.bbrep.2015.09.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2015] [Revised: 09/23/2015] [Accepted: 09/25/2015] [Indexed: 01/09/2023] Open
Abstract
Environments surrounding G-rich sequences remarkably affect the conformations of these structures. A proper evaluation system mimicking the crowded environment in a cell with macromolecules should be developed to perform structural and functional studies on G-quadruplexes. In this study, the topology and stability of a G-quadruplex formed by human telomeric repeat sequences were investigated in a macromolecule-crowded environment created by polyethylene glycol 200 (PEG200), tumor cell extract, and Xenopus laevis egg extract. The interactions between small molecules and telomeric G-quadruplexes were also evaluated in the different systems. The results suggested that the actual behavior of G-quadruplex structures in cells extract is quite different from that in the PEG crowding system, and proteins or other factors in extracts might play a very important role in G-quadruplex structures. Cell-free system was constructed using HL60 cell extract. Topologies and stability of G-quadruplexes were identified in different systems. G-quadruplex’s ligands’ effects were evaluated in different systems.
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Affiliation(s)
- Shi-Ke Wang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, 132 Waihuan East Road, Guangzhou 510006, PR China
| | - Hua-Fei Su
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, 132 Waihuan East Road, Guangzhou 510006, PR China
| | - Yu-Chao Gu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, 132 Waihuan East Road, Guangzhou 510006, PR China
| | - Shu-Ling Lin
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, 132 Waihuan East Road, Guangzhou 510006, PR China
| | - Jia-Heng Tan
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, 132 Waihuan East Road, Guangzhou 510006, PR China
| | - Zhi-Shu Huang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, 132 Waihuan East Road, Guangzhou 510006, PR China
| | - Tian-Miao Ou
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, 132 Waihuan East Road, Guangzhou 510006, PR China
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Pal N, Shweta H, Singh MK, Verma SD, Sen S. Power-Law Solvation Dynamics in G-Quadruplex DNA: Role of Hydration Dynamics on Ligand Solvation inside DNA. J Phys Chem Lett 2015; 6:1754-1760. [PMID: 26263345 DOI: 10.1021/acs.jpclett.5b00653] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
G-quadruplex DNA (GqDNA) structures act as promising anticancer targets for small-molecules (ligands). Solvation dynamics of a ligand (DAPI: 4',6-diamidino-2-phenylindole) inside antiparallel-GqDNA is studied through direct comparison of time-resolved experiments to molecular dynamics (MD) simulation. Dynamic Stokes shifts of DAPI in GqDNA prepared in H2O buffer and D2O are compared to find the effect of water on ligand solvation. Experimental dynamics (in H2O) is then directly compared with the dynamics computed from 65 ns simulation on the same DAPI-GqDNA complex. Ligand solvation follows power-law relaxation (summed with fast exponential relaxation) from ~100 fs to 10 ns. Simulation results show relaxation below ~5 ps is dominated by water motion, while both water and DNA contribute comparably to dictate long-time power-law dynamics. Ion contribution is, however, found to be negligible. Simulation results also suggest that anomalous solvation dynamics may have origin in subdiffusive motion of perturbed water near GqDNA.
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Affiliation(s)
- Nibedita Pal
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Him Shweta
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Moirangthem Kiran Singh
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Sachin Dev Verma
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Sobhan Sen
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
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Zhou ZX, Gao F, Chen X, Tian XJ, Ji LN. Selective binding and reverse transcription inhibition of single-strand poly(A) RNA by metal TMPyP complexes. Inorg Chem 2014; 53:10015-7. [PMID: 25203754 DOI: 10.1021/ic501337c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Ni-, Cu-, and Zn-TMPyP are capable of binding to single-strand poly(A) RNA with high preference and affinity and inhibiting the reverse transcription of RNA by both M-MuLV and HIV-1 reverse transcriptase. With 10 nM azidothymidine, the IC50 value of M-TMPyP could be lowered to 10(-1) μM order.
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Affiliation(s)
- Zhu-Xin Zhou
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry and Chemical Engineering, Sun Yat-Sen University , Guangzhou 510275, P. R. China
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Parrotta L, Ortuso F, Moraca F, Rocca R, Costa G, Alcaro S, Artese A. Targeting unimolecular G-quadruplex nucleic acids: a new paradigm for the drug discovery? Expert Opin Drug Discov 2014; 9:1167-87. [PMID: 25109710 DOI: 10.1517/17460441.2014.941353] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
INTRODUCTION G-quadruplexes (G4s) are targets of great interest because of their roles in crucial biological processes, such as aging and cancer. G4s are based on the formation of G-quartets, stabilised by Hoogsteen-type hydrogen bonds and by interaction with cations between the tetrads. These biologically relevant conformations were first discovered in eukaryotic chromosomal telomeric DNA, but have also been found in the proximal location of promoters in a number of human genes. Therefore, the extensive analysis of an intriguing target could move towards the rational drug design of new selective anticancer agents. AREAS COVERED The authors review G4 structural characterisation, with detailed insight related to the polymorphism issue. The authors describe the topologically distinct G4 structural forms and the factors involved in their interconversion mechanisms, such as the sequence of the oligonucleotides, the strand stoichiometry and orientation, the syn-anti conformation of the guanine glycosidic bonds and the G4 loop types and the environmental factors. Furthermore, the authors report several studies related to folding and unfolding kinetic profiles in order to understand the conformational view of monomolecular G4 formations. EXPERT OPINION G4 unimolecular nucleic acids can be considered as valid targets for the rational drug development of novel anticancer agents. Structural biology represents an essential link between the biology and medicinal chemistry knowledge in this field. In silico methods have already been demonstrated to be useful, especially if well integrated with biophysical tests. If this proves successful, the G4-targeting paradigm could also be extended to drug discovery beyond neoplastic pathologies.
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Affiliation(s)
- Lucia Parrotta
- Università degli Studi "Magna Græcia", Dipartimento di Scienze della Salute , Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro , Italy
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Ma DL, Lin S, Leung KH, Zhong HJ, Liu LJ, Chan DSH, Bourdoncle A, Mergny JL, Wang HMD, Leung CH. An oligonucleotide-based label-free luminescent switch-on probe for RNA detection utilizing a G-quadruplex-selective iridium(III) complex. NANOSCALE 2014; 6:8489-8494. [PMID: 24816304 DOI: 10.1039/c4nr00541d] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We report herein the synthesis and application of a novel G-quadruplex-selective luminescent iridium(iii) complex for the construction of an oligonucleotide-based, label-free, rapid and convenient luminescent RNA detection platform.
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Affiliation(s)
- Dik-Lung Ma
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China.
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Huang XX, Zhu LN, Wu B, Huo YF, Duan NN, Kong DM. Two cationic porphyrin isomers showing different multimeric G-quadruplex recognition specificity against monomeric G-quadruplexes. Nucleic Acids Res 2014; 42:8719-31. [PMID: 24939896 PMCID: PMC4117758 DOI: 10.1093/nar/gku526] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Ligands that can interact specifically with telomeric multimeric G-quadruplexes could be developed as promising anticancer drugs with few side effects related to other G-quadruplex-forming regions. In this paper, a new cationic porphyrin derivative, m-TMPipEOPP, was synthesized and characterized. Its multimeric G-quadruplex recognition specificity under molecular crowding conditions was compared to its isomer p-TMPipEOPP. The slight structural difference accounts for different multimeric G-quadruplex recognition specificity for the two isomers. p-TMPipEOPP can barely discriminate between multimeric and monomeric G-quadruplexes. By contrast, m-TMPipEOPP can bind with multimeric but not with monomeric G-quadruplexes. p-TMPipEOPP might bind to multimeric G-quadruplexes by two modes: sandwich-like end-stacking mode and pocket-dependent intercalative mode. Increasing the pocket size between adjacent two G-quadruplex uints is beneficial for the latter mode. m-TMPipEOPP might bind to multimeric G-quadruplexes by a side binding mode, which confers m-TMPipEOPP with higher multimeric G-quadruplex recognition specificity compared to p-TMPipEOPP. m-TMPipEOPP increases the stability of multimeric G-quadruplex under both dilute and molecular crowding conditions but its G-quadruplex-stabilizing ability is a little weaker than p-TMPipEOPP. These results provide important information for the design of highly specific multimeric G-quadruplex ligands. Another interesting finding is that pocket size is an important factor in determining the stability of multimeric G-quadruplexes.
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Affiliation(s)
- Xiao-Xi Huang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, PR China Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300071, PR China
| | - Li-Na Zhu
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300071, PR China Department of Chemistry, Tianjin University, Tianjin 300072, PR China
| | - Bin Wu
- Department of Chemistry, Tianjin University, Tianjin 300072, PR China
| | - Yan-Fang Huo
- Department of Chemistry, Tianjin University, Tianjin 300072, PR China
| | - Na-Na Duan
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, PR China Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300071, PR China
| | - De-Ming Kong
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, PR China Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300071, PR China
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The effect of macromolecular crowding on the electrostatic component of barnase-barstar binding: a computational, implicit solvent-based study. PLoS One 2014; 9:e98618. [PMID: 24915485 PMCID: PMC4051634 DOI: 10.1371/journal.pone.0098618] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 05/05/2014] [Indexed: 02/02/2023] Open
Abstract
Macromolecular crowding within the cell can impact both protein folding and binding. Earlier models of cellular crowding focused on the excluded volume, entropic effect of crowding agents, which generally favors compact protein states. Recently, other effects of crowding have been explored, including enthalpically-related crowder–protein interactions and changes in solvation properties. In this work, we explore the effects of macromolecular crowding on the electrostatic desolvation and solvent-screened interaction components of protein–protein binding. Our simple model enables us to focus exclusively on the electrostatic effects of water depletion on protein binding due to crowding, providing us with the ability to systematically analyze and quantify these potentially intuitive effects. We use the barnase–barstar complex as a model system and randomly placed, uncharged spheres within implicit solvent to model crowding in an aqueous environment. On average, we find that the desolvation free energy penalties incurred by partners upon binding are lowered in a crowded environment and solvent-screened interactions are amplified. At a constant crowder density (fraction of total available volume occupied by crowders), this effect generally increases as the radius of model crowders decreases, but the strength and nature of this trend can depend on the water probe radius used to generate the molecular surface in the continuum model. In general, there is huge variation in desolvation penalties as a function of the random crowder positions. Results with explicit model crowders can be qualitatively similar to those using a lowered “effective” solvent dielectric to account for crowding, although the “best” effective dielectric constant will likely depend on multiple system properties. Taken together, this work systematically demonstrates, quantifies, and analyzes qualitative intuition-based insights into the effects of water depletion due to crowding on the electrostatic component of protein binding, and it provides an initial framework for future analyses.
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Yu HJ, Yu L, Hao ZF, Zhao Y. Interactions of ruthenium complexes containing indoloquinoline moiety with human telomeric G-quadruplex DNA. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 124:187-193. [PMID: 24486786 DOI: 10.1016/j.saa.2013.12.096] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 12/26/2013] [Accepted: 12/27/2013] [Indexed: 06/03/2023]
Abstract
G-quadruplex structures are attractive targets for the development of anticancer drugs, as their formation in human telomere could impair telomerase activity, thus inducing apoptosis in cancer cells. Vast majority of G-quadruplex binding molecules have been designed and synthesized. Ruthenium complexes have also been reported to induction or stabilization of G-quadruplex structure of human telomeric sequence, whereas most of them generally promote the formation of antiparallel or hybrid-type G-quadruplex structure. Ruthenium complex that selectively promotes the formation of parallel G-quadruplex structure has rarely been reported. We reported here the interaction of two ruthenium complexes [Ru(bpy)2(mitatp)](2+)1 and [Ru(phen)2(mitatp)](2+)2 (bpy=2,2' bipyridine, phen=1,10-phenanthroline, mitatp=5-methoxy-isatino[1,2-b]-1,4,8,9-tetraazatriphenylene) containing indoloquinoline moiety with human telomeric G-quadruplex DNA (Telo22). Complex 1 binds to Telo22 tightly via a stable π-π stacking interaction and efficiently stabilizes the G-quadruplex structure. Circular dichroism (CD) spectra titration results suggest that complex 1 could induce Telo22 to fold into antiparallel G-quadruplex conformation. Complex 2 exhibits moderate G-quadruplex binding and stabilizing ability, while CD titration data reveals that complex 2 could promote the formation of parallel G-quadruplex structure.
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Affiliation(s)
- Hui-juan Yu
- School of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou 510006, PR China.
| | - Lin Yu
- School of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou 510006, PR China.
| | - Zhi-feng Hao
- School of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou 510006, PR China
| | - Ying Zhao
- School of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou 510006, PR China
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A convenient sandwich assay of thrombin in biological media using nanoparticle-enhanced fluorescence polarization. Biosens Bioelectron 2014; 56:231-6. [PMID: 24508546 DOI: 10.1016/j.bios.2014.01.021] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 12/24/2013] [Accepted: 01/13/2014] [Indexed: 11/21/2022]
Abstract
A new aptamer biosensor was presented for the detection of thrombin in this work, which was based on fluorescence polarization (FP) using silica nanoparticles as enhancement probe. The silica nanoparticles covered by streptavidin were tagged with a thrombin aptamer (5'-biotin-GGTTGGTGTGGTTGG-3'), which was bound to the surface of silica nanoparticle through the specific interaction between streptavidin and biotin. In the presence of thrombin, it induced the aptamer to form quadruplex structure. When the other thrombin aptamer labeled with fluorescein (5'-FAM-AGTCCGTGGTAGGGCAGGTTGGGGTGACT-3') was added to the above system, a sandwich structure can form at the surface of silica nanoparticles. The fluorescence polarization was therefore enhanced and quantification between fluorescence polarization signal and concentration of thrombin was built. The sensor provided a linear range from 0.6 to 100 nM for thrombin with a detection limit of 0.20 nM (3.29 SB/m, according to the recent recommendation of IUPAC) in a homogeneous media. The same linear range was obtained in spiked human serum samples with a slightly higher detection limit (0.26 nM), demonstrating high anti-interference of the sensor in a complex biological sample matrix. And the sensor can be used to monitor spiked concentration of thrombin level in real human plasma with satisfactory results obtained.
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Lai H, Xiao Y, Yan S, Tian F, Zhong C, Liu Y, Weng X, Zhou X. Symmetric cyanovinyl-pyridinium triphenylamine: a novel fluorescent switch-on probe for an antiparallel G-quadruplex. Analyst 2014; 139:1834-8. [DOI: 10.1039/c3an02269b] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
We describe a probe based on a cyanovinyl pyridinium triphenylamine (CPT) derivative, which showed fluorescent switch-on properties toward an antiparallel G-quadruplex.
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Affiliation(s)
- Hai Lai
- College of Chemistry and Molecular Sciences
- Wuhan University
- Wuhan 430072, P. R. China
| | - Yijie Xiao
- College of Chemistry and Molecular Sciences
- Wuhan University
- Wuhan 430072, P. R. China
| | - Shengyong Yan
- College of Chemistry and Molecular Sciences
- Wuhan University
- Wuhan 430072, P. R. China
| | - Fangfang Tian
- College of Chemistry and Molecular Sciences
- Wuhan University
- Wuhan 430072, P. R. China
| | - Cheng Zhong
- College of Chemistry and Molecular Sciences
- Wuhan University
- Wuhan 430072, P. R. China
| | - Yi Liu
- College of Chemistry and Molecular Sciences
- Wuhan University
- Wuhan 430072, P. R. China
| | - Xiaocheng Weng
- College of Chemistry and Molecular Sciences
- Wuhan University
- Wuhan 430072, P. R. China
- The State Key Laboratory of Natural and Biomimetic Drugs
- State
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences
- Wuhan University
- Wuhan 430072, P. R. China
- The State Key Laboratory of Natural and Biomimetic Drugs
- State
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Nakano SI, Miyoshi D, Sugimoto N. Effects of molecular crowding on the structures, interactions, and functions of nucleic acids. Chem Rev 2013; 114:2733-58. [PMID: 24364729 DOI: 10.1021/cr400113m] [Citation(s) in RCA: 367] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Shu-ichi Nakano
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST) and Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University , 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
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Yaku H, Murashima T, Miyoshi D, Sugimoto N. In vitro assays predictive of telomerase inhibitory effect of G-quadruplex ligands in cell nuclei. J Phys Chem B 2013; 118:2605-14. [PMID: 24328194 DOI: 10.1021/jp410669t] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
G-quadruplex-binding and telomerase-inhibiting capacities of G-quadruplex ligands were examined under a cell nuclei-mimicking condition including excess double-stranded DNA (λ DNA) and molecular crowding cosolute (PEG 200). Under the cell nuclei-mimicking condition, a cationic porphyrin (TMPyP4) did not bind to the G-quadruplex despite the high affinity (Ka = 3.6 × 10(6) M(-1)) under a diluted condition without λ DNA and PEG 200. Correspondingly, TMPyP4 inhibited telomerase activity under the diluted condition (IC50 = 1.6 μM) but not under the cell nuclei-mimicking condition. In contrast, the Ka and IC50 values of an anionic copper phthalocyanine (Cu-APC) under the diluted (2.8 × 10(4) M(-1) and 0.86 μM) and the cell nuclei-mimicking (2.8 × 10(4) M(-1) and 2.1 μM) conditions were similar. In accordance with these results, 10 μM TMPyP4 did not affect the proliferation of HeLa cells, while Cu-APC efficiently inhibited the proliferation (IC50 = 1.4 μM). These results show that the cell nuclei-mimicking condition is effective to predict capacities of G-quadruplex ligands in the cell. In addition, the antiproliferative effect of Cu-APC on normal cells was smaller than that on HeLa cells, indicating that the cell nuclei-mimicking condition is also useful to predict side effects of ligands.
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Affiliation(s)
- Hidenobu Yaku
- Advanced Technology Research Laboratories, Panasonic Corporation, 3-4 Hikaridai, Seika-cho, Soraku-gun, Kyoto 619-0237, Japan
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Biver T. Stabilisation of non-canonical structures of nucleic acids by metal ions and small molecules. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2013.04.016] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Yaku H, Murashima T, Tateishi-Karimata H, Nakano SI, Miyoshi D, Sugimoto N. Study on effects of molecular crowding on G-quadruplex-ligand binding and ligand-mediated telomerase inhibition. Methods 2013; 64:19-27. [PMID: 23562626 DOI: 10.1016/j.ymeth.2013.03.028] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Revised: 03/21/2013] [Accepted: 03/25/2013] [Indexed: 01/24/2023] Open
Abstract
The telomere G-quadruplex-binding and telomerase-inhibiting capacity of two cationic (TMPyP4 and PIPER) and two anionic (phthalocyanine and Hemin) G-quadruplex-ligands were examined under conditions of molecular crowding (MC). Osmotic experiments showed that binding of the anionic ligands, which bind to G-quadruplex DNA via π-π stacking interactions, caused some water molecules to be released from the G-quadruplex/ligand complex; in contrast, a substantial number of water molecules were taken up upon electrostatic binding of the cationic ligands to G-quadruplex DNA. These behaviors of water molecules maintained or reduced the binding affinity of the anionic and the cationic ligands, respectively, under MC conditions. Consequently, the anionic ligands (phthalocyanine and Hemin) robustly inhibited telomerase activity even with MC; in contrast, the inhibition of telomerase caused by cationic TMPyP4 was drastically reduced by MC. These results allow us to conclude that the binding of G-quadruplex-ligands to G-quadruplex via non-electrostatic interactions is preferable for telomerase inhibition under physiological conditions.
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Key Words
- 5,10,15,20-tetra-(N-methyl-4-pyridyl)porphyrin
- Cancer
- Cu-APC
- EG
- Fe(III)-protoporphyrin IX
- G-quadruplex-ligand
- Hemin
- MC
- Molecular crowding
- N,N′-bis[2-(1-piperidino)ethyl]-3,4,9,10-perylenetetracarboxylic diimide
- PEG
- PIPER
- TMPyP4
- Telomerase
- Water molecule
- copper(II) phthalocyanine 3,4′,4′′,4′′′-tetrasulfonic acid tetrasodium salt
- double-stranded DNA
- dsDNA
- ethylene glycol
- molecular crowding
- poly ethylene glycol
- tsTRAP assay
- two-step telomere repeat amplification protocol assay
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Affiliation(s)
- Hidenobu Yaku
- Advanced Technology Research Laboratories, Panasonic Corporation, 3-4 Hikaridai, Seika-cho, Soraku-gun, Kyoto 619-0237, Japan; Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan; Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
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Zhu LN, Wu B, Kong DM. Specific recognition and stabilization of monomeric and multimeric G-quadruplexes by cationic porphyrin TMPipEOPP under molecular crowding conditions. Nucleic Acids Res 2013; 41:4324-35. [PMID: 23430152 PMCID: PMC3627595 DOI: 10.1093/nar/gkt103] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Ligands targeting telomeric G-quadruplexs are considered good candidates for anticancer drugs. However, current studies on G-quadruplex ligands focus exclusively on the interactions of ligands and monomeric G-quadruplexes under dilute conditions. Living cells are crowded with biomacromolecules, and the ∼200-nucleotide G-rich single-stranded overhang of human telomeric DNA has the potential to fold into multimeric G-quadruplex structures containing several G-quadruplex units. Studies on interactions between ligands and multimeric G-quadruplexes under molecular crowding conditions could provide a new route for screening specific telomeric G-quadruplex-targeting ligands. Herein, TMPipEOPP, a cationic porphyrin derivative designed by us, was demonstrated as a promising multimeric telomeric G-quadruplex ligand under molecular crowding conditions. It could highly specifically recognize G-quadruplexes. It could also promote the formation of G-quadruplexes and stabilize them. Detailed studies showed that TMPipEOPP interacted with monomeric G-quadruplexes in sandwich-like end-stacking mode of quadruplex/TMPipEOPP/quadruplex and interacted with multimeric human telomeric G-quadruplexes by intercalating into the pocket between two adjacent G-quadruplex units. The pocket size greatly affected TMPipEOPP binding. A larger pocket was advantageous for the intercalation of TMPipEOPP. This work provides new insights into the ligand-binding properties of multimeric G-quadruplexes under molecular crowding conditions and introduces a new route for screening anticancer drugs targeting telomeric G-quadruplexes.
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Affiliation(s)
- Li-Na Zhu
- Department of Chemistry, Tianjin University, Tianjin 300072, PR China.
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Nagatoishi S, Sugimoto N. Interaction of water with the G-quadruplex loop contributes to the binding energy of G-quadruplex to protein. MOLECULAR BIOSYSTEMS 2013; 8:2766-70. [PMID: 22851057 DOI: 10.1039/c2mb25234a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Unlike DNA duplexes that release water upon interaction with protein, the binding of DNA G-quadruplex of the thrombin-binding aptamer (TBA) to thrombin takes up water. Here, to reveal the mechanism of water uptake, we designed four mutants of TBA (ΔT3, ΔT7, ΔT9, ΔT12), in which thymine residues (T3, T7, T9 and T12) were deleted from the loop regions of TBA G-quadruplex. For the mutants the thermodynamics and the osmolyte effects on the interactions with thrombin were investigated. The mutants ΔT3, ΔT9 and ΔT12 decreased the binding constants of the G-quadruplex to thrombin. Furthermore, an osmotic stress analysis indicated that the number of water molecules binding to the complex decreased in the mutants ΔT3 and ΔT9. The decrease in the binding affinity was related to loss of binding of the loop nucleotides to water molecules. Therefore, the interaction between loops of the G-quadruplex and water molecules contributed to the binding energy of G-quadruplex to protein. Our study suggests that water binding is essential for the binding of G-quadruplex to protein.
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Affiliation(s)
- Satoru Nagatoishi
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
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Agarwal T, Pradhan D, Géci I, El-Madani AM, Petersen M, Pedersen EB, Maiti S. Improved inhibition of telomerase by short twisted intercalating nucleic acids under molecular crowding conditions. Nucleic Acid Ther 2012; 22:399-404. [PMID: 23098240 DOI: 10.1089/nat.2012.0372] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Human telomeric DNA has the ability to fold into a 4-stranded G-quadruplex structure. Several G-quadruplex ligands are known to stabilize the structure and thereby inhibit telomerase activity. Such ligands have demonstrated efficient telomerase inhibition in dilute conditions, but under molecular crowding conditions mimicking physiological milieu, stabilization of the telomeric G-quadruplex is often lost. We attempted to demonstrate the enhanced G-quadruplex stabilizing ability under molecular conditions by using twisted intercalating nucleic acids (TINA)-modified oligonucleotides. We have shown using circular dichroism and ultraviolet spectroscopic methods that these TINA-modified short oligonucleotides function as G-quadruplex, inducing agents and participate in the formation of stabilized 3:1 G-quadruplex with the human telomeric oligonucleotide. Using enzyme-linked immunosorbent assay-based telomerase repeat amplification assay (TRAP) assay as well as nondenaturing polyacrylamide gel electrophoresis-based TRAP, we demonstrate remarkable enhancement in their anti-telomerase activity even under molecular crowding conditions. This is the first time in which a G-quadruplex stabilizing agent has demonstrated enhanced activity even under molecular crowding conditions.
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Affiliation(s)
- Tani Agarwal
- Proteomics and Structural Biology Unit, Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research, New Delhi, India
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Miyoshi D, Fujimoto T, Sugimoto N. Molecular Crowding and Hydration Regulating of G-Quadruplex Formation. Top Curr Chem (Cham) 2012; 330:87-110. [DOI: 10.1007/128_2012_335] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Jain AK, Paul A, Maji B, Muniyappa K, Bhattacharya S. Dimeric 1,3-Phenylene-bis(piperazinyl benzimidazole)s: Synthesis and Structure–Activity Investigations on their Binding with Human Telomeric G-Quadruplex DNA and Telomerase Inhibition Properties. J Med Chem 2012; 55:2981-93. [DOI: 10.1021/jm200860b] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Akash K Jain
- Department
of Organic Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - Ananya Paul
- Department
of Organic Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - Basudeb Maji
- Department
of Organic Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - K. Muniyappa
- Department of Biochemistry, 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, Bangalore 560012, India
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Petraccone L, Pagano B, Giancola C. Studying the effect of crowding and dehydration on DNA G-quadruplexes. Methods 2012; 57:76-83. [PMID: 22406490 DOI: 10.1016/j.ymeth.2012.02.011] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Revised: 02/20/2012] [Accepted: 02/21/2012] [Indexed: 01/01/2023] Open
Abstract
Intracellular environment is crowded with biomolecules that occupy a significant fraction (up to 40%) of the cellular volume, with a total concentration in the range 300-400mg/ml. Recently, the effect of crowding/dehydrating agents on the DNA G-quadruplexes has become a subject of an increasing interest. Crowding and/or dehydrating agents have been used to simulate how G-quadruplexes behave under cell-mimicking conditions characterized by a large excluded volume and a lower water activity. Indeed, the presence of both steric crowding and a lower water activity can affect G-quadruplex stability, their folding/unfolding kinetics, as well as their binding processes with proteins or small ligands. Many of these effects can be explored experimentally by measuring the dependence of the conformational stability, isomerisation kinetics and equilibria on the concentration of cosolutes which do not interact with the molecules (G-quadruplexes) under investigation. Spectroscopic methodologies, like circular dichroism, UV and fluorescence, have been widely employed to study G-quadruplexes in dilute solution. Here we focus on some aspects that need to be taken into account when employing such techniques in the presence of large amount of a cosolute. Additionally, we discuss possible problems/artifacts that arise in setting experiments in presence of these commonly employed cosolutes and in interpreting the results.
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Affiliation(s)
- Luigi Petraccone
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli "Federico II", Via Cintia, I-80126 Napoli, Italy
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Nagesh N, Ganesh Kumar A. Interaction of TMPyP4, TMPyP3, and TMPyP2 with Intramolecular G-Quadruplex Formed by Promoter Region of Bcl2 and KRAS NHPPE. ACTA ACUST UNITED AC 2012. [DOI: 10.5402/2012/786596] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Oncogenes are rich in guanine and capable of forming quadruplex structure. Promoter regions oncogenes such as Bcl2 and KRAS NHPPE are rich in guanine content and they can form quadruplex structures. Alterations in the mode and nature of molecular binding to DNA, certainly has effect on the posttranscriptional activities. Recent experiments indicate that structure of quadruplex complex and ligand has predominant role on ligand-quadruplex DNA interaction. In order to understand the nature of each ligand interaction with quadruplex DNA, Bcl2, KRAS NHPPE quadruplex DNA interaction with three porphyrin was studied using spectroscopy, microcalorimetry and mass spectrometry. Our studies, indicate that mode of ligand interaction varies with structure, environment and concentration of ligand. Fluorescence quenching experiments show that TMPyP4 interaction is ligand concentration dependent. Job plots and ITC experiments demonstrate that four molecules of TMPyP4 and two molecules of TMPyP3, TMPyP2 interact with each quadruplex complex. Through ITC titrations, ligand binding constant are higher for TMPyP4 (≈107 M−1) compared to TMPyP3, TMPyP2 (≈105 M−1). ESI-MS experiments confirm the stoichiometry of TMPyP4 : 39Bcl2 is 4 : 1 at saturation and it is 2 : 1 in case of KRAS NHPPE quadruplex.
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Affiliation(s)
- Narayana Nagesh
- Department of Medicinal Chemistry, Centre for Cellular and Molecular Biology, Hyderabad 500007, India
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Abstract
G-quadruplex ligands are potential anticancer agents as telomerase inhibitors and potential transcriptional regulators of oncogenes. The search for best-in-class drugs is addressed to identify small molecules able to promote and stabilize G-quadruplex structures. What features should the G-quadruplex ligands possess? They should have selective antiproliferative effects on cancer cells and induce telomerase inhibition or oncogene suppression. One of the main challenges in their design and synthesis is to make the ligands selective for G-quadruplex DNA. These features should be amplified by careful analyses of physico-chemical aspects of G-quadruplex-drug interactions. In particular, the study of the energetics of G-quadruplex-drug interactions can enhance drug design by providing thermodynamic parameters that give quantitative information on the biomolecular interactions important for binding. The main methodologies used to gain information on energetics of binding are based on spectroscopic or calorimetric principles. Spectroscopic techniques such as fluorescence and circular dichroism are rapid and cheap methods, but are not sufficient to characterize completely the thermodynamics of interaction. Calorimetric techniques such as isothermal titration calorimetry offer a direct measure of binding enthalpy, in addition to the stoichiometry and affinity constants. With the complete thermodynamic signature of drug-target interaction, dissecting the enthalpic and entropic components of binding is possible, which can be a useful aid to decision-making during drug optimization.
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Affiliation(s)
- Concetta Giancola
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli "Federico II", Via Cintia, 80126, Napoli, Italy,
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