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Stipaničev N, Raabe K, Rozas I. Aiming to Improve Binding of Porphyrin Diphenyl Guanidinium Conjugates to Guanine-Quadruplexes: When Size Matters. Bioorg Med Chem Lett 2022; 75:128954. [PMID: 36031019 DOI: 10.1016/j.bmcl.2022.128954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/12/2022] [Accepted: 08/22/2022] [Indexed: 11/28/2022]
Abstract
Aiming to improve the binding to Guanine quadruplexes of different topologies, docking studies of porphyrin diphenyl guanidine conjugates previously prepared with an O or a S bridge between the diphenyl moiety and a newly design derivative with an SO2 bridge were carried out using different guanine quadruplexes of different topologies (four parallel, one antiparallel and one hybrid). Positive results were obtained from these computational studies drove us to prepare the SO2 bridge conjugate improving the synthetic route previously reported by us. Biophysical experiments such as UV-thermal melting and circular dichroism indicated the lack of binding to the double stranded DNA and poor binding of the new derivative prepared to any of the guanine quadruplexes studied. These results show that the size of this SO2 bridge could be responsible of the poor experimental binding to guanine quadruplexes.
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Affiliation(s)
- Nikolina Stipaničev
- School of Chemistry, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Konstantin Raabe
- School of Chemistry, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Isabel Rozas
- School of Chemistry, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland.
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2
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Shankar U, Mishra SK, Jain N, Tawani A, Yadav P, Kumar A. Ni +2 permease system of Helicobacter pylori contains highly conserved G-quadruplex motifs. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 101:105298. [PMID: 35526824 DOI: 10.1016/j.meegid.2022.105298] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 03/30/2022] [Accepted: 05/02/2022] [Indexed: 06/14/2023]
Abstract
The genome of a micro-organism contains all the information required for its survival inside its host cells. The guanine rich regions of the genome can form stable G-quadruplex structures that act as the regulators of gene expression. Herein, the completely sequenced genomes of Helicobacter pylori were explored for the identification and characterization of the conserved G-quadruplex motifs in this gastrointestinal pathogen. Initial in silico analysis revealed the presence of ~8241 GQ motifs in the H. pylori genome. Metal binding proteins of H. pylori are significantly enriched in the GQ motifs. Our study emphasizes the identification and characterization of four highly conserved G-quadruplex forming motifs (HPGQs) in the nickel transporter genes (nixA, niuB1, niuB2, and niuD) of the H. pylori. Nickel is a virulence determinant in H. pylori and is required as a co-factor for the urease and [NiFe] hydrogenase enzymes that are crucial for its survival in the stomach lining of humans. The presence of GQ motifs in these nickel transporter genes can affect their expression and may alter the functioning of Urease and [NiFe] hydrogenase. Similar to human and virus G-quadruplexes, targeting these conserved PGQs with bioactive molecules may represent a novel therapeutic avenue for combating infection of H. pylori. The identified HPGQs were characterized in-vitro by using CD spectroscopy, electrophoresis technique, and NMR spectroscopy at both acidic (4.5) and neutral pH (7.0). ITC revealed the specific interaction of these HPGQs with high affinity to the known G-quadruplex binding ligand, TMPyP4. The mTFP based reporter assay showed decrease in the gene expression of mTFP in the TMPyP4 treated cells as compared to the untreated and further affirmed the formation of stable G-quadruplex structures in the HPGQ motifs in vivo. This is the first report for characterizing G-quadruplex motifs in nickel transport-associated genes in the H. pylori bacterium.
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Affiliation(s)
- Uma Shankar
- Department of Biosciences and Biomedical Engineering Indore, Simrol, Indore, Madhya Pradesh 455235, India
| | - Subodh Kumar Mishra
- Department of Biosciences and Biomedical Engineering Indore, Simrol, Indore, Madhya Pradesh 455235, India
| | - Neha Jain
- Department of Biosciences and Biomedical Engineering Indore, Simrol, Indore, Madhya Pradesh 455235, India
| | - Arpita Tawani
- Department of Biosciences and Biomedical Engineering Indore, Simrol, Indore, Madhya Pradesh 455235, India
| | - Puja Yadav
- Department of Microbiology, Central University of Haryana, Mahendergarh, Haryana, India
| | - Amit Kumar
- Department of Biosciences and Biomedical Engineering Indore, Simrol, Indore, Madhya Pradesh 455235, India.
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3
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Fagan SG, Helm M, Prehn JHM. tRNA-derived fragments: A new class of non-coding RNA with key roles in nervous system function and dysfunction. Prog Neurobiol 2021; 205:102118. [PMID: 34245849 DOI: 10.1016/j.pneurobio.2021.102118] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 06/30/2021] [Accepted: 07/06/2021] [Indexed: 01/12/2023]
Abstract
tRNA-derived small RNAs (tsRNA) are a recently identified family of non-coding RNA that have been associated with a variety of cellular functions including the regulation of protein translation and gene expression. Recent sequencing and bioinformatic studies have identified the broad spectrum of tsRNA in the nervous system and demonstrated that this new class of non-coding RNA is produced from tRNA by specific cleavage events catalysed by ribonucleases such as angiogenin and dicer. Evidence is also accumulating that production of tsRNA is increased during disease processes where they regulate stress responses, proteostasis, and neuronal survival. Mutations to tRNA cleaving and modifying enzymes have been implicated in several neurodegenerative disorders, and tsRNA levels in the blood are advancing as biomarkers for neurological disease. In this review we summarize the physiological importance of tsRNA in the central nervous system and their relevance to neurological disease.
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Affiliation(s)
- Steven G Fagan
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, St. Stephen'S Green, Dublin 2, Ireland; SFI FutureNeuro Research Centre, Royal College of Surgeons in Ireland, St. Stephen's Green, Dublin 2, Ireland
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences - IPBS, Johannes Gutenberg-University, 55128, Mainz, Germany
| | - Jochen H M Prehn
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, St. Stephen'S Green, Dublin 2, Ireland; SFI FutureNeuro Research Centre, Royal College of Surgeons in Ireland, St. Stephen's Green, Dublin 2, Ireland.
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4
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Maddah M, Karami L. An atomistic investigation on the interaction of distamycin A and its derivative with the telomeric G-Quadruplex as anticancer agents by molecular dynamics simulation. Arch Biochem Biophys 2021; 701:108797. [PMID: 33607110 DOI: 10.1016/j.abb.2021.108797] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 02/05/2021] [Accepted: 02/06/2021] [Indexed: 10/22/2022]
Abstract
Human telomerase that activates within cancer cells has a telomeric sequence at the 3' end. Each factor that stabilizes the G-quadruplex in guanine-rich telomeric sequences can inhibit the regular telomerase activity. Therefore, the telomeric G-quadruplex is known as a promising target in cancer treatment. In this work, we studied the binding of positively charged distamycin A and its uncharged derivative to the G-quadruplex in a solution environment by Molecular Dynamics (MD) simulation. The binding mechanism and subtle conformational changes were investigated as a result of the ligand attachment. Moreover, binding free energy and clustering analysis describe the stability and flexibility of G-quadruplexes upon ligand binding. Structural analyses displayed that the favorable binding of both ligands imposes significant stability and rigidity in G-quadruplex conformation compared to free G-quadruplex, especially charged distamycin. Hydration pattern and ion distribution were different for free G-quadruplex and both of the ligand complexes. Energy decomposition reveals the electrostatic effect on the stability of G-quadruplex. The radial distribution function displayed the solvent shell and ion moving away from the groove. The hydrogen bond played an essential role in the binding of both ligands, especially for the charged derivative. van der Waals interaction is the only factor that is more important in binding uncharged distamycin into G-quadruplex than the charged one. The calculated ΔGbind showed the stability of both ligands within grooves and good agreement with the experimental binding free energy data. Finally, the results suggest that ligand modification improves the binding mode toward stabilizing G-quadruplexes.
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Affiliation(s)
- Mina Maddah
- Depatment of Chemistry, K. N. Toosi University of Technology, Tehran, Iran; Super Computing Institute, University of Tehran, Tehran, Iran.
| | - Leila Karami
- Department of Cell and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran.
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5
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Platella C, Trajkovski M, Doria F, Freccero M, Plavec J, Montesarchio D. On the interaction of an anticancer trisubstituted naphthalene diimide with G-quadruplexes of different topologies: a structural insight. Nucleic Acids Res 2020; 48:12380-12393. [PMID: 33170272 PMCID: PMC7708068 DOI: 10.1093/nar/gkaa1001] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/29/2020] [Accepted: 10/22/2020] [Indexed: 12/12/2022] Open
Abstract
Naphthalene diimides showed significant anticancer activity in animal models, with therapeutic potential related to their ability to strongly interact with G-quadruplexes. Recently, a trifunctionalized naphthalene diimide, named NDI-5, was identified as the best analogue of a mini-library of novel naphthalene diimides for its high G-quadruplex binding affinity along with marked, selective anticancer activity, emerging as promising candidate drug for in vivo studies. Here we used NMR, dynamic light scattering, circular dichroism and fluorescence analyses to investigate the interactions of NDI-5 with G-quadruplexes featuring either parallel or hybrid topology. Interplay of different binding modes of NDI-5 to G-quadruplexes was observed for both parallel and hybrid topologies, with end-stacking always operative as the predominant binding event. While NDI-5 primarily targets the 5'-end quartet of the hybrid G-quadruplex model (m-tel24), the binding to a parallel G-quadruplex model (M2) occurs seemingly simultaneously at the 5'- and 3'-end quartets. With parallel G-quadruplex M2, NDI-5 formed stable complexes with 1:3 DNA:ligand binding stoichiometry. Conversely, when interacting with hybrid G-quadruplex m-tel24, NDI-5 showed multiple binding poses on a single G-quadruplex unit and/or formed different complexes comprising two or more G-quadruplex units. NDI-5 produced stabilizing effects on both G-quadruplexes, forming complexes with dissociation constants in the nM range.
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Affiliation(s)
- Chiara Platella
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy
| | - Marko Trajkovski
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Filippo Doria
- Department of Chemistry, University of Pavia, Viale Taramelli 10, I-27100 Pavia, Italy
| | - Mauro Freccero
- Department of Chemistry, University of Pavia, Viale Taramelli 10, I-27100 Pavia, Italy
| | - Janez Plavec
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
- EN→FIST Centre of Excellence, Trg OF 13, SI-1000 Ljubljana, Slovenia
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy
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6
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Liu L, Li J, He Y. Multifunctional epiberberine mediates multi-therapeutic effects. Fitoterapia 2020; 147:104771. [DOI: 10.1016/j.fitote.2020.104771] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/25/2020] [Accepted: 10/29/2020] [Indexed: 12/13/2022]
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7
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Berei J, Eckburg A, Miliavski E, Anderson AD, Miller RJ, Dein J, Giuffre AM, Tang D, Deb S, Racherla KS, Patel M, Vela MS, Puri N. Potential Telomere-Related Pharmacological Targets. Curr Top Med Chem 2020; 20:458-484. [DOI: 10.2174/1568026620666200109114339] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 11/21/2019] [Accepted: 11/21/2019] [Indexed: 12/22/2022]
Abstract
Telomeres function as protective caps at the terminal portion of chromosomes, containing
non-coding nucleotide sequence repeats. As part of their protective function, telomeres preserve genomic
integrity and minimize chromosomal exposure, thus limiting DNA damage responses. With
continued mitotic divisions in normal cells, telomeres progressively shorten until they reach a threshold
at a point where they activate senescence or cell death pathways. However, the presence of the enzyme
telomerase can provide functional immortality to the cells that have reached or progressed past
senescence. In senescent cells that amass several oncogenic mutations, cancer formation can occur due
to genomic instability and the induction of telomerase activity. Telomerase has been found to be expressed
in over 85% of human tumors and is labeled as a near-universal marker for cancer. Due to this
feature being present in a majority of tumors but absent in most somatic cells, telomerase and telomeres
have become promising targets for the development of new and effective anticancer therapeutics.
In this review, we evaluate novel anticancer targets in development which aim to alter telomerase
or telomere function. Additionally, we analyze the progress that has been made, including preclinical
studies and clinical trials, with therapeutics directed at telomere-related targets. Furthermore, we review
the potential telomere-related therapeutics that are used in combination therapy with more traditional
cancer treatments. Throughout the review, topics related to medicinal chemistry are discussed,
including drug bioavailability and delivery, chemical structure-activity relationships of select therapies,
and the development of a unique telomere assay to analyze compounds affecting telomere elongation.
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Affiliation(s)
- Joseph Berei
- Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, United States
| | - Adam Eckburg
- Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, United States
| | - Edward Miliavski
- Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, United States
| | - Austin D. Anderson
- Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, United States
| | - Rachel J. Miller
- Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, United States
| | - Joshua Dein
- Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, United States
| | - Allison M. Giuffre
- Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, United States
| | - Diana Tang
- Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, United States
| | - Shreya Deb
- Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, United States
| | - Kavya Sri Racherla
- Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, United States
| | - Meet Patel
- Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, United States
| | - Monica Saravana Vela
- Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, United States
| | - Neelu Puri
- Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, United States
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8
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Chasing Particularities of Guanine- and Cytosine-Rich DNA Strands. Molecules 2020; 25:molecules25030434. [PMID: 31972988 PMCID: PMC7037129 DOI: 10.3390/molecules25030434] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/17/2020] [Accepted: 01/20/2020] [Indexed: 01/17/2023] Open
Abstract
By substitution of natural nucleotides by their abasic analogs (i.e., 1',2'-dideoxyribose phosphate residue) at critically chosen positions within 27-bp DNA constructs originating from the first intron of N-myc gene, we hindered hybridization within the guanine- and cytosine-rich central region and followed formation of non-canonical structures. The impeded hybridization between the complementary strands leads to time-dependent structural transformations of guanine-rich strand that are herein characterized with the use of solution-state NMR, CD spectroscopy, and native polyacrylamide gel electrophoresis. Moreover, the DNA structural changes involve transformation of intra- into inter-molecular G-quadruplex structures that are thermodynamically favored. Intriguingly, the transition occurs in the presence of complementary cytosine-rich strands highlighting the inability of Watson-Crick base-pairing to preclude the transformation between G-quadruplex structures that occurs via intertwining mechanism and corroborates a role of G-quadruplex structures in DNA recombination processes.
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9
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Ma Y, Iida K, Nagasawa K. Topologies of G-quadruplex: Biological functions and regulation by ligands. Biochem Biophys Res Commun 2020; 531:3-17. [PMID: 31948752 DOI: 10.1016/j.bbrc.2019.12.103] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 12/20/2019] [Accepted: 12/28/2019] [Indexed: 01/06/2023]
Abstract
G-Quadruplex (G4) is one of the higher-order structures occurring in guanine-rich sequences of nucleic acids, and plays critical roles in biological processes. The G4-forming sequences can generate three kinds of topologies, i.e., parallel, anti-parallel, and hybrid, and these polymorphic structures have an important influence on G4-related biological functions. In this review, we highlight variety of structures generated by G4s containing various sequences and under diverse conditions. We also discuss the G4 ligands which induce specific topologies and/or conversion between different topologies.
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Affiliation(s)
- Yue Ma
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Japan.
| | - Keisuke Iida
- Department of Chemistry, Chiba University, Japan
| | - Kazuo Nagasawa
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Japan.
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10
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Litovchick A, Tian X, Monteiro MI, Kennedy KM, Guié MA, Centrella P, Zhang Y, Clark MA, Keefe AD. Novel Nucleic Acid Binding Small Molecules Discovered Using DNA-Encoded Chemistry. Molecules 2019; 24:molecules24102026. [PMID: 31137911 PMCID: PMC6572338 DOI: 10.3390/molecules24102026] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 05/15/2019] [Accepted: 05/20/2019] [Indexed: 11/16/2022] Open
Abstract
Inspired by the many reported successful applications of DNA-encoded chemical libraries in drug discovery projects with protein targets, we decided to apply this platform to nucleic acid targets. We used a 120-billion-compound set of 33 distinct DNA-encoded chemical libraries and affinity-mediated selection to discover binders to a panel of DNA targets. Here, we report the successful discovery of small molecules that specifically interacted with DNA G-quartets, which are stable structural motifs found in G-rich regions of genomic DNA, including in the promoter regions of oncogenes. For this study, we chose the G-quartet sequence found in the c-myc promoter as a primary target. Compounds enriched using affinity-mediated selection against this target demonstrated high-affinity binding and high specificity over DNA sequences not containing G-quartet motifs. These compounds demonstrated a moderate ability to discriminate between different G-quartet motifs and also demonstrated activity in a cell-based assay, suggesting direct target engagement in the cell. DNA-encoded chemical libraries and affinity-mediated selection are uniquely suited to discover binders to targets that have no inherent activity outside of a cellular context, and they may also be of utility in other nucleic acid structural motifs.
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Affiliation(s)
| | - Xia Tian
- Arrakis Therapeutics, Waltham, MA 02451, USA.
| | | | | | | | | | - Ying Zhang
- X-Chem Pharmaceuticals, Waltham, MA 02435, USA.
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11
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Umek T, Sollander K, Bergquist H, Wengel J, Lundin KE, Smith CIE, Zain R. Oligonucleotide Binding to Non-B-DNA in MYC. Molecules 2019; 24:E1000. [PMID: 30871121 PMCID: PMC6429085 DOI: 10.3390/molecules24051000] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 02/25/2019] [Accepted: 03/06/2019] [Indexed: 11/16/2022] Open
Abstract
MYC, originally named c-myc, is an oncogene deregulated in many different forms of cancer. Translocation of the MYC gene to an immunoglobulin gene leads to an overexpression and the development of Burkitt's lymphoma (BL). Sporadic BL constitutes one subgroup where one of the translocation sites is located at the 5'-vicinity of the two major MYC promoters P₁ and P₂. A non-B-DNA forming sequence within this region has been reported with the ability to form an intramolecular triplex (H-DNA) or a G-quadruplex. We have examined triplex formation at this site first by using a 17 bp triplex-forming oligonucleotide (TFO) and a double strand DNA (dsDNA) target corresponding to the MYC sequence. An antiparallel purine-motif triplex was detected using electrophoretic mobility shift assay. Furthermore, we probed for H-DNA formation using the BQQ-OP based triplex-specific cleavage assay, which indicated the formation of the structure in the supercoiled plasmid containing the corresponding region of the MYC promoter. Targeting non-B-DNA structures has therapeutic potential; therefore, we investigated their influence on strand-invasion of anti-gene oligonucleotides (ON)s. We show that in vitro, non-B-DNA formation at the vicinity of the ON target site facilitates dsDNA strand-invasion of the anti-gene ONs.
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Affiliation(s)
- Tea Umek
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital Huddinge, 141 86 Huddinge, Sweden.
| | - Karin Sollander
- Department of Molecular Biology and Functional Genomics, Stockholm University, 171 65 Stockholm, Sweden.
| | - Helen Bergquist
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital Huddinge, 141 86 Huddinge, Sweden.
| | - Jesper Wengel
- Biomolecular Nanoscale Engineerng Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, M5230 Odense, Denmark.
| | - Karin E Lundin
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital Huddinge, 141 86 Huddinge, Sweden.
| | - C I Edvard Smith
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital Huddinge, 141 86 Huddinge, Sweden.
| | - Rula Zain
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital Huddinge, 141 86 Huddinge, Sweden.
- Department of Clinical Genetics, Centre for Rare Diseases, Karolinska University Hospital, SE-171 76 Stockholm, Sweden.
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12
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Rahman A, O'Sullivan P, Rozas I. Recent developments in compounds acting in the DNA minor groove. MEDCHEMCOMM 2018; 10:26-40. [PMID: 30774852 DOI: 10.1039/c8md00425k] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 12/11/2018] [Indexed: 12/12/2022]
Abstract
The macromolecule that carries genetic information, DNA, is considered as an exceptional target for diseases depending on cellular division of malignant cells (i.e. cancer), microbes (i.e. bacteria) or parasites (i.e. protozoa). To aim for a comprehensive review to cover all aspects related to DNA targeting would be an impossible task and, hence, the objective of the present review is to present, from a medicinal chemistry point of view, recent developments of compounds targeting the minor groove of DNA. Accordingly, we discuss the medicinal chemistry aspects of heterocyclic small-molecules binding the DNA minor groove, as novel anticancer, antibacterial and antiparasitic agents.
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Affiliation(s)
- Adeyemi Rahman
- School of Chemistry , Trinity Biomedical Sciences Institute , Trinity College Dublin , 152-160-Pearse Street , Dublin 2 , Ireland .
| | - Patrick O'Sullivan
- School of Chemistry , Trinity Biomedical Sciences Institute , Trinity College Dublin , 152-160-Pearse Street , Dublin 2 , Ireland .
| | - Isabel Rozas
- School of Chemistry , Trinity Biomedical Sciences Institute , Trinity College Dublin , 152-160-Pearse Street , Dublin 2 , Ireland .
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13
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Sullivan HJ, Readmond C, Radicella C, Persad V, Fasano TJ, Wu C. Binding of Telomestatin, TMPyP4, BSU6037, and BRACO19 to a Telomeric G-Quadruplex-Duplex Hybrid Probed by All-Atom Molecular Dynamics Simulations with Explicit Solvent. ACS OMEGA 2018; 3:14788-14806. [PMID: 30555989 PMCID: PMC6289566 DOI: 10.1021/acsomega.8b01574] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Accepted: 09/11/2018] [Indexed: 06/09/2023]
Abstract
A promising anticancer therapeutic strategy is the stabilization of telomeric G-quadruplexes using G-quadruplex-binding small molecules. Although many G-quadruplex-specific ligands have been developed, their low potency and selectivity to G-quadruplexes over duplex remains unsolved. Recently, a crystal structure of a telomeric 3' quadruplex-duplex hybrid was reported and the quadruplex-duplex interface was suggested to a good target to address the issues. However, there are no high-resolution complex structures reported for G-quadruplex ligands except for a docked BSU6037. In this study, molecular dynamic (MD) binding simulations with a free ligand were used to study binding poses and dynamics of four representative ligands: telomestatin, TMPyP4, BSU6037, and BRACO19. The MD data showed that BSU6037 was able to fully intercalate into the interface whereas TMPyP4 and BRACO19 could only maintain partial intercalation into the interface and telomestatin only binds at the quadruplex and duplex ends. Both linear ligands, BSU6037 and BRACO19, were able to interact with the interface, yet they were not selective over duplex DNA. The DNA geometry, binding modes, and binding pathways were systematically characterized, and the binding energy was calculated and compared for each system. The interaction of the ligands to the interface was by the means of an induced-fit binding mechanism rather than a lock-key mechanism, consisting of the DNA unfolding at the interface to allow entrance of the drug and then the refolding and repacking of the DNA and the ligand to further stabilize the G-quadruplex. On the basis of the findings in this study, modifications were suggested to optimize the interface binding for TMPyp4 and telomestatin.
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Affiliation(s)
- Holli-Joi Sullivan
- Chemistry
& Biochemistry and Department of Molecular & Cellular Biosciences, College of Science and Mathematics, Rowan University, Glassboro, New Jersey 08028, United States
| | - Carolyn Readmond
- Chemistry
& Biochemistry and Department of Molecular & Cellular Biosciences, College of Science and Mathematics, Rowan University, Glassboro, New Jersey 08028, United States
| | - Christina Radicella
- Chemistry
& Biochemistry and Department of Molecular & Cellular Biosciences, College of Science and Mathematics, Rowan University, Glassboro, New Jersey 08028, United States
| | - Victoria Persad
- Chemistry
& Biochemistry and Department of Molecular & Cellular Biosciences, College of Science and Mathematics, Rowan University, Glassboro, New Jersey 08028, United States
| | - Thomas J. Fasano
- Chemistry
& Biochemistry and Department of Molecular & Cellular Biosciences, College of Science and Mathematics, Rowan University, Glassboro, New Jersey 08028, United States
| | - Chun Wu
- Chemistry
& Biochemistry and Department of Molecular & Cellular Biosciences, College of Science and Mathematics, Rowan University, Glassboro, New Jersey 08028, United States
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14
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Asamitsu S, Bando T, Sugiyama H. Ligand Design to Acquire Specificity to Intended G-Quadruplex Structures. Chemistry 2018; 25:417-430. [PMID: 30051593 DOI: 10.1002/chem.201802691] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 07/14/2018] [Indexed: 12/17/2022]
Abstract
A G-quadruplex is a nucleic acid secondary structure that is adopted by guanine-rich sequences, and is considered to be relevant in various pharmacological and biological contexts. G-Quadruplexes have also attracted great attention in the field of DNA nanotechnology because of their extremely high thermal stability and the availability of many defined structures. To date, a large repertory of DNA/RNA G-quadruplex-interactive ligands has been developed by numerous laboratories. Several relevant reviews have also been published that have helped researchers to grasp the full scope of G-quadruplex research from its outset to the present. This review focuses on the G-quadruplex ligands that allow targeting of specific G-quadruplexes. Moreover, unique ligands, successful methodologies, and future perspectives in relation to specific G-quadruplex recognition are also addressed.
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Affiliation(s)
- Sefan Asamitsu
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo, Kyoto, 606-8502, Japan
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo, Kyoto, 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo, Kyoto, 606-8502, Japan.,Institute for Integrated Cell-Material Science (WPI-iCeMS), Kyoto University, Sakyo, Kyoto, 606-8501, Japan
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15
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Kumar M, Kaushik M, Kukreti S. A topological transition from bimolecular quadruplex to G-triplex/tri-G-quadruplex exhibited by truncated double repeats of human telomere. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2018; 47:903-915. [PMID: 29934676 DOI: 10.1007/s00249-018-1312-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 04/11/2018] [Accepted: 05/21/2018] [Indexed: 12/12/2022]
Abstract
Human telomeric G-rich sequences can fold back into various conformations depending upon the salt (Na+ or K+) at physiological pH. On the basis of results obtained by native PAGE electrophoresis, circular dichroism, and UV-melting experiments, we report here that truncated sequences of human telomere (d-GGGTTAGGG; GM9, d-AGGGTTAGGG; GM10, d-TAGGGTTAGGG; GM11) adopt a varied range of quadruplex conformations as a function of the cation present. By correlating CD and gel electrophoresis experiments; it was concluded that the GM9 oligonucleotide can self-associate to form a tetramer quadruplex (antiparallel; AP) in Na+ solution and a mixture of G-triplex (AP) or tri-G-quadruplex (parallel; P) along with a tetramer G-quadruplex structure (AP) in K+. The GM10 oligonucleotide formed a bimolecular G-quadruplex in both Na+ and K+ solutions, while GM11 associated to form a bimolecular G-quadruplex (AP) structure in Na+ solution and a mixture of bimolecular G-quadruplex (AP) and bimolecular G-quadruplex (P) along with parallel G-triplex or antiparallel tri-G-quadruplex in K+. All the UV-melting profiles, thermal difference spectra, and CD melting curves suggested the formation of a variety of G-quadruplex conformations by the DNA sequences studied in Na+ and K+ ions. Hypothetical models for different conformations adopted by these DNA molecules have also been proposed, which may further enhance our knowledge about the divergent topologies of guanine quadruplexes.
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Affiliation(s)
- Mohan Kumar
- Nucleic Acid Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Mahima Kaushik
- Nucleic Acid Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India.,Cluster Innovation Centre, University of Delhi, Delhi, India
| | - Shrikant Kukreti
- Nucleic Acid Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India.
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16
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Vasimalla S, Sato S, Takenaka F, Kurose Y, Takenaka S. Cyclic perylene diimide: Selective ligand for tetraplex DNA binding over double stranded DNA. Bioorg Med Chem 2017; 25:6404-6411. [DOI: 10.1016/j.bmc.2017.10.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 10/12/2017] [Accepted: 10/13/2017] [Indexed: 01/27/2023]
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17
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Machireddy B, Kalra G, Jonnalagadda S, Ramanujachary K, Wu C. Probing the Binding Pathway of BRACO19 to a Parallel-Stranded Human Telomeric G-Quadruplex Using Molecular Dynamics Binding Simulation with AMBER DNA OL15 and Ligand GAFF2 Force Fields. J Chem Inf Model 2017; 57:2846-2864. [PMID: 29028340 DOI: 10.1021/acs.jcim.7b00287] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Human telomeric DNA G-quadruplex has been identified as a good therapeutic target in cancer treatment. G-quadruplex-specific ligands that stabilize the G-quadruplex have great potential to be developed as anticancer agents. Two crystal structures (an apo form of parallel stranded human telomeric G-quadruplex and its holo form in complex with BRACO19, a potent G-quadruplex ligand) have been solved, yet the binding mechanism and pathway remain elusive. In this study, we simulated the binding of a free BRACO19 molecule to the apo form of the G-quadruplex using the latest AMBER DNA (OL15) and ligand (GAFF2) force fields. Three binding modes have been identified: top stacking, bottom intercalation, and groove binding. Bottom intercalation (51% of the population) resembles the bottom binding pose in the complex crystal structure very well. The groove binding mode is less stable than the bottom binding mode and is likely to be an intermediate state leading to the bottom binding mode. A flip-insertion mechanism was observed in the bottom intercalation mode, during which flipping of the bases outward makes space for ligand insertion, after which the bases flip back to increase the stability of the complex. In addition to reproducing the base-flipping behavior for some loop residues upon ligand binding, the direct alignment type of the ATAT-tetrad was observed in our simulations for the first time. These successes provide initial support for using this combination of the OL15 and GAFF2 force fields to study quadruplex-ligand interactions.
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Affiliation(s)
- Babitha Machireddy
- College of Science and Mathematics, Rowan University , Glassboro, New Jersey 08028, United States
| | - Gurmannat Kalra
- College of Science and Mathematics, Rowan University , Glassboro, New Jersey 08028, United States
| | - Subash Jonnalagadda
- College of Science and Mathematics, Rowan University , Glassboro, New Jersey 08028, United States
| | - Kandalam Ramanujachary
- College of Science and Mathematics, Rowan University , Glassboro, New Jersey 08028, United States
| | - Chun Wu
- College of Science and Mathematics, Rowan University , Glassboro, New Jersey 08028, United States
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18
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Yadav K, Meka PNR, Sadhu S, Guggilapu SD, Kovvuri J, Kamal A, Srinivas R, Devayani P, Babu BN, Nagesh N. Telomerase Inhibition and Human Telomeric G-Quadruplex DNA Stabilization by a β-Carboline-Benzimidazole Derivative at Low Concentrations. Biochemistry 2017; 56:4392-4404. [PMID: 28737386 DOI: 10.1021/acs.biochem.7b00008] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Guanine rich regions in DNA, which can form highly stable secondary structures, namely, G-quadruplex or G4 DNA structures, affect DNA replication and transcription. Molecules that stabilize G4 DNA have become important in recent years. In this study, G4 DNA stabilization, inhibition of telomerase, and anticancer activity of synthetic β-carboline-benzimidazole derivatives (5a, 5d, 5h, and 5r) were studied. Among them, derivatives containing a 4-methoxyphenyl ring at C1 and a 6-methoxy-substituted benzimidazole at C3 (5a) were found to stabilize telomeric G-quadruplex DNA efficiently. The stoichiometry and interaction of a synthetic, β-carboline-benzimidazole derivative, namely, 3-(6-methoxy-1H-benzo[d]imidazol-2-yl)-1-(4-methoxyphenyl)-9H-pyrido[3,4-b]indole (5a), with human intermolecular G-quadruplex DNA at low concentrations were examined using electrospray ionization mass spectrometry. Spectroscopy techniques indicate that 5a may intercalate between the two stacks of G-quadruplex DNA. This model is supported by docking studies. When cancer cells are treated with 5a, the cell cycle arrest occurs at the sub-G1 phase. In addition, an apoptosis assay and fluorescence microscopy studies using cancer cells indicate that 5a can induce apoptosis. Results of biochemical assays such as the polymerase chain reaction stop assay and telomerase activity assay indicate that 5a has the potential to stabilize G-quadruplex DNA, and thereby, it may interfere with in vitro DNA synthesis and decrease telomerase activity. The results of this study reveal that the β-carboline-benzimidazole derivative (5a) is efficient in G-quadruplex DNA stabilization over double-stranded DNA, inhibits telomerase activity, and induces apoptosis in cancer cells.
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Affiliation(s)
- Kranthikumar Yadav
- Analytical Chemistry and Mass Spectrometry Division, CSIR-Indian Institute of Chemical Technology , Hyderabad 500007, India
| | - Penchala Narasimha Rao Meka
- Medicinal Chemistry and Pharmacology, CSIR-Indian Institute of Chemical Technology , Hyderabad 500007, India
| | - Sudeshna Sadhu
- CSIR-Centre for Cellular and Molecular Biology , Hyderabad 500007, India
| | - Sravanthi Devi Guggilapu
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER) , Hyderabad 500037, India
| | - Jeshma Kovvuri
- Medicinal Chemistry and Pharmacology, CSIR-Indian Institute of Chemical Technology , Hyderabad 500007, India
| | - Ahmed Kamal
- Medicinal Chemistry and Pharmacology, CSIR-Indian Institute of Chemical Technology , Hyderabad 500007, India.,Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER) , Hyderabad 500037, India
| | - Ragampeta Srinivas
- Analytical Chemistry and Mass Spectrometry Division, CSIR-Indian Institute of Chemical Technology , Hyderabad 500007, India
| | - Panuganti Devayani
- CSIR-Centre for Cellular and Molecular Biology , Hyderabad 500007, India
| | - Bathini Nagendra Babu
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER) , Hyderabad 500037, India
| | - Narayana Nagesh
- CSIR-Centre for Cellular and Molecular Biology , Hyderabad 500007, India
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19
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Shen Z, Mulholland KA, Zheng Y, Wu C. Binding of anticancer drug daunomycin to a TGGGGT G-quadruplex DNA probed by all-atom molecular dynamics simulations: additional pure groove binding mode and implications on designing more selective G-quadruplex ligands. J Mol Model 2017; 23:256. [PMID: 28785893 DOI: 10.1007/s00894-017-3417-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 07/12/2017] [Indexed: 12/12/2022]
Abstract
DNA G-quadruplex structures are emerging cancer-specific targets for chemotherapeutics. Ligands that bind to and stabilize DNA G-quadruplexes have the potential to be anti-cancer drugs. Lack of binding selectivity to DNA G-quadruplex over DNA duplex remains a major challenge when attempting to develop G-quadruplex ligands into successful anti-cancer drugs. Thorough understanding of the binding nature of existing non-selective ligands that bind to both DNA quadruplex and DNA duplex will help to address this challenge. Daunomycin and doxorubicin, two commonly used anticancer drugs, are examples of non-selective DNA ligands. In this study, we extended our early all-atom binding simulation studies between doxorubicin and a DNA duplex (d(CGATCG)2) to probe the binding between daunomycin and a parallel DNA quadruplex (d(TGGGGT)4) and DNA duplex. In addition to the end stacking mode, which mimics the mode in the crystal structure, a pure groove binding mode was observed in our free binding simulations. The dynamic and energetic properties of these two binding modes are thoroughly examined, and a detailed comparison is made between DNA quadruplex binding modes and DNA duplex binding modes. Implications on the design of more selective DNA quadruplex ligands are also discussed. Graphical abstract Top stacking and groov binding modes from the MD simulations.
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Affiliation(s)
- Zhanhang Shen
- School of Physics, Shandong University, Jinan, 250100, China
| | - Kelly A Mulholland
- College of Science and Mathematics, Rowan University, Glassboro, NJ, 08028, USA
| | - Yujun Zheng
- School of Physics, Shandong University, Jinan, 250100, China.
| | - Chun Wu
- College of Science and Mathematics, Rowan University, Glassboro, NJ, 08028, USA.
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20
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Zhu Y, Hamlow LA, He CC, Lee JK, Gao J, Berden G, Oomens J, Rodgers MT. Gas-Phase Conformations and N-Glycosidic Bond Stabilities of Sodium Cationized 2'-Deoxyguanosine and Guanosine: Sodium Cations Preferentially Bind to the Guanine Residue. J Phys Chem B 2017; 121:4048-4060. [PMID: 28355483 DOI: 10.1021/acs.jpcb.7b02906] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
2'-Deoxyguanosine (dGuo) and guanosine (Guo) are fundamental building blocks of DNA and RNA nucleic acids. In order to understand the effects of sodium cationization on the gas-phase conformations and stabilities of dGuo and Guo, infrared multiple photon dissociation (IRMPD) action spectroscopy experiments and complementary electronic structure calculations are performed. The measured IRMPD spectra of [dGuo+Na]+ and [Guo+Na]+ are compared to calculated IR spectra predicted for the stable low-energy structures computed for these species to determine the most favorable sodium cation binding sites, identify the structures populated in the experiments, and elucidate the influence of the 2'-hydroxyl substituent on the structures and IRMPD spectral features. These results are compared with those from a previous IRMPD study of the protonated guanine nucleosides to elucidate the differences between sodium cationization and protonation on structure. Energy-resolved collision-induced dissociation (ER-CID) experiments and survival yield analyses of protonated and sodium cationized dGuo and Guo are performed to compare the effects of these cations toward activating the N-glycosidic bonds of these nucleosides. For both [dGuo+Na]+ and [Guo+Na]+, the gas-phase structures populated in the experiments are found to involve bidentate binding of the sodium cation to the O6 and N7 atoms of guanine, forming a 5-membered chelation ring, with guanine found in both anti and syn orientations and C2'-endo (2T3 or 3T2) puckering of the sugar. The ER-CID results, IRMPD yields and the computed C1'-N9 bond lengths indicate that sodium cationization activates the N-glycosidic bond less effectively than protonation for both dGuo and Guo. The 2'-hydroxyl substituent of Guo is found to impact the preferred structures very little except that it enables a 2'OH···3'OH hydrogen bond to be formed, and stabilizes the N-glycosidic bond relative to that of dGuo in both the sodium cationized and protonated complexes.
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Affiliation(s)
- Y Zhu
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
| | - L A Hamlow
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
| | - C C He
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
| | - J K Lee
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
| | - J Gao
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University , Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
| | - G Berden
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University , Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
| | - J Oomens
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University , Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
| | - M T Rodgers
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
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21
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Song J, Perreault JP, Topisirovic I, Richard S. RNA G-quadruplexes and their potential regulatory roles in translation. ACTA ACUST UNITED AC 2016; 4:e1244031. [PMID: 28090421 PMCID: PMC5173311 DOI: 10.1080/21690731.2016.1244031] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 09/26/2016] [Accepted: 09/28/2016] [Indexed: 12/11/2022]
Abstract
DNA guanine (G)-rich 4-stranded helical nucleic acid structures called G-quadruplexes (G4), have been extensively studied during the last decades. However, emerging evidence reveals that 5′- and 3′-untranslated regions (5′- and 3′-UTRs) as well as open reading frames (ORFs) contain putative RNA G-quadruplexes. These stable secondary structures play key roles in telomere homeostasis and RNA metabolism including pre-mRNA splicing, polyadenylation, mRNA targeting and translation. Interestingly, multiple RNA binding proteins such as nucleolin, FMRP, DHX36, and Aven were identified to bind RNA G-quadruplexes. Moreover, accumulating reports suggest that RNA G-quadruplexes regulate translation in cap-dependent and -independent manner. Herein, we discuss potential roles of RNA G-quadruplexes and associated trans-acting factors in the regulation of mRNA translation.
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Affiliation(s)
- Jingwen Song
- Terry Fox Molecular Oncology Group and Segal Cancer Center, McGill University, Montréal, Québec, Canada; Bloomfield Center for Research on Aging, Lady Davis Institute for Medical Research, McGill University, Montréal, Québec, Canada; Department of Oncology, McGill University, Montréal, Québec, Canada; Department of Medicine, McGill University, Montréal, Québec, Canada
| | | | - Ivan Topisirovic
- Terry Fox Molecular Oncology Group and Segal Cancer Center, McGill University, Montréal, Québec, Canada; Department of Oncology, McGill University, Montréal, Québec, Canada; Department of Biochemistry, McGill University, Montréal, Québec, Canada
| | - Stéphane Richard
- Terry Fox Molecular Oncology Group and Segal Cancer Center, McGill University, Montréal, Québec, Canada; Bloomfield Center for Research on Aging, Lady Davis Institute for Medical Research, McGill University, Montréal, Québec, Canada; Department of Oncology, McGill University, Montréal, Québec, Canada; Department of Medicine, McGill University, Montréal, Québec, Canada
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22
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Mulholland K, Wu C. Binding of Telomestatin to a Telomeric G-Quadruplex DNA Probed by All-Atom Molecular Dynamics Simulations with Explicit Solvent. J Chem Inf Model 2016; 56:2093-2102. [DOI: 10.1021/acs.jcim.6b00473] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Kelly Mulholland
- College of Science and Mathematics, Rowan University, Glassboro, New Jersey 08028, United States
| | - Chun Wu
- College of Science and Mathematics, Rowan University, Glassboro, New Jersey 08028, United States
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23
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A two-pronged attack on DNA: targeting guanine quadruplexes with nonplanar porphyrins and DNA-binding small molecules. Future Med Chem 2016; 8:609-12. [DOI: 10.4155/fmc-2016-0040] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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24
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Ferraroni M, Bazzicalupi C, Papi F, Fiorillo G, Guamán-Ortiz LM, Nocentini A, Scovassi AI, Lombardi P, Gratteri P. Solution and Solid-State Analysis of Binding of 13-Substituted Berberine Analogues to Human Telomeric G-quadruplexes. Chem Asian J 2016; 11:1107-15. [DOI: 10.1002/asia.201600116] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Indexed: 12/29/2022]
Affiliation(s)
- Marta Ferraroni
- Department of Chemistry; University of Florence; Via della Lastruccia 3 50019 Sesto Fiorentino FI Italy
| | - Carla Bazzicalupi
- Department of Chemistry; University of Florence; Via della Lastruccia 3 50019 Sesto Fiorentino FI Italy
| | - Francesco Papi
- Department of Chemistry; University of Florence; Via della Lastruccia 3 50019 Sesto Fiorentino FI Italy
- Department NEUROFARBA-Pharmaceutical and nutraceutical section; Laboratory of Molecular Modeling Cheminformatics&QSAR; University of Firenze; via Ugo Schiff 6 50019 Sesto Fiorentino, Firenze Italy
| | - Gaetano Fiorillo
- Naxospharma srl; via G. Di Vittorio, 70 20026 Novate Milanese Italy
| | - Luis Miguel Guamán-Ortiz
- Universidad Técnica Particular de Loja; Departamento de Ciencias de la Salud; San Cayetano Alto Calle Paris 1101608 Loja Ecuador
- Istituto di Genetica Molecolare del CNR, Via Abbiategrasso 207; 27100 Pavia Italy
| | - Alessio Nocentini
- Department NEUROFARBA-Pharmaceutical and nutraceutical section; Laboratory of Molecular Modeling Cheminformatics&QSAR; University of Firenze; via Ugo Schiff 6 50019 Sesto Fiorentino, Firenze Italy
| | - Anna Ivana Scovassi
- Istituto di Genetica Molecolare del CNR, Via Abbiategrasso 207; 27100 Pavia Italy
| | - Paolo Lombardi
- Naxospharma srl; via G. Di Vittorio, 70 20026 Novate Milanese Italy
| | - Paola Gratteri
- Department NEUROFARBA-Pharmaceutical and nutraceutical section; Laboratory of Molecular Modeling Cheminformatics&QSAR; University of Firenze; via Ugo Schiff 6 50019 Sesto Fiorentino, Firenze Italy
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25
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Abstract
DNA has been exploited as a biological target of chemotherapeutics since the 1940s. Traditional chemotherapeutics, such as cisplatin and DNA-alkylating agents, rely primarily on increased uptake by rapidly proliferating cancer cells for therapeutic effects, but this strategy can result in off-target toxicity in healthy tissue. Recently, research interests have shifted towards targeted chemotherapeutics, in which a drug targets a specific biological signature of cancer, resulting in selective toxicity towards cancerous cells. Here, we review a family of complexes, termed rhodium metalloinsertors, that selectively target DNA base pair mismatches, a hallmark of mismatch-repair (MMR) deficient cancers. These rhodium metalloinsertors, bind DNA mismatches with high specificity and display high selectively in killing MMR-deficient versus MMR-proficient cells. This cell selectivity is unique for small molecules that bind DNA. Current generations of rhodium metalloinsertors have shown nanomolar potency along with high selectivity towards MMR-deficient cells, and show promise as a foundation for a new family of chemotherapeutics for MMR-deficient cancers.
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Affiliation(s)
- Kelsey M Boyle
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena CA 91125
| | - Jacqueline K Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena CA 91125
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26
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Formation and stabilization of the telomeric antiparallel G-quadruplex and inhibition of telomerase by novel benzothioxanthene derivatives with anti-tumor activity. Sci Rep 2015; 5:13693. [PMID: 26329134 PMCID: PMC4557076 DOI: 10.1038/srep13693] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 08/03/2015] [Indexed: 12/20/2022] Open
Abstract
G-quadruplexes formed in telomeric DNA sequences at human chromosome ends can be a novel target for the development of therapeutics for the treatment of cancer patients. Herein, we examined the ability of six novel benzothioxanthene derivatives S1–S6 to induce the formation of and stabilize an antiparallel G-quadruplex by EMSA, UV-melting and CD techniques and the influence of S1–S6 on A549 and SGC7901 cells through real-time cell analysis, wound healing, trap assay methods. Results show that six compounds could differentially induce 26 nt G-rich oligonucleotides to form the G-quadruplex with high selectivity vs C-rich DNA, mutated DNA and double-stranded DNA, stabilize it with high affinity, promote apoptosis and inhibit mobility and telomerase activity of A549 cells and SGC7901 cells. Especially, S1, S3, S4 displayed stronger abilities, of which S3 was the most optimal with the maximum ΔTm value being up to 29.8 °C for G-quadruplex, the minimum IC50 value being 0.53 μM and the maximum cell inhibitory rate being up to 97.2%. This study suggests that this type of compounds that induce the formation of and stabilize the telomeric antiparallel G-quadruplex, and consequently inhibit telomerase activity, leading to cell apoptosis, can be screened for the discovery of novel antitumor therapeutics.
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27
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Porru M, Artuso S, Salvati E, Bianco A, Franceschin M, Diodoro MG, Passeri D, Orlandi A, Savorani F, D'Incalci M, Biroccio A, Leonetti C. Targeting G-Quadruplex DNA Structures by EMICORON Has a Strong Antitumor Efficacy against Advanced Models of Human Colon Cancer. Mol Cancer Ther 2015; 14:2541-51. [PMID: 26304235 DOI: 10.1158/1535-7163.mct-15-0253] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 08/10/2015] [Indexed: 01/11/2023]
Abstract
We previously identified EMICORON as a novel G-quadruplex (G4) ligand showing high selectivity for G4 structures over the duplex DNA, causing telomere damage and inhibition of cell proliferation in transformed and tumor cells. Here, we evaluated the antitumoral effect of EMICORON on advanced models of human colon cancer that could adequately predict human clinical outcomes. Our results showed that EMICORON was well tolerated in mice, as no adverse effects were reported, and a low ratio of sensitivity across human and mouse bone marrow cells was observed, indicating a good potential for reaching similar blood levels in humans. Moreover, EMICORON showed a marked therapeutic efficacy, as it inhibited the growth of patient-derived xenografts (PDX) and orthotopic colon cancer and strongly reduced the dissemination of tumor cells to lymph nodes, intestine, stomach, and liver. Finally, activation of DNA damage and impairment of proliferation and angiogenesis are proved to be key determinants of EMICORON antitumoral activity. Altogether, our results, performed on advanced experimental models of human colon cancer that bridge the translational gap between preclinical and clinical studies, demonstrated that EMICORON had an unprecedented antitumor activity warranting further studies of EMICORON-based combination treatments.
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Affiliation(s)
- Manuela Porru
- Experimental Chemotherapy Laboratory, Regina Elena National Cancer Institute, Rome, Italy
| | - Simona Artuso
- Experimental Chemotherapy Laboratory, Regina Elena National Cancer Institute, Rome, Italy
| | - Erica Salvati
- Experimental Chemotherapy Laboratory, Regina Elena National Cancer Institute, Rome, Italy
| | | | | | | | - Daniela Passeri
- Department of Biopathology and Image Diagnostics, Anatomic Pathology Institute, University of Rome "Tor Vergata", Rome, Italy
| | - Augusto Orlandi
- Department of Biopathology and Image Diagnostics, Anatomic Pathology Institute, University of Rome "Tor Vergata", Rome, Italy
| | - Francesco Savorani
- Department of Food Science, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Maurizio D'Incalci
- Department of Oncology, Pharmacological Research Institute "Mario Negri", Milan, Italy
| | - Annamaria Biroccio
- Experimental Chemotherapy Laboratory, Regina Elena National Cancer Institute, Rome, Italy.
| | - Carlo Leonetti
- Experimental Chemotherapy Laboratory, Regina Elena National Cancer Institute, Rome, Italy.
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28
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Tera M, Hirokawa T, Okabe S, Sugahara K, Seimiya H, Shimamoto K. Design and synthesis of a berberine dimer: a fluorescent ligand with high affinity towards G-quadruplexes. Chemistry 2015; 21:14519-28. [PMID: 26272465 DOI: 10.1002/chem.201501693] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Indexed: 12/20/2022]
Abstract
G-quadruplexes (G4) are thought to be important factors for telomerase inhibition and transcriptional/translational modulations. Bioinformatic analyses imply that the human genome and mRNA contain a multitude of G4-forming sequences; however, their analysis requires selective and detectable ligands. Given that two molecules of fluorescent berberine (BBR) coordinate to telomeric G4 in their co-crystals, we designed hydrocarbon-linked BBR-analogue dimers because we expected the alignment of two BBR chromophores would avoid Watson-Crick base pair intercalation, which should result in high selectivity towards G4. An alkene-cis-C2 BBR dimer showed the highest affinity (Kd ≤2.6 nM) and selectivity (ca. 900-fold vs. duplex) towards G4. The intrinsic "light-up" fluorescence properties of this BBR dimer, derived from its conformational switching by G4, allowed a selective visualization of various G4 in the gel without using additional bulky fluorescence dyes, which, combined with the observed lack of conformational change of the ligand, suggested future applications in in vitro detection systems.
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Affiliation(s)
- Masayuki Tera
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seikacho, Soraku, Kyoto 619-0284 (Japan).
| | - Takatsugu Hirokawa
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ward, Tokyo, 135-0064 (Japan)
| | - Sachiko Okabe
- Division of Molecular Biotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ward, Tokyo, 135-8550 (Japan)
| | - Kohtaro Sugahara
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seikacho, Soraku, Kyoto 619-0284 (Japan)
| | - Hiroyuki Seimiya
- Division of Molecular Biotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ward, Tokyo, 135-8550 (Japan)
| | - Keiko Shimamoto
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seikacho, Soraku, Kyoto 619-0284 (Japan)
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Chiorcea-Paquim AM, Rodrigues Pontinha AD, Oliveira-Brett AM. Quadruplex-targeting anticancer drug BRACO-19 voltammetric and AFM characterization. Electrochim Acta 2015. [DOI: 10.1016/j.electacta.2015.05.146] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Le DD, Di Antonio M, Chan LKM, Balasubramanian S. G-quadruplex ligands exhibit differential G-tetrad selectivity. Chem Commun (Camb) 2015; 51:8048-50. [PMID: 25864836 DOI: 10.1039/c5cc02252e] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A rapid and simple equilibrium-binding assay mediated by ligand-induced fluorescence quenching of fluorophore-labelled G-quadruplex (G4) structures enabled quantitative interrogation of mutually exclusive ligand binding interactions at opposed G-tetrads. This technique revealed that the ligands TmPyP4, PhenDC3, and PDS have differential chemotype-specific binding preferences for individual G-tetrads of a model genomic G4 structure.
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Affiliation(s)
- D D Le
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
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31
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Trajkovski M, Morel E, Hamon F, Bombard S, Teulade-Fichou MP, Plavec J. Interactions of Pt-ttpy with G-Quadruplexes Originating from Promoter Region of the c-myc Gene Deciphered by NMR and Gel Electrophoresis Analysis. Chemistry 2015; 21:7798-807. [DOI: 10.1002/chem.201500347] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Indexed: 12/20/2022]
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Nagasawa K, Sedghi Masoud S, Tsushima Y, Iida K. Synthesis of Macrocyclic Penta- and Tetraoxazoles as G-Quadruplex Ligands. HETEROCYCLES 2015. [DOI: 10.3987/com-14-s(k)90] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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33
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Gratteri P, Massai L, Michelucci E, Rigo R, Messori L, Cinellu MA, Musetti C, Sissi C, Bazzicalupi C. Interactions of selected gold(iii) complexes with DNA G quadruplexes. Dalton Trans 2015; 44:3633-9. [DOI: 10.1039/c4dt02698e] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The interactions of three Au(iii) complexes with human telomeric DNA sequences: Auoxo6 turned out to be very effective in inducing and binding the G-quadruplex DNA conformation.
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Affiliation(s)
- P. Gratteri
- Department NEUROFARBA – Pharmaceutical and nutraceutical section and Laboratory of Molecular Modeling Cheminformatics & QSAR
- University of Firenze
- I-50019 Sesto Fiorentino
- Italy
| | - L. Massai
- Department of Chemistry “Ugo Schiff”
- University of Firenze
- I-50019 Sesto Fiorentino
- Italy
| | - E. Michelucci
- Mass Spectrometry Centre (CISM)
- University of Florence
- 50019 Sesto Fiorentino
- Italy
| | - R. Rigo
- Department of Pharmaceutical and Pharmacological Sciences
- 35131 Padova
- Italy
| | - L. Messori
- Department of Chemistry “Ugo Schiff”
- University of Firenze
- I-50019 Sesto Fiorentino
- Italy
| | - M. A. Cinellu
- Department of Chemistry and Pharmacy
- University of Sassari
- 07100 Sassari
- Italy
| | - C. Musetti
- Department of Pharmaceutical and Pharmacological Sciences
- 35131 Padova
- Italy
- Glaxo Smith Kline
- Collegeville
| | - C. Sissi
- Department of Pharmaceutical and Pharmacological Sciences
- 35131 Padova
- Italy
| | - C. Bazzicalupi
- Department of Chemistry “Ugo Schiff”
- University of Firenze
- I-50019 Sesto Fiorentino
- Italy
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34
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Doluca O, Withers JM, Loo TS, Edwards PJB, González C, Filichev VV. Interdependence of pyrene interactions and tetramolecular G4-DNA assembly. Org Biomol Chem 2015; 13:3742-8. [DOI: 10.1039/c4ob02499k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Our results demonstrate the expanded capabilities of G-quadruplex DNAs for directed chromophore arrangements and show new perspectives in the design of G-quadruplexes governed by non-guanine moieties.
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Affiliation(s)
- Osman Doluca
- College of Sciences
- Institute of Fundamental Sciences
- Massey University
- 4442 Palmerston North
- New Zealand
| | - Jamie M. Withers
- College of Sciences
- Institute of Fundamental Sciences
- Massey University
- 4442 Palmerston North
- New Zealand
| | - Trevor S. Loo
- College of Sciences
- Institute of Fundamental Sciences
- Massey University
- 4442 Palmerston North
- New Zealand
| | - Patrick J. B. Edwards
- College of Sciences
- Institute of Fundamental Sciences
- Massey University
- 4442 Palmerston North
- New Zealand
| | | | - Vyacheslav V. Filichev
- College of Sciences
- Institute of Fundamental Sciences
- Massey University
- 4442 Palmerston North
- New Zealand
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35
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Métifiot M, Amrane S, Litvak S, Andreola ML. G-quadruplexes in viruses: function and potential therapeutic applications. Nucleic Acids Res 2014; 42:12352-66. [PMID: 25332402 PMCID: PMC4227801 DOI: 10.1093/nar/gku999] [Citation(s) in RCA: 174] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 09/26/2014] [Accepted: 10/06/2014] [Indexed: 12/15/2022] Open
Abstract
G-rich nucleic acids can form non-canonical G-quadruplex structures (G4s) in which four guanines fold in a planar arrangement through Hoogsteen hydrogen bonds. Although many biochemical and structural studies have focused on DNA sequences containing successive, adjacent guanines that spontaneously fold into G4s, evidence for their in vivo relevance has recently begun to accumulate. Complete sequencing of the human genome highlighted the presence of ∼300,000 sequences that can potentially form G4s. Likewise, the presence of putative G4-sequences has been reported in various viruses genomes [e.g., Human immunodeficiency virus (HIV-1), Epstein-Barr virus (EBV), papillomavirus (HPV)]. Many studies have focused on telomeric G4s and how their dynamics are regulated to enable telomere synthesis. Moreover, a role for G4s has been proposed in cellular and viral replication, recombination and gene expression control. In parallel, DNA aptamers that form G4s have been described as inhibitors and diagnostic tools to detect viruses [e.g., hepatitis A virus (HAV), EBV, cauliflower mosaic virus (CaMV), severe acute respiratory syndrome virus (SARS), simian virus 40 (SV40)]. Here, special emphasis will be given to the possible role of these structures in a virus life cycle as well as the use of G4-forming oligonucleotides as potential antiviral agents and innovative tools.
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Affiliation(s)
- Mathieu Métifiot
- CNRS UMR-5234, Université de Bordeaux, 146 Rue Léo Saignat, 33076 Bordeaux, France
| | - Samir Amrane
- INSERM, U869, IECB, ARNA laboratory, Université de Bordeaux, 2 Rue Robert Escarpit 33600 Pessac, France
| | - Simon Litvak
- CNRS UMR-5234, Université de Bordeaux, 146 Rue Léo Saignat, 33076 Bordeaux, France
| | - Marie-Line Andreola
- CNRS UMR-5234, Université de Bordeaux, 146 Rue Léo Saignat, 33076 Bordeaux, France
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36
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Müller S, Rodriguez R. G-quadruplex interacting small molecules and drugs: from bench toward bedside. Expert Rev Clin Pharmacol 2014; 7:663-79. [DOI: 10.1586/17512433.2014.945909] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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