101
|
Kotar A, Wang B, Shivalingam A, Gonzalez-Garcia J, Vilar R, Plavec J. NMR Structure of a Triangulenium-Based Long-Lived Fluorescence Probe Bound to a G-Quadruplex. Angew Chem Int Ed Engl 2016; 55:12508-11. [PMID: 27577037 DOI: 10.1002/anie.201606877] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Indexed: 12/31/2022]
Abstract
An NMR structural study of the interaction between a small-molecule optical probe (DAOTA-M2) and a G-quadruplex from the promoter region of the c-myc oncogene revealed that they interact at 1:2 binding stoichiometry. NMR-restrained structural calculations show that binding of DAOTA-M2 occurs mainly through π-π stacking between the polyaromatic core of the ligand and guanine residues of the outer G-quartets. Interestingly, the binding affinities of DAOTA-M2 differ by a factor of two for the outer G-quartets of the unimolecular parallel G-quadruplex under study. Unrestrained MD calculations indicate that DAOTA-M2 displays significant dynamic behavior when stacked on a G-quartet plane. These studies provide molecular guidelines for the design of triangulenium derivatives that can be used as optical probes for G-quadruplexes.
Collapse
Affiliation(s)
- Anita Kotar
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia
| | - Baifan Wang
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia
| | - Arun Shivalingam
- Department of Chemistry, Imperial College London, South Kensington, London, SW7 2AZ, UK
| | - Jorge Gonzalez-Garcia
- Department of Chemistry, Imperial College London, South Kensington, London, SW7 2AZ, UK
| | - Ramon Vilar
- Department of Chemistry, Imperial College London, South Kensington, London, SW7 2AZ, UK
| | - Janez Plavec
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia. .,EN-FIST Center of Excellence, Trg OF 13, 1000, Ljubljana, Slovenia. .,Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, Ljubljana, Slovenia.
| |
Collapse
|
102
|
Chauhan A, Paul R, Debnath M, Bessi I, Mandal S, Schwalbe H, Dash J. Synthesis of Fluorescent Binaphthyl Amines That Bind c-MYC G-Quadruplex DNA and Repress c-MYC Expression. J Med Chem 2016; 59:7275-81. [PMID: 27442915 DOI: 10.1021/acs.jmedchem.6b00328] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Two novel binaphthyl amines have been designed and synthesized using Buchwald amination and oxidative homocoupling as key steps. The binaphthyl amine containing two triazole rings shows higher affinity for c-MYC G-quadruplex, exhibits fluorescence "turn-on" response with c-MYC, and stains the nucleus in cells. The triazolyl binaphthyl amine shows cytotoxicity for cancer cells by inducing G2/M phase cell cycle arrest and apoptosis. Moreover, both ligands can downregulate c-MYC expression at transcriptional and translational levels.
Collapse
Affiliation(s)
- Ajay Chauhan
- Department of Chemical Sciences, Indian Institute of Science Education and Research , Mohanpur, West Bengal 741252, India
| | - Rakesh Paul
- Department of Organic Chemistry, Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700032, India
| | - Manish Debnath
- Department of Organic Chemistry, Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700032, India
| | - Irene Bessi
- Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt , Max-von-Laue Strasse 7, 60438 Frankfurt am Main, Germany
| | - Samir Mandal
- Department of Organic Chemistry, Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700032, India
| | - Harald Schwalbe
- Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt , Max-von-Laue Strasse 7, 60438 Frankfurt am Main, Germany
| | - Jyotirmayee Dash
- Department of Chemical Sciences, Indian Institute of Science Education and Research , Mohanpur, West Bengal 741252, India.,Department of Organic Chemistry, Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700032, India
| |
Collapse
|
103
|
Yoshida W, Yoshioka H, Bay DH, Iida K, Ikebukuro K, Nagasawa K, Karube I. Detection of DNA Methylation of G-Quadruplex and i-Motif-Forming Sequences by Measuring the Initial Elongation Efficiency of Polymerase Chain Reaction. Anal Chem 2016; 88:7101-7. [PMID: 27351368 DOI: 10.1021/acs.analchem.6b00982] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
DNA methylation has been proposed as one of the promising biomarkers for cancer diagnosis. In this study, we developed a DNA methylation detection system utilizing G-quadruplex and i-motif-forming sequences that requires neither sodium bisulfite treatment nor methylated DNA ligands. We hypothesized that G-quadruplex and i-motif structures would be stabilized by DNA methylation and arrest DNA polymerase activity during quantitative polymerase chain reaction (qPCR). The PCR products from VEGF, RET G-quadruplex, and i-motif-forming sequences were used as templates and analyzed by qPCR. Our results indicated that the initial elongation efficiency of PCR decreased with increasing DNA methylation levels in the G-quadruplex and i-motif-forming sequences. Moreover, we demonstrated that the initial elongation efficiency of PCR decreased with increased DNA methylation of the VEGF region on genomic DNA. These results indicated that DNA methylation of the G-quadruplex and i-motif-forming sequences on genomic DNA can be detected by qPCR.
Collapse
Affiliation(s)
- Wataru Yoshida
- School of Bioscience and Biotechnology, Tokyo University of Technology , 1404-1 Katakuramachi, Hachioji, Tokyo, 192-0982, Japan
| | - Hitomi Yoshioka
- School of Bioscience and Biotechnology, Tokyo University of Technology , 1404-1 Katakuramachi, Hachioji, Tokyo, 192-0982, Japan
| | - Daniyah Habiballah Bay
- School of Bioscience and Biotechnology, Tokyo University of Technology , 1404-1 Katakuramachi, Hachioji, Tokyo, 192-0982, Japan.,Biology Department, Umm Al-Qura University , P.O. Box 715, Makkah, 21955, Kingdom of Saudi Arabia
| | - Keisuke Iida
- Graduate School of Science and Engineering, Saitama University , Kitaadachi-gun, Saitama, 362-0806, Japan
| | - Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology , 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Kazuo Nagasawa
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology , 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Isao Karube
- School of Bioscience and Biotechnology, Tokyo University of Technology , 1404-1 Katakuramachi, Hachioji, Tokyo, 192-0982, Japan
| |
Collapse
|
104
|
Amato J, Morigi R, Pagano B, Pagano A, Ohnmacht S, De Magis A, Tiang YP, Capranico G, Locatelli A, Graziadio A, Leoni A, Rambaldi M, Novellino E, Neidle S, Randazzo A. Toward the Development of Specific G-Quadruplex Binders: Synthesis, Biophysical, and Biological Studies of New Hydrazone Derivatives. J Med Chem 2016; 59:5706-20. [PMID: 27223049 DOI: 10.1021/acs.jmedchem.6b00129] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
G-Quadruplex-binding compounds are currently perceived as possible anticancer therapeutics. Here, starting from a promising lead, a small series of novel hydrazone-based compounds were synthesized and evaluated as G-quadruplex binders. The in vitro G-quadruplex-binding properties of the synthesized compounds were investigated employing both human telomeric and oncogene promoter G-quadruplexes with different folding topologies as targets. The present investigation led to the identification of potent G-quadruplex stabilizers with high selectivity over duplex DNA and preference for one G-quadruplex topology over others. Among them, selected derivatives have been shown to trap G-quadruplex structures in the nucleus of cancer cells. Interestingly, this behavior correlates with efficient cytotoxic activity in human osteosarcoma and colon carcinoma cells.
Collapse
Affiliation(s)
- Jussara Amato
- Department of Pharmacy, University of Naples "Federico II" , via D. Montesano 49, 80131 Napoli, Italy
| | - Rita Morigi
- Department of Pharmacy and Biotechnology, University of Bologna , 40126 Bologna, Italy
| | - Bruno Pagano
- Department of Pharmacy, University of Naples "Federico II" , via D. Montesano 49, 80131 Napoli, Italy
| | - Alessia Pagano
- Department of Pharmacy, University of Naples "Federico II" , via D. Montesano 49, 80131 Napoli, Italy
| | - Stephan Ohnmacht
- UCL School of Pharmacy, University College London , London WC1N 1AX, U.K
| | - Alessio De Magis
- Department of Pharmacy and Biotechnology, University of Bologna , 40126 Bologna, Italy
| | - Yee-Peng Tiang
- Department of Pharmacy and Biotechnology, University of Bologna , 40126 Bologna, Italy
| | - Giovanni Capranico
- Department of Pharmacy and Biotechnology, University of Bologna , 40126 Bologna, Italy
| | - Alessandra Locatelli
- Department of Pharmacy and Biotechnology, University of Bologna , 40126 Bologna, Italy
| | - Alessandra Graziadio
- Department of Pharmacy and Biotechnology, University of Bologna , 40126 Bologna, Italy
| | - Alberto Leoni
- Department of Pharmacy and Biotechnology, University of Bologna , 40126 Bologna, Italy
| | - Mirella Rambaldi
- Department of Pharmacy and Biotechnology, University of Bologna , 40126 Bologna, Italy
| | - Ettore Novellino
- Department of Pharmacy, University of Naples "Federico II" , via D. Montesano 49, 80131 Napoli, Italy
| | - Stephen Neidle
- UCL School of Pharmacy, University College London , London WC1N 1AX, U.K
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples "Federico II" , via D. Montesano 49, 80131 Napoli, Italy
| |
Collapse
|
105
|
Betzer JF, Nuter F, Chtchigrovsky M, Hamon F, Kellermann G, Ali S, Calméjane MA, Roque S, Poupon J, Cresteil T, Teulade-Fichou MP, Marinetti A, Bombard S. Linking of Antitumor trans NHC-Pt(II) Complexes to G-Quadruplex DNA Ligand for Telomeric Targeting. Bioconjug Chem 2016; 27:1456-70. [PMID: 27115175 DOI: 10.1021/acs.bioconjchem.6b00079] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
G-quadruplex structures (G4) are promising anticancerous targets. A great number of small molecules targeting these structures have already been identified through biophysical methods. In cellulo, some of them are able to target either telomeric DNA and/or some sequences involved in oncogene promotors, both resulting in cancer cell death. However, only a few of them are able to bind to these structures G4 irreversibly. Here we combine within the same molecule the G4-binding agent PDC (pyridodicarboxamide) with a N-heterocyclic carbene-platinum complex NHC-Pt already identified for its antitumor properties. The resulting conjugate platinum complex NHC-Pt-PDC stabilizes strongly G-quadruplex structures in vitro, with affinity slightly affected as compared to PDC. In addition, we show that the new conjugate binds preferentially and irreversibly the quadruplex form of the human telomeric sequence with a profile in a way different from that of NHC-Pt thereby indicating that the platination reaction is oriented by stacking of the PDC moiety onto the G4-structure. In cellulo, NHC-Pt-PDC induces a significant loss of TRF2 from telomeres that is considerably more important than the effect of its two components alone, PDC and NHC-Pt, respectively.
Collapse
Affiliation(s)
- Jean-François Betzer
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Sud, Université Paris-Saclay , 1, av. de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Frédérick Nuter
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Sud, Université Paris-Saclay , 1, av. de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Mélanie Chtchigrovsky
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Sud, Université Paris-Saclay , 1, av. de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Florian Hamon
- CNRS UMR9187/INSERM U1196, Institut Curie, Centre Universitaire Paris XI , Bâtiments 110-112, 91405 Orsay, France
| | - Guillaume Kellermann
- INSERM UMR-S-1007, Université Paris Descartes , 45, rue des Saints Pères, 75270 Paris, France
| | - Samar Ali
- INSERM UMR-S-1007, Université Paris Descartes , 45, rue des Saints Pères, 75270 Paris, France
| | - Marie-Ange Calméjane
- INSERM UMR-S-1007, Université Paris Descartes , 45, rue des Saints Pères, 75270 Paris, France
| | - Sylvain Roque
- INSERM UMR-S-1007, Université Paris Descartes , 45, rue des Saints Pères, 75270 Paris, France
| | - Joël Poupon
- Laboratoire de Toxicologie Biologique, Hôpital Lariboisière , 2 rue Ambroise Paré, 75475 Paris, France
| | - Thierry Cresteil
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Sud, Université Paris-Saclay , 1, av. de la Terrasse, 91198 Gif-sur-Yvette, France.,Université Paris-Sud d'Innovation Thérapeutique , 5 rue J.B. Clément, 92290 Châtenay-Malabry, France
| | - Marie-Paule Teulade-Fichou
- CNRS UMR9187/INSERM U1196, Institut Curie, Centre Universitaire Paris XI , Bâtiments 110-112, 91405 Orsay, France
| | - Angela Marinetti
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Sud, Université Paris-Saclay , 1, av. de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Sophie Bombard
- CNRS UMR9187/INSERM U1196, Institut Curie, Centre Universitaire Paris XI , Bâtiments 110-112, 91405 Orsay, France.,INSERM UMR-S-1007, Université Paris Descartes , 45, rue des Saints Pères, 75270 Paris, France
| |
Collapse
|
106
|
Terenzi A, Lötsch D, van Schoonhoven S, Roller A, Kowol CR, Berger W, Keppler BK, Barone G. Another step toward DNA selective targeting: Ni(II) and Cu(II) complexes of a Schiff base ligand able to bind gene promoter G-quadruplexes. Dalton Trans 2016; 45:7758-67. [PMID: 27054617 PMCID: PMC5048337 DOI: 10.1039/c6dt00648e] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 04/01/2016] [Indexed: 12/31/2022]
Abstract
DNA G-rich sequences are able to form four-stranded structures organized in stacked guanine tetrads. These structures, called G-quadruplexes, were found to have an important role in the regulation of oncogenes expression and became, for such a reason, appealing targets for anticancer drugs. Aiming at finding selective G-quadruplex binders, we have designed, synthesized and characterized a new water soluble Salen-like Schiff base ligand and its Ni(II) and Cu(II) metal complexes. UV-Vis, circular dichroism and FRET measurements indicated that the nickel complex can stabilize oncogene promoter G-quadruplexes with high selectivity, presenting no interactions with duplex DNA at all. The same compound exhibited dose-dependent cytotoxic activity in MCF-7 breast cancer cells when combined with lipofectamine as lipophilic carrier.
Collapse
Affiliation(s)
- Alessio Terenzi
- Institute of Inorganic Chemistry, University of Vienna, Waehringerstr. 42, A-1090 Vienna, Austria. and Research Platform "Translational Cancer Therapy Research", University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Daniela Lötsch
- Department of Medicine I, Institute of Cancer Research and Comprehensive Cancer Center, Medical University Vienna, Borschkegasse 8a, A-1090 Vienna, Austria
| | - Sushilla van Schoonhoven
- Department of Medicine I, Institute of Cancer Research and Comprehensive Cancer Center, Medical University Vienna, Borschkegasse 8a, A-1090 Vienna, Austria
| | - Alexander Roller
- Institute of Inorganic Chemistry, University of Vienna, Waehringerstr. 42, A-1090 Vienna, Austria.
| | - Christian R Kowol
- Institute of Inorganic Chemistry, University of Vienna, Waehringerstr. 42, A-1090 Vienna, Austria. and Research Platform "Translational Cancer Therapy Research", University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Walter Berger
- Research Platform "Translational Cancer Therapy Research", University of Vienna and Medical University of Vienna, Vienna, Austria and Department of Medicine I, Institute of Cancer Research and Comprehensive Cancer Center, Medical University Vienna, Borschkegasse 8a, A-1090 Vienna, Austria
| | - Bernhard K Keppler
- Institute of Inorganic Chemistry, University of Vienna, Waehringerstr. 42, A-1090 Vienna, Austria. and Research Platform "Translational Cancer Therapy Research", University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Giampaolo Barone
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Viale delle Scienze, Edificio 17, 90128 Palermo, Italy.
| |
Collapse
|
107
|
Sabharwal NC, Mendoza O, Nicoludis JM, Ruan T, Mergny JL, Yatsunyk LA. Investigation of the interactions between Pt(II) and Pd(II) derivatives of 5,10,15,20-tetrakis (N-methyl-4-pyridyl) porphyrin and G-quadruplex DNA. J Biol Inorg Chem 2016; 21:227-39. [PMID: 26748794 PMCID: PMC4801998 DOI: 10.1007/s00775-015-1325-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 12/16/2015] [Indexed: 01/26/2023]
Abstract
G-quadruplexes are non-canonical DNA structures formed by guanine-rich DNA sequences that are implicated in cancer and aging. Understanding how small molecule ligands interact with quadruplexes is essential both to the development of novel anticancer therapeutics and to the design of new quadruplex-selective probes needed for elucidation of quadruplex biological functions. In this work, UV-visible, fluorescence, and circular dichroism spectroscopies, fluorescence resonance energy transfer (FRET) melting assays, and resonance light scattering were used to investigate how the Pt(II) and Pd(II) derivatives of the well-studied 5,10,15,20-tetrakis(N-methyl-4-pyridyl)porphyrin (TMPyP4) interact with quadruplexes formed by the human telomeric DNA, Tel22, and by the G-rich sequences from oncogene promoters. Our results suggest that Pt- and PdTMPyP4 interact with Tel22 via efficient π-π stacking with a binding affinity of 10(6)-10(7) M(-1). Under porphyrin excess, PtTMPyP4 aggregates using Tel22 as a template; the aggregates reach maximum size at [PtTMPyP4]/[Tel22] ~8 and dissolve at [PtTMPyP4]/[Tel22] ≤ 2. FRET assays reveal that both porphyrins are excellent stabilizers of human telomeric DNA, with stabilization temperature of 30.7 ± 0.6 °C for PtTMPyP4 and 30.9 ± 0.4 °C for PdTMPyP4 at [PtTMPyP4]/[Tel22] = 2 in K(+) buffer, values significantly higher as compared to those for TMPyP4. The porphyrins display modest selectivity for quadruplex vs. duplex DNA, with selectivity ratios of 150 and 330 for Pt- and PdTMPyP4, respectively. This selectivity was confirmed by observed 'light switch' effect: fluorescence of PtTMPyP4 increases significantly in the presence of a variety of DNA secondary structures, yet the strongest effect is produced by quadruplex DNA.
Collapse
Affiliation(s)
- Navin C Sabharwal
- Department of Chemistry and Biochemistry, Swarthmore College, 500 College Ave., Swarthmore, PA, 19081, USA
- Lerner College of Medicine, Cleveland Clinic, 9500 Euclid Ave., Cleveland, OH, 44195, USA
| | - Oscar Mendoza
- INSERM U1212, CNRS, 33600, Pessac, France
- Université de Bordeaux, Bordeaux, France
| | - John M Nicoludis
- Department of Chemistry and Biochemistry, Swarthmore College, 500 College Ave., Swarthmore, PA, 19081, USA
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St., Cambridge, MA, 02138, USA
| | - Thomas Ruan
- Department of Chemistry and Biochemistry, Swarthmore College, 500 College Ave., Swarthmore, PA, 19081, USA
| | - Jean-Louis Mergny
- INSERM U1212, CNRS, 33600, Pessac, France
- Université de Bordeaux, Bordeaux, France
| | - Liliya A Yatsunyk
- Department of Chemistry and Biochemistry, Swarthmore College, 500 College Ave., Swarthmore, PA, 19081, USA.
| |
Collapse
|
108
|
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
| |
Collapse
|
109
|
Kaserer T, Rigo R, Schuster P, Alcaro S, Sissi C, Schuster D. Optimized Virtual Screening Workflow for the Identification of Novel G-Quadruplex Ligands. J Chem Inf Model 2016; 56:484-500. [PMID: 26841201 DOI: 10.1021/acs.jcim.5b00658] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
G-quadruplexes, alternative DNA secondary structures present in telomeres, emerge as promising targets for the treatment of cancer, because they prevent telomere elongation and accordingly cell proliferation. Within this study, theoretically validated pharmacophore- and shape-based models as well as a theoretically validated docking protocol were generated and applied in parallel for virtual screening and the identification of novel G-quadruplex ligands. Top-ranked hits retrieved with all methods independently and in addition in a consensus approach were selected for biological testing. Of the 32 tested virtual hits seven selectively stabilized G-quadruplexes over duplex DNA in the fluorescence melting assay. For the five most active compounds, chemically closely related analogues were collected and subjected to in vitro analysis. Thereby, seven further novel G-quadruplex ligands could be identified. These molecules do not only represent novel scaffolds, but some of them are in addition even more potent G-quadruplex stabilizers than the established reference compound berberine. This study proposes an optimized in silico workflow for the identification of novel G-quadruplex stabilizers, which can also be applied in future studies. In addition, structurally novel and promising lead candidates with strong and selective G-quadruplex stabilizing properties are reported.
Collapse
Affiliation(s)
- Teresa Kaserer
- Computer-Aided Molecular Design Group, Institute of Pharmacy/Pharmaceutical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck , Innrain 80-82, 6020 Innsbruck, Austria
| | - Riccardo Rigo
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova , via Marzolo 5, 35131 Padova, Italy
| | - Philipp Schuster
- Computer-Aided Molecular Design Group, Institute of Pharmacy/Pharmaceutical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck , Innrain 80-82, 6020 Innsbruck, Austria
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute, Università "Magna Graecia" di Catanzaro , Campus "S. Venuta", Viale Europa, 88100 Catanzaro, Italy
| | - Claudia Sissi
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova , via Marzolo 5, 35131 Padova, Italy
| | - Daniela Schuster
- Computer-Aided Molecular Design Group, Institute of Pharmacy/Pharmaceutical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck , Innrain 80-82, 6020 Innsbruck, Austria
| |
Collapse
|
110
|
Abstract
G-quadruplexes are non-canonical secondary structures found in guanine rich regions of DNA and RNA. Reports have indicated the wide occurrence of RNA G-quadruplexes across the transcriptome in various regions of mRNAs and non-coding RNAs. RNA G-quadruplexes have been implicated in playing an important role in translational regulation, mRNA processing events and maintenance of chromosomal end integrity. In this review, we summarize the structural and functional aspects of RNA G-quadruplexes with emphasis on recent progress to understand the protein/trans factors binding these motifs. With the revelation of the importance of these secondary structures as regulatory modules in biology, we have also evaluated the various advancements towards targeting these structures and the challenges associated with them. Apart from this, numerous potential applications of this secondary motif have also been discussed.
Collapse
Affiliation(s)
- Prachi Agarwala
- Proteomics and Structural Biology Unit, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India.
| | | | | |
Collapse
|
111
|
Shivalingam A, Vyšniauskas A, Albrecht T, White AJP, Kuimova MK, Vilar R. Trianguleniums as Optical Probes for G-Quadruplexes: A Photophysical, Electrochemical, and Computational Study. Chemistry 2016; 22:4129-39. [PMID: 26880483 PMCID: PMC4991273 DOI: 10.1002/chem.201504099] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Indexed: 01/27/2023]
Abstract
Nucleic acids can adopt non-duplex topologies, such as G-quadruplexes in vitro. Yet it has been challenging to establish their existence and function in vivo due to a lack of suitable tools. Recently, we identified the triangulenium compound DAOTA-M2 as a unique fluorescence probe for such studies. This probe's emission lifetime is highly dependent on the topology of the DNA it interacts with opening up the possibility of carrying out live-cell imaging studies. Herein, we describe the origin of its fluorescence selectivity for G-quadruplexes. Cyclic voltammetry predicts that the appended morpholino groups can act as intra- molecular photo-induced electron transfer (PET) quenchers. Photophysical studies show that a delicate balance between this effect and inter-molecular PET with nucleobases is key to the overall fluorescence enhancement observed upon nucleic acid binding. We utilised computational modelling to demonstrate a conformational dependence of intra-molecular PET. Finally, we performed orthogonal studies with a triangulenium compound, in which the morpholino groups were removed, and demonstrated that this change inverts triangulenium fluorescence selectivity from G-quadruplex to duplex DNA, thus highlighting the importance of fine tuning the molecular structure not only for target affinity, but also for fluorescence response.
Collapse
Affiliation(s)
- Arun Shivalingam
- Department of Chemistry, Imperial College London, South Kensington, London, SW7 2AZ, UK
| | - Aurimas Vyšniauskas
- Department of Chemistry, Imperial College London, South Kensington, London, SW7 2AZ, UK
| | - Tim Albrecht
- Department of Chemistry, Imperial College London, South Kensington, London, SW7 2AZ, UK
| | - Andrew J P White
- Department of Chemistry, Imperial College London, South Kensington, London, SW7 2AZ, UK
| | - Marina K Kuimova
- Department of Chemistry, Imperial College London, South Kensington, London, SW7 2AZ, UK.
| | - Ramon Vilar
- Department of Chemistry, Imperial College London, South Kensington, London, SW7 2AZ, UK.
| |
Collapse
|
112
|
Abstract
Quadruplex-forming sequences are widely prevalent in human and other genomes, including bacterial ones. These sequences are over-represented in eukaryotic telomeres, promoters, and 5' untranslated regions. They can form quadruplex structures, which may be transient in many situations in normal cells since they can be effectively resolved by helicase action. Mutated helicases in cancer cells are unable to unwind quadruplexes, which are impediments to transcription, translation, or replication, depending on their location within a particular gene. Small molecules that can stabilize quadruplex structures augment these effects and produce cell and proliferation growth inhibition. This article surveys the chemical biology of quadruplexes. It critically examines the major classes of quadruplex-binding small molecules that have been developed to date and the various approaches to discovering selective agents. The challenges of requiring (and achieving) small-molecule targeted selectivity for a particular quadruplex are discussed in relation to the potential of these small molecules as clinically useful therapeutic agents.
Collapse
Affiliation(s)
- Stephen Neidle
- UCL School of Pharmacy, University College London , 29-39 Brunswick Square, London WC1N 1AX, U.K
| |
Collapse
|
113
|
Pavan Kumar Y, Saha P, Saha D, Bessi I, Schwalbe H, Chowdhury S, Dash J. Fluorescent Dansyl-Guanosine Conjugates that Bindc-MYCPromoter G-Quadruplex and Downregulatec-MYCExpression. Chembiochem 2016; 17:388-93. [DOI: 10.1002/cbic.201500631] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Indexed: 01/15/2023]
Affiliation(s)
- Y. Pavan Kumar
- Department of Organic Chemistry; Indian Association for the Cultivation of Science; Jadavpur University; 2A ∞ B Raja S. C. Mullick Road Jadavpur Kolkata 700032 India
| | - Puja Saha
- Department of Organic Chemistry; Indian Association for the Cultivation of Science; Jadavpur University; 2A ∞ B Raja S. C. Mullick Road Jadavpur Kolkata 700032 India
| | - Dhurjhoti Saha
- CSIR-Institute of Genomics and Integrative Biology; Mathura Road Delhi 110 025 India
| | - Irene Bessi
- Institute of Organic Chemistry and Chemical Biology; Goethe University Frankfurt; and Center for Biomolecular Magnetic Resonance; Max-von-Laue Strasse 7 60438 Frankfurt am Main Germany
| | - Harald Schwalbe
- Institute of Organic Chemistry and Chemical Biology; Goethe University Frankfurt; and Center for Biomolecular Magnetic Resonance; Max-von-Laue Strasse 7 60438 Frankfurt am Main Germany
| | - Shantanu Chowdhury
- CSIR-Institute of Genomics and Integrative Biology; Mathura Road Delhi 110 025 India
| | - Jyotirmayee Dash
- Department of Organic Chemistry; Indian Association for the Cultivation of Science; Jadavpur University; 2A ∞ B Raja S. C. Mullick Road Jadavpur Kolkata 700032 India
| |
Collapse
|
114
|
Zhou JK, Yang DY, Sheu SY. The molecular mechanism of ligand unbinding from the human telomeric G-quadruplex by steered molecular dynamics and umbrella sampling simulations. Phys Chem Chem Phys 2016; 17:12857-69. [PMID: 25908641 DOI: 10.1039/c5cp00378d] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
G-quadruplexes are attractive drug targets in cancer therapy. Understanding the mechanisms of the binding-unbinding processes involving biomolecules and molecular recognition is essential for designing new drugs of G-quadruplexes. We performed steered molecular dynamics and umbrella sampling simulations to investigate the molecular mechanism and kinetics of ligand unbinding processes of the basket, propeller and hybrid G-quadruplex structures. Our studies of the ligand charge effect showed that Coulomb interaction plays a significant role in stabilizing the G-quadruplex structure in the unbinding process. The free energy profiles were carried out and the free energy changes associated with the unbinding process were computed quantitatively, whereas these results could help to identify accessible binding sites and transient interactions. The dynamics of the hydration shell water molecules around the G-quadruplex exhibits an abnormal Brownian motion, and the thickness and free energy of the hydration shell were estimated. A two-step relaxation scheme was theoretically developed to describe the kinetic reaction of BMVC and G-quadruplex interactions. Our computed results fall in a reasonable range of experimental data. The present investigation could be helpful in the structure-based drug design.
Collapse
Affiliation(s)
- Jia-Kai Zhou
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 112, Taiwan.
| | | | | |
Collapse
|
115
|
Bonnat L, Dejeu J, Bonnet H, Génnaro B, Jarjayes O, Thomas F, Lavergne T, Defrancq E. Templated Formation of Discrete RNA and DNA:RNA Hybrid G-Quadruplexes and Their Interactions with Targeting Ligands. Chemistry 2016; 22:3139-47. [PMID: 26808196 DOI: 10.1002/chem.201504351] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Indexed: 11/10/2022]
Abstract
G-rich RNA and DNA oligonucleotides derived from the human telomeric sequence were assembled onto addressable cyclopeptide platforms through oxime ligations and copper-catalyzed azide-alkyne cycloaddition (CuAAc) reactions. The resulting conjugates were able to fold into highly stable RNA and DNA:RNA hybrid G-quadruplex (G4) architectures as demonstrated by UV, circular dichroism (CD), and NMR spectroscopic analysis. Whereas rationally designed parallel RNA and DNA:RNA hybrid G4 topologies could be obtained, we could not force the formation of an antiparallel RNA G4 structure, thus supporting the idea that this topology is strongly disfavored. The binding affinities of four representative G4 ligands toward the discrete RNA and DNA:RNA hybrid G4 topologies were compared to the one obtained with the corresponding DNA G4 structure. Surface plasmon resonance (SPR) binding analysis suggests that the accessibility to G4 recognition elements is different among the three structures and supports the idea that G4 ligands might be shaped to achieve structure selectivity in a biological context.
Collapse
Affiliation(s)
- Laureen Bonnat
- Université Grenoble Alpes, Département de Chimie Moléculaire, UMR-5250, 38000, Grenoble, France.,CNRS, 38000, Grenoble, France
| | - Jérôme Dejeu
- Université Grenoble Alpes, Département de Chimie Moléculaire, UMR-5250, 38000, Grenoble, France.,CNRS, 38000, Grenoble, France
| | - Hugues Bonnet
- Université Grenoble Alpes, Département de Chimie Moléculaire, UMR-5250, 38000, Grenoble, France.,CNRS, 38000, Grenoble, France
| | - Béatrice Génnaro
- Université Grenoble Alpes, Département de Chimie Moléculaire, UMR-5250, 38000, Grenoble, France.,CNRS, 38000, Grenoble, France
| | - Olivier Jarjayes
- Université Grenoble Alpes, Département de Chimie Moléculaire, UMR-5250, 38000, Grenoble, France.,CNRS, 38000, Grenoble, France
| | - Fabrice Thomas
- Université Grenoble Alpes, Département de Chimie Moléculaire, UMR-5250, 38000, Grenoble, France.,CNRS, 38000, Grenoble, France
| | - Thomas Lavergne
- Université Grenoble Alpes, Département de Chimie Moléculaire, UMR-5250, 38000, Grenoble, France. .,CNRS, 38000, Grenoble, France.
| | - Eric Defrancq
- Université Grenoble Alpes, Département de Chimie Moléculaire, UMR-5250, 38000, Grenoble, France. .,CNRS, 38000, Grenoble, France.
| |
Collapse
|
116
|
Abstract
This paper highlights recent developments in the design and construction of functional materials such as supramolecular hydrogels and ion channels using a guanine motif as a self-assembling building block.
Collapse
Affiliation(s)
- Jyotirmayee Dash
- Department of Organic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India.
| | | |
Collapse
|
117
|
Felsenstein KM, Saunders LB, Simmons JK, Leon E, Calabrese DR, Zhang S, Michalowski A, Gareiss P, Mock BA, Schneekloth JS. Small Molecule Microarrays Enable the Identification of a Selective, Quadruplex-Binding Inhibitor of MYC Expression. ACS Chem Biol 2016; 11:139-48. [PMID: 26462961 PMCID: PMC4719142 DOI: 10.1021/acschembio.5b00577] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
![]()
The
transcription factor MYC plays a pivotal role in cancer initiation,
progression, and maintenance. However, it has proven difficult to
develop small molecule inhibitors of MYC. One attractive route to
pharmacological inhibition of MYC has been the prevention of its expression
through small molecule-mediated stabilization of the G-quadruplex
(G4) present in its promoter. Although molecules that bind globally
to quadruplex DNA and influence gene expression are well-known, the
identification of new chemical scaffolds that selectively modulate
G4-driven genes remains a challenge. Here, we report an approach for
the identification of G4-binding small molecules using small molecule
microarrays (SMMs). We use the SMM screening platform to identify
a novel G4-binding small molecule that inhibits MYC expression in
cell models, with minimal impact on the expression of other G4-associated
genes. Surface plasmon resonance (SPR) and thermal melt assays demonstrated
that this molecule binds reversibly to the MYC G4 with single digit
micromolar affinity, and with weaker or no measurable binding to other
G4s. Biochemical and cell-based assays demonstrated that the compound
effectively silenced MYC transcription and translation via a G4-dependent
mechanism of action. The compound induced G1 arrest and was selectively
toxic to MYC-driven cancer cell lines containing the G4 in the promoter
but had minimal effects in peripheral blood mononucleocytes or a cell
line lacking the G4 in its MYC promoter. As a measure of selectivity,
gene expression analysis and qPCR experiments demonstrated that MYC
and several MYC target genes were downregulated upon treatment with
this compound, while the expression of several other G4-driven genes
was not affected. In addition to providing a novel chemical scaffold
that modulates MYC expression through G4 binding, this work suggests
that the SMM screening approach may be broadly useful as an approach
for the identification of new G4-binding small molecules.
Collapse
Affiliation(s)
- Kenneth M. Felsenstein
- Laboratory
of Cancer Biology and Genetics, National Cancer Institute, Building
37, Room 3146, Bethesda, Maryland 20892-4258, United States
- NCI/JHU Molecular Targets and Drug Discovery Program, Baltimore, Maryland, United States
| | - Lindsey B. Saunders
- Chemical
Biology Laboratory, National Cancer Institute, Building 376, Room 225C, P.O. Box B, Frederick, Maryland 21702-1201, United States
| | - John K. Simmons
- Laboratory
of Cancer Biology and Genetics, National Cancer Institute, Building
37, Room 3146, Bethesda, Maryland 20892-4258, United States
| | - Elena Leon
- Laboratory
of Cancer Biology and Genetics, National Cancer Institute, Building
37, Room 3146, Bethesda, Maryland 20892-4258, United States
- NCI/JHU Molecular Targets and Drug Discovery Program, Baltimore, Maryland, United States
| | - David R. Calabrese
- Chemical
Biology Laboratory, National Cancer Institute, Building 376, Room 225C, P.O. Box B, Frederick, Maryland 21702-1201, United States
| | - Shuling Zhang
- Laboratory
of Cancer Biology and Genetics, National Cancer Institute, Building
37, Room 3146, Bethesda, Maryland 20892-4258, United States
| | - Aleksandra Michalowski
- Laboratory
of Cancer Biology and Genetics, National Cancer Institute, Building
37, Room 3146, Bethesda, Maryland 20892-4258, United States
| | - Peter Gareiss
- Yale Center for Molecular Discovery, West Haven, Connecticut, United States
| | - Beverly A. Mock
- Laboratory
of Cancer Biology and Genetics, National Cancer Institute, Building
37, Room 3146, Bethesda, Maryland 20892-4258, United States
| | - John S. Schneekloth
- Chemical
Biology Laboratory, National Cancer Institute, Building 376, Room 225C, P.O. Box B, Frederick, Maryland 21702-1201, United States
| |
Collapse
|
118
|
Galer P, Wang B, Šket P, Plavec J. Reversible pH Switch of Two-Quartet G-Quadruplexes Formed by Human Telomere. Angew Chem Int Ed Engl 2016; 55:1993-7. [PMID: 26836334 DOI: 10.1002/anie.201507569] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 11/04/2015] [Indexed: 12/30/2022]
Abstract
A four-repeat human telomere DNA sequence without the 3'-end guanine, d[TAGGG(TTAGGG)2 TTAGG] (htel1-ΔG23) has been found to adopt two distinct two G-quartet antiparallel basket-type G-quadruplexes, TD and KDH(+) in presence of KCl. NMR, CD, and UV spectroscopy have demonstrated that topology of KDH(+) form is distinctive with unique protonated T18⋅A20(+) ⋅G5 base triple and other capping structural elements that provide novel insight into structural polymorphism and heterogeneity of G-quadruplexes in general. Specific stacking interactions amongst two G-quartets flanking base triples and base pairs in TD and KDH(+) forms are reflected in 10 K higher thermal stability of KDH(+) . Populations of TD and KDH(+) forms are controlled by pH. The (de)protonation of A20 is the key for pH driven structural transformation of htel1-ΔG23. Reversibility offers possibilities for its utilization as a conformational switch within different compartments of living cell enabling specific ligand and protein interactions.
Collapse
Affiliation(s)
- Petra Galer
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, Ljubljana, Slovenia
| | - Baifan Wang
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, Ljubljana, Slovenia
| | - Primož Šket
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, Ljubljana, Slovenia. .,EN-FIST Center of Excellence, Trg OF 13, 1000, Ljubljana, Slovenia.
| | - Janez Plavec
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, Ljubljana, Slovenia. .,EN-FIST Center of Excellence, Trg OF 13, 1000, Ljubljana, Slovenia. .,Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, Ljubljana, Slovenia.
| |
Collapse
|
119
|
Galer P, Wang B, Šket P, Plavec J. Reversible pH Switch of Two-Quartet G-Quadruplexes Formed by Human Telomere. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201507569] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Petra Galer
- Slovenian NMR Center; National Institute of Chemistry; Hajdrihova 19 Ljubljana Slovenia
| | - Baifan Wang
- Slovenian NMR Center; National Institute of Chemistry; Hajdrihova 19 Ljubljana Slovenia
| | - Primož Šket
- Slovenian NMR Center; National Institute of Chemistry; Hajdrihova 19 Ljubljana Slovenia
- EN-FIST Center of Excellence; Trg OF 13 1000 Ljubljana Slovenia
| | - Janez Plavec
- Slovenian NMR Center; National Institute of Chemistry; Hajdrihova 19 Ljubljana Slovenia
- EN-FIST Center of Excellence; Trg OF 13 1000 Ljubljana Slovenia
- Faculty of Chemistry and Chemical Technology; University of Ljubljana; Večna pot 113 Ljubljana Slovenia
| |
Collapse
|
120
|
Bhat J, Chatterjee S. Skeleton selectivity in complexation of chelerythrine and chelerythrine-like natural plant alkaloids with the G-quadruplex formed at the promoter of c-MYC oncogene: in silico exploration. RSC Adv 2016. [DOI: 10.1039/c6ra04671a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Chelerythrine binds at the 5′ end and arrests the G-quadruplex formed in the promoter region ofc-MYConcogene thus restrict thec-MYCexpression. Position of methoxy group over the core skeleton of chelerythrine determines the binding pattern of ligand.
Collapse
Affiliation(s)
- Jyotsna Bhat
- Department of Biophysics
- Bose Institute
- Kolkata
- India
| | | |
Collapse
|
121
|
Pany SPP, Bommisetti P, Diveshkumar KV, Pradeepkumar PI. Benzothiazole hydrazones of furylbenzamides preferentially stabilize c-MYC and c-KIT1 promoter G-quadruplex DNAs. Org Biomol Chem 2016; 14:5779-93. [DOI: 10.1039/c6ob00138f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The stabilization of G-quadruplex DNA structures by using small molecule ligands having simple structural scaffolds has the potential to be harnessed for developing next generation anticancer agents.
Collapse
Affiliation(s)
| | - Praneeth Bommisetti
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
| | - K. V. Diveshkumar
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
| | - P. I. Pradeepkumar
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
| |
Collapse
|
122
|
Chauhan A, Paladhi S, Debnath M, Dash J. Selective recognition of c-MYC G-quadruplex DNA using prolinamide derivatives. Org Biomol Chem 2016; 14:5761-7. [DOI: 10.1039/c6ob00177g] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein we report the design, synthesis, biophysical and biological evaluation of triazole containing prolinamide derivatives as selectivec-MYCG-quadruplex binding ligands.
Collapse
Affiliation(s)
- Ajay Chauhan
- Department of Chemical Sciences
- Indian Institute of Science Education and Research Kolkata
- Mohanpur
- India
| | - Sushovan Paladhi
- Department of Chemical Sciences
- Indian Institute of Science Education and Research Kolkata
- Mohanpur
- India
- Department of Organic Chemistry
| | - Manish Debnath
- Department of Organic Chemistry
- Indian Association for the Cultivation of Science
- Kolkata-700032
- India
| | - Jyotirmayee Dash
- Department of Chemical Sciences
- Indian Institute of Science Education and Research Kolkata
- Mohanpur
- India
- Department of Organic Chemistry
| |
Collapse
|
123
|
Spinello A, Barone G, Grunenberg J. Molecular recognition of naphthalene diimide ligands by telomeric quadruplex-DNA: the importance of the protonation state and mediated hydrogen bonds. Phys Chem Chem Phys 2016; 18:2871-7. [DOI: 10.1039/c5cp05576h] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
How important are mediated hydrogen bonds in terms of molecular recognition? Compliance Constants (relaxed force constants) give the answer.
Collapse
Affiliation(s)
- A. Spinello
- Università di Palermo
- Dipartimento di Scienze e Tecnologie Biologiche
- Chimiche e Farmaceutiche
- Italy
- Istituto Euro-Mediterraneo di Scienza e Tecnologia (IEMEST)
| | - G. Barone
- Università di Palermo
- Dipartimento di Scienze e Tecnologie Biologiche
- Chimiche e Farmaceutiche
- Italy
- Istituto Euro-Mediterraneo di Scienza e Tecnologia (IEMEST)
| | - J. Grunenberg
- Technische Universität Braunschweig
- Institut für Organische Chemie
- Germany
| |
Collapse
|
124
|
Largy E, Mergny JL, Gabelica V. Role of Alkali Metal Ions in G-Quadruplex Nucleic Acid Structure and Stability. Met Ions Life Sci 2016; 16:203-58. [PMID: 26860303 DOI: 10.1007/978-3-319-21756-7_7] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
G-quadruplexes are guanine-rich nucleic acids that fold by forming successive quartets of guanines (the G-tetrads), stabilized by intra-quartet hydrogen bonds, inter-quartet stacking, and cation coordination. This specific although highly polymorphic type of secondary structure deviates significantly from the classical B-DNA duplex. G-quadruplexes are detectable in human cells and are strongly suspected to be involved in a number of biological processes at the DNA and RNA levels. The vast structural polymorphism exhibited by G-quadruplexes, together with their putative biological relevance, makes them attractive therapeutic targets compared to canonical duplex DNA. This chapter focuses on the essential and specific coordination of alkali metal cations by G-quadruplex nucleic acids, and most notably on studies highlighting cation-dependent dissimilarities in their stability, structure, formation, and interconversion. Section 1 surveys G-quadruplex structures and their interactions with alkali metal ions while Section 2 presents analytical methods used to study G-quadruplexes. The influence of alkali cations on the stability, structure, and kinetics of formation of G-quadruplex structures of quadruplexes will be discussed in Sections 3 and 4. Section 5 focuses on the cation-induced interconversion of G-quadruplex structures. In Sections 3 to 5, we will particularly emphasize the comparisons between cations, most often K(+) and Na(+) because of their prevalence in the literature and in cells.
Collapse
Affiliation(s)
- Eric Largy
- ARNA Laboratory, Université Bordeaux, IECB, 2, rue Robert Escarpit, F-33600, Pessac, France.,ARNA Laboratory, INSERM, U869, F-33000, Bordeaux, France
| | - Jean-Louis Mergny
- ARNA Laboratory, Université Bordeaux, IECB, 2, rue Robert Escarpit, F-33600, Pessac, France. .,ARNA Laboratory, INSERM, U869, F-33000, Bordeaux, France.
| | - Valérie Gabelica
- ARNA Laboratory, Université Bordeaux, IECB, 2, rue Robert Escarpit, F-33600, Pessac, France. .,ARNA Laboratory, INSERM, U869, F-33000, Bordeaux, France.
| |
Collapse
|
125
|
Wang MQ, Zhu WX, Song ZZ, Li S, Zhang YZ. A triphenylamine-based colorimetric and fluorescent probe with donor–bridge–acceptor structure for detection of G-quadruplex DNA. Bioorg Med Chem Lett 2015; 25:5672-6. [DOI: 10.1016/j.bmcl.2015.11.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 10/16/2015] [Accepted: 11/04/2015] [Indexed: 11/15/2022]
|
126
|
Duskova K, Sierra S, Arias-Pérez MS, Gude L. Human telomeric G-quadruplex DNA interactions of N-phenanthroline glycosylamine copper(II) complexes. Bioorg Med Chem 2015; 24:33-41. [PMID: 26678174 DOI: 10.1016/j.bmc.2015.11.037] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 11/24/2015] [Accepted: 11/26/2015] [Indexed: 01/12/2023]
Abstract
We report in this article the interactions of five N-(1,10-phenanthrolin-5-yl)-β-glycopyranosylamine copper(II) complexes with G-quadruplex DNA. Specifically, the interactions of these compounds with a human telomeric oligonucleotide have been assessed by fluorescence-based assays (FRET melting and G4-FID), circular dichroism and competitive equilibrium dialysis experiments. The metal complexes bind and stabilize G-quadruplex DNA structures with apparent association constants in the order of 10(4)-10(5)M(-1) and the affinity observed is dependent on the ionic conditions utilized and the specific nature of the carbohydrate moiety tethered to the 1,10-phenanthroline system. The compounds showed only a slight preference to bind G-quadruplex DNA over duplex DNA when the quadruplex DNA was folded in sodium ionic conditions. However, the binding affinity and selectivity, although modest, were notably increased when the G-quadruplex DNA was folded in the presence of potassium metal ions. Moreover, the study points towards a significant contribution of groove and/or loop binding in the recognition mode of quadruplex structures by these non-classical quadruplex ligands. The results reported herein highlight the potential and the versatility of carbohydrate bis-phenanthroline metal-complex conjugates to recognize G-quadruplex DNA structures.
Collapse
Affiliation(s)
- Katerina Duskova
- Departamento de Química Orgánica y Química Inorgánica, Universidad de Alcalá, 28805 Alcalá de Henares (Madrid), Spain
| | - Sara Sierra
- Departamento de Química Orgánica y Química Inorgánica, Universidad de Alcalá, 28805 Alcalá de Henares (Madrid), Spain
| | - María-Selma Arias-Pérez
- Departamento de Química Orgánica y Química Inorgánica, Universidad de Alcalá, 28805 Alcalá de Henares (Madrid), Spain
| | - Lourdes Gude
- Departamento de Química Orgánica y Química Inorgánica, Universidad de Alcalá, 28805 Alcalá de Henares (Madrid), Spain.
| |
Collapse
|
127
|
Chen CH, Hu TH, Huang TC, Chen YL, Chen YR, Cheng CC, Chen CT. Delineation of G-Quadruplex Alkylation Sites Mediated by 3,6-Bis(1-methyl-4-vinylpyridinium iodide)carbazole-Aniline Mustard Conjugates. Chemistry 2015; 21:17379-90. [PMID: 26769627 DOI: 10.1002/chem.201502595] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Indexed: 11/12/2022]
Abstract
A new G-quadruplex (G-4)-directing alkylating agent BMVC-C3M was designed and synthesized to integrate 3,6-bis(1-methyl-4-vinylpyridinium iodide)carbazole (BMVC) with aniline mustard. Various telomeric G-4 structures (hybrid-2 type and antiparallel) and an oncogene promoter, c-MYC (parallel), were constructed to react with BMVC-C3M, yielding 35 % alkylation yield toward G-4 DNA over other DNA categories (<6 %) and high specificity under competition conditions. Analysis of the intact alkylation adducts by electrospray ionization mass spectroscopy (ESI-MS) revealed the stepwise DNA alkylation mechanism of aniline mustard for the first time. Furthermore, the monoalkylation sites and intrastrand cross-linking sites were determined and found to be dependent on G-4 topology based on the results of footprinting analysis in combination with mass spectroscopic techniques and in silico modeling. The results indicated that BMVC-C3M preferentially alkylated at A15 (H26), G12 (H24), and G2 (c-MYC), respectively, as monoalkylated adducts and formed A15-C3M-A21 (H26), G12-C3M-G4 (H24), and G2-C3M-G4/G17 (c-MYC), respectively, as cross-linked dialkylated adducts. Collectively, the stability and site-selective cross-linking capacity of BMVC-C3M provides a credible tool for the structural and functional characterization of G-4 DNAs in biological systems.
Collapse
Affiliation(s)
- Chien-Han Chen
- Department of Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 10617 Taiwan (R.O.C.), Fax: (+886) 2-23636359
| | - Tsung-Hao Hu
- Department of Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 10617 Taiwan (R.O.C.), Fax: (+886) 2-23636359
| | - Tzu-Chiao Huang
- Department of Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 10617 Taiwan (R.O.C.), Fax: (+886) 2-23636359
| | - Ying-Lan Chen
- Agricultural Biotechnology Research Center, Academia Sinica, No. 128, Sec. 2, Academia Road, Taipei, 11529 Taiwan (R.O.C.).,Institute of Plant Biology and Department of Life Science, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 10617 Taiwan (R.O.C.)
| | - Yet-Ran Chen
- Agricultural Biotechnology Research Center, Academia Sinica, No. 128, Sec. 2, Academia Road, Taipei, 11529 Taiwan (R.O.C.)
| | - Chien-Chung Cheng
- Department of Applied Chemistry, Chia-Yi University, No. 300, Xuefu Road, Chiayi City, 60004 Taiwan (R.O.C.), Fax: (+886) 5-2717901.
| | - Chao-Tsen Chen
- Department of Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 10617 Taiwan (R.O.C.), Fax: (+886) 2-23636359.
| |
Collapse
|
128
|
Zizza P, Cingolani C, Artuso S, Salvati E, Rizzo A, D'Angelo C, Porru M, Pagano B, Amato J, Randazzo A, Novellino E, Stoppacciaro A, Gilson E, Stassi G, Leonetti C, Biroccio A. Intragenic G-quadruplex structure formed in the human CD133 and its biological and translational relevance. Nucleic Acids Res 2015; 44:1579-90. [PMID: 26511095 PMCID: PMC4770210 DOI: 10.1093/nar/gkv1122] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 10/14/2015] [Indexed: 11/14/2022] Open
Abstract
Cancer stem cells (CSCs) have been identified in several solid malignancies and are now emerging as a plausible target for drug discovery. Beside the questionable existence of CSCs specific markers, the expression of CD133 was reported to be responsible for conferring CSC aggressiveness. Here, we identified two G-rich sequences localized within the introns 3 and 7 of the CD133 gene able to form G-quadruplex (G4) structures, bound and stabilized by small molecules. We further showed that treatment of patient-derived colon CSCs with G4-interacting agents triggers alternative splicing that dramatically impairs the expression of CD133. Interestingly, this is strongly associated with a loss of CSC properties, including self-renewing, motility, tumor initiation and metastases dissemination. Notably, the effects of G4 stabilization on some of these CSC properties are uncoupled from DNA damage response and are fully recapitulated by the selective interference of the CD133 expression.In conclusion, we provided the first proof of the existence of G4 structures within the CD133 gene that can be pharmacologically targeted to impair CSC aggressiveness. This discloses a class of potential antitumoral agents capable of targeting the CSC subpopulation within the tumoral bulk.
Collapse
Affiliation(s)
- Pasquale Zizza
- Area of Translational Research, Regina Elena National Cancer Institute, via E. Chianesi 53, 00144 Rome, Italy
| | - Chiara Cingolani
- Area of Translational Research, Regina Elena National Cancer Institute, via E. Chianesi 53, 00144 Rome, Italy
| | - Simona Artuso
- Area of Translational Research, Regina Elena National Cancer Institute, via E. Chianesi 53, 00144 Rome, Italy
| | - Erica Salvati
- Area of Translational Research, Regina Elena National Cancer Institute, via E. Chianesi 53, 00144 Rome, Italy
| | - Angela Rizzo
- Area of Translational Research, Regina Elena National Cancer Institute, via E. Chianesi 53, 00144 Rome, Italy
| | - Carmen D'Angelo
- Area of Translational Research, Regina Elena National Cancer Institute, via E. Chianesi 53, 00144 Rome, Italy
| | - Manuela Porru
- Area of Translational Research, Regina Elena National Cancer Institute, via E. Chianesi 53, 00144 Rome, Italy
| | - Bruno Pagano
- Department of Pharmacy, University of Naples 'Federico II', via D. Montesano 49, I-80131 Napoli, Italy
| | - Jussara Amato
- Department of Pharmacy, University of Naples 'Federico II', via D. Montesano 49, I-80131 Napoli, Italy
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples 'Federico II', via D. Montesano 49, I-80131 Napoli, Italy
| | - Ettore Novellino
- Department of Pharmacy, University of Naples 'Federico II', via D. Montesano 49, I-80131 Napoli, Italy
| | - Antonella Stoppacciaro
- Dipartimento di Medicina Clinica e Molecolare, Università 'La Sapienza', piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Eric Gilson
- Institute for Research on Cancer and Aging, Nice (IRCAN), CNRS UMR7284/INSERM U1081, University of Nice, 06107 Nice, France
| | - Giorgio Stassi
- Department of Medical Genetics, Archet 2 Hospital, CHU of Nice, 06202 Nice cedex 3, France
| | - Carlo Leonetti
- Area of Translational Research, Regina Elena National Cancer Institute, via E. Chianesi 53, 00144 Rome, Italy
| | - Annamaria Biroccio
- Area of Translational Research, Regina Elena National Cancer Institute, via E. Chianesi 53, 00144 Rome, Italy
| |
Collapse
|
129
|
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]
|
130
|
Bhowmik D, Fiorillo G, Lombardi P, Suresh Kumar G. Recognition of human telomeric G-quadruplex DNA by berberine analogs: effect of substitution at the 9 and 13 positions of the isoquinoline moiety. J Mol Recognit 2015; 28:722-30. [DOI: 10.1002/jmr.2486] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 05/11/2015] [Accepted: 05/23/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Debipreeta Bhowmik
- Biophysical Chemistry Laboratory; CSIR-Indian Institute of Chemical Biology; Kolkata 700 032 India
| | - Gaetano Fiorillo
- Naxospharma srl; Via G. Di Vittorio 70 20026 Novate Milanese MI Italy
| | - Paolo Lombardi
- Naxospharma srl; Via G. Di Vittorio 70 20026 Novate Milanese MI Italy
| | - G. Suresh Kumar
- Biophysical Chemistry Laboratory; CSIR-Indian Institute of Chemical Biology; Kolkata 700 032 India
| |
Collapse
|
131
|
Bessi I, Jonker HRA, Richter C, Schwalbe H. Involvement of Long-Lived Intermediate States in the Complex Folding Pathway of the Human Telomeric G-Quadruplex. Angew Chem Int Ed Engl 2015; 54:8444-8. [PMID: 26036989 DOI: 10.1002/anie.201502286] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Indexed: 12/21/2022]
Abstract
The energy landscapes of human telomeric G-quadruplexes are complex, and their folding pathways have remained largely unexplored. By using real-time NMR spectroscopy, we investigated the K(+)-induced folding of the human telomeric DNA sequence 5'-TTGGG(TTAGGG)3 A-3'. Three long-lived states were detected during folding: a major conformation (hybrid-1), a previously structurally uncharacterized minor conformation (hybrid-2), and a partially unfolded state. The minor hybrid-2 conformation is formed faster than the more stable hybrid-1 conformation. Equilibration of the two states is slow and proceeds via a partially unfolded intermediate state, which can be described as an ensemble of hairpin-like structures.
Collapse
Affiliation(s)
- Irene Bessi
- Institute for Organic Chemistry and Chemical Biology, Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt/Main, Institution Max-von-Laue-Strasse 7, 60438 Frankfurt (Germany) http://schwalbe.org.chemie.uni-frankfurt.de
| | - Hendrik R A Jonker
- Institute for Organic Chemistry and Chemical Biology, Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt/Main, Institution Max-von-Laue-Strasse 7, 60438 Frankfurt (Germany) http://schwalbe.org.chemie.uni-frankfurt.de
| | - Christian Richter
- Institute for Organic Chemistry and Chemical Biology, Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt/Main, Institution Max-von-Laue-Strasse 7, 60438 Frankfurt (Germany) http://schwalbe.org.chemie.uni-frankfurt.de
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt/Main, Institution Max-von-Laue-Strasse 7, 60438 Frankfurt (Germany) http://schwalbe.org.chemie.uni-frankfurt.de.
| |
Collapse
|
132
|
Bessi I, Jonker HRA, Richter C, Schwalbe H. Involvement of Long-Lived Intermediate States in the Complex Folding Pathway of the Human Telomeric G-Quadruplex. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201502286] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
133
|
Brito H, Martins AC, Lavrado J, Mendes E, Francisco AP, Santos SA, Ohnmacht SA, Kim NS, Rodrigues CMP, Moreira R, Neidle S, Borralho PM, Paulo A. Targeting KRAS Oncogene in Colon Cancer Cells with 7-Carboxylate Indolo[3,2-b]quinoline Tri-Alkylamine Derivatives. PLoS One 2015; 10:e0126891. [PMID: 26024321 PMCID: PMC4449006 DOI: 10.1371/journal.pone.0126891] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 04/08/2015] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND A guanine-rich strand within the promoter of the KRAS gene can fold into an intra-molecular G-quadruplex structure (G4), which has an important role in the regulation of KRAS transcription. We have previously identified indolo[3,2-b]quinolines with a 7-carboxylate group and three alkylamine side chains (IQ3A) as effective G4 stabilizers and promising selective anticancer leads. Herein we investigated the anticancer mechanism of action of these compounds, which we hypothesized due to stabilization of the G4 sequence in the KRAS promoter and subsequent down-regulation of gene expression. METHODOLOGY/PRINCIPAL FINDINGS IQ3A compounds showed greater stabilization of G4 compared to duplex DNA structures and reduced KRAS promoter activity in a dual luciferase reporter assay. Moreover, IQ3A compounds showed high anti-proliferative activity in HCT116 and SW620 colon cancer cells (IC50 < 2.69 μM), without eliciting cell death in non-malignant HEK293T human embryonic kidney, and human colon fibroblasts CCD18co. IQ3A compounds significantly reduced KRAS mRNA and protein steady-state levels at IC50 concentrations, and increased p53 protein steady-state levels and cell death by apoptosis in HCT116 cells (mut KRAS, wt p53). Furthermore, KRAS silencing in HCT116 p53 wild-type (p53(+/+)) and null (p53(-/-)) isogenic cell lines induced a higher level of cell death, and a higher IQ3A-induced cell death in HCT116 p53(+/+) compared to HCT116 p53(-/-). CONCLUSIONS Herein we provide evidence that G4 ligands such as IQ3A compounds can target G4 motifs present in KRAS promoter, down-regulate the expression of the mutant KRAS gene through inhibition of transcription and translation, and induce cell death by apoptosis in colon cancer cell lines. Thus, targeting KRAS at the genomic level with G4 ligands may be a new anticancer therapy strategy for colon cancer.
Collapse
Affiliation(s)
- Hugo Brito
- Cell Function and Therapeutic Targeting Group, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - Ana Cláudia Martins
- Medicinal Chemistry Group, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - João Lavrado
- Medicinal Chemistry Group, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - Eduarda Mendes
- Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - Ana Paula Francisco
- Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - Sofia A. Santos
- Medicinal Chemistry Group, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA 02114, United States of America
| | - Stephan A. Ohnmacht
- UCL School of Pharmacy, University College London, 29/39 Brunswick Square, London WC1N 1AX, United Kingdom
| | - Nam-Soon Kim
- Medical Genomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-333, Republic of Korea
| | - Cecília M. P. Rodrigues
- Cell Function and Therapeutic Targeting Group, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - Rui Moreira
- Medicinal Chemistry Group, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - Stephen Neidle
- UCL School of Pharmacy, University College London, 29/39 Brunswick Square, London WC1N 1AX, United Kingdom
| | - Pedro M. Borralho
- Cell Function and Therapeutic Targeting Group, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
- * E-mail: (PMB); (AP)
| | - Alexandra Paulo
- Medicinal Chemistry Group, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
- * E-mail: (PMB); (AP)
| |
Collapse
|
134
|
Chiorcea-Paquim AM, Pontinha ADR, Eritja R, Lucarelli G, Sparapani S, Neidle S, Oliveira-Brett AM. Atomic Force Microscopy and Voltammetric Investigation of Quadruplex Formation between a Triazole-Acridine Conjugate and Guanine-Containing Repeat DNA Sequences. Anal Chem 2015; 87:6141-9. [DOI: 10.1021/acs.analchem.5b00743] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
| | | | - Ramon Eritja
- Institute for Research in Biomedicine, IQAC−CSIC, CIBER-BBN
Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona, Spain
| | - Genny Lucarelli
- UCL
School of Pharmacy, University College London, London WC1N 1AX, U.K
| | - Silvia Sparapani
- UCL
School of Pharmacy, University College London, London WC1N 1AX, U.K
| | - Stephen Neidle
- UCL
School of Pharmacy, University College London, London WC1N 1AX, U.K
| | | |
Collapse
|
135
|
Simone R, Fratta P, Neidle S, Parkinson GN, Isaacs AM. G-quadruplexes: Emerging roles in neurodegenerative diseases and the non-coding transcriptome. FEBS Lett 2015; 589:1653-68. [PMID: 25979174 DOI: 10.1016/j.febslet.2015.05.003] [Citation(s) in RCA: 164] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 04/29/2015] [Accepted: 05/02/2015] [Indexed: 12/14/2022]
Abstract
G-rich sequences in DNA and RNA have a propensity to fold into stable secondary structures termed G-quadruplexes. G-quadruplex forming sequences are widespread throughout the human genome, within both, protein coding and non-coding genes, and regulatory regions. G-quadruplexes have been implicated in multiple cellular functions including chromatin epigenetic regulation, DNA recombination, transcriptional regulation of gene promoters and enhancers, and translation. Here we will review the evidence for the occurrence of G-quadruplexes both in vitro and in vivo; their role in neurological diseases including G-quadruplex-forming repeat expansions in the C9orf72 gene in frontotemporal dementia and amyotrophic lateral sclerosis and loss of the G-quadruplex binding protein FMRP in the intellectual disability fragile X syndrome. We also review mounting evidence that supports a role for G-quadruplexes in regulating the processing or function of a range of non-coding RNAs. Finally we will highlight current perspectives for therapeutic interventions that target G-quadruplexes.
Collapse
Affiliation(s)
- Roberto Simone
- Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK.
| | - Pietro Fratta
- Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK; Sobell Department of Motor Neuroscience and Movement, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Stephen Neidle
- UCL School of Pharmacy, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Gary N Parkinson
- UCL School of Pharmacy, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Adrian M Isaacs
- Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK.
| |
Collapse
|
136
|
Arba M, Kartasasmita RE, Tjahjono DH. Molecular docking and dynamics simulations on the interaction of cationic porphyrin-anthraquinone hybrids with DNA G-quadruplexes. J Biomol Struct Dyn 2015; 34:427-38. [PMID: 25808513 DOI: 10.1080/07391102.2015.1033015] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
A series of cationic porphyrin-anthraquinone hybrids bearing either pyridine, imidazole, or pyrazole rings at the meso-positions have been investigated for their interaction with DNA G-quadruplexes by employing molecular docking and molecular dynamics simulations. Three types of DNA G-quadruplexes were utilized, which comprise parallel, antiparallel, and mixed hybrid topologies. The porphyrin hybrids have a preference to bind with parallel and mixed hybrid structures compared to the antiparallel structure. This preference arises from the end stacking of porphyrin moiety following G-stem and loop binding of anthraquinone tail, which is not found in the antiparallel due to the presence of diagonal and lateral loops that crowd the G-quartet. The binding to the antiparallel, instead, occurred with poorer affinity through both the loop and wide groove. All sites of porphyrin binding were confirmed by 6 ns molecular dynamics simulation, as well as by the negative value of the total binding free energies that were calculated using the MMPBSA method. Free energy analysis shows that the favorable contribution came from the electrostatic term, which supposedly originated from the interaction of either cationic pyridinium, pyrazole, or imidazole groups and the anionic phosphate backbone, and also from the van der Waals energy, which primarily contributed through end stacking interaction.
Collapse
Affiliation(s)
- Muhammad Arba
- a School of Pharmacy , Bandung Institute of Technology , Jalan Ganesha 10, Bandung 40132 , Indonesia.,b Department of Chemistry , Halu Oleo University , Jl. HEA Mokodompit, Kendari 93232 , Indonesia
| | - Rahmana E Kartasasmita
- a School of Pharmacy , Bandung Institute of Technology , Jalan Ganesha 10, Bandung 40132 , Indonesia
| | - Daryono H Tjahjono
- a School of Pharmacy , Bandung Institute of Technology , Jalan Ganesha 10, Bandung 40132 , Indonesia
| |
Collapse
|
137
|
Marchetti C, Minarini A, Tumiatti V, Moraca F, Parrotta L, Alcaro S, Rigo R, Sissi C, Gunaratnam M, Ohnmacht SA, Neidle S, Milelli A. Macrocyclic naphthalene diimides as G-quadruplex binders. Bioorg Med Chem 2015; 23:3819-30. [PMID: 25935290 DOI: 10.1016/j.bmc.2015.03.076] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 03/05/2015] [Accepted: 03/28/2015] [Indexed: 11/15/2022]
Abstract
The synthesis, biological and molecular modeling evaluation of a series of macrocyclic naphthalene diimides is reported. The present investigation expands on the study of structure-activity relationships of prototype compound 2 by constraining the molecule into a macrocyclic structure with the aim of improving its G-quadruplex binding activity and selectivity. The new derivatives, compounds 4-7 carry spermidine- and spermine-like linkers while in compound 8 the inner basic nitrogen atoms of spermine have been replaced with oxygen atoms. The design strategy has led to potent compounds stabilizing both human telomeric (F21T) and c-KIT2 quadruplex sequences, and high selectivity for quadruplex in comparison to duplex DNA. Antiproliferative effects of the new derivatives 4-8 have been evaluated in a panel of cancer cell lines and all the tested compounds showed activity in the low micromolar or sub-micromolar range of concentrations. In order to rationalize the molecular basis of the DNA G-quadruplex versus duplex recognition preference, docking and molecular dynamics studies have been performed. The computational results support the observation that the main driving force in the recognition is due to electrostatic factors.
Collapse
Affiliation(s)
- Chiara Marchetti
- Department of Pharmacy and Biotechnology, University of Bologna, via Belmeloro 6, 40126 Bologna, Italy; School of Pharmacy, University College London, London WC1N 1AX, UK
| | - Anna Minarini
- Department of Pharmacy and Biotechnology, University of Bologna, via Belmeloro 6, 40126 Bologna, Italy
| | - Vincenzo Tumiatti
- Department for Life Quality Studies, University of Bologna, Rimini Campus, Corso d'Augusto 237, 47921 Rimini, Italy
| | - Federica Moraca
- Dipartimento di Scienze della Salute, Università 'Magna Græcia' di Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Lucia Parrotta
- Dipartimento di Scienze della Salute, Università 'Magna Græcia' di Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute, Università 'Magna Græcia' di Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Riccardo Rigo
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, 35131 Padova, Italy
| | - Claudia Sissi
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, 35131 Padova, Italy
| | | | | | - Stephen Neidle
- School of Pharmacy, University College London, London WC1N 1AX, UK
| | - Andrea Milelli
- Department for Life Quality Studies, University of Bologna, Rimini Campus, Corso d'Augusto 237, 47921 Rimini, Italy.
| |
Collapse
|
138
|
Lavrado J, Brito H, Borralho PM, Ohnmacht SA, Kim NS, Leitão C, Pisco S, Gunaratnam M, Rodrigues CMP, Moreira R, Neidle S, Paulo A. KRAS oncogene repression in colon cancer cell lines by G-quadruplex binding indolo[3,2-c]quinolines. Sci Rep 2015; 5:9696. [PMID: 25853628 PMCID: PMC5382548 DOI: 10.1038/srep09696] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Accepted: 03/05/2015] [Indexed: 01/29/2023] Open
Abstract
KRAS is one of the most frequently mutated oncogenes in human cancer, yet remaining undruggable. To explore a new therapeutic strategy, a library of 5-methyl-indolo[3,2-c]quinoline derivatives (IQc) with a range of alkyldiamine side chains was designed to target DNA and RNA G-quadruplexes (G4) in the promoter and 5′-UTR mRNA of the KRAS gene. Biophysical experiments showed that di-substituted IQc compounds are potent and selective KRAS G4 stabilizers. They preferentially inhibit the proliferation of KRAS mutant cancer cell lines (0.22 < IC50 < 4.80 μM), down-regulate KRAS promoter activity in a luciferase reporter assay, and reduce both KRAS mRNA and p21KRAS steady-state levels in mutant KRAS colon cancer cell lines. Additionally, IQcs induce cancer cell death by apoptosis, explained in part by their capacity to repress KRAS expression. Overall, the results suggest that targeting mutant KRAS at the gene level with G4 binding small molecules is a promising anticancer strategy.
Collapse
Affiliation(s)
- João Lavrado
- Medicinal Chemistry Group, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Portugal, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - Hugo Brito
- Cell Function and Therapeutic Targeting Group, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Portugal, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - Pedro M Borralho
- Cell Function and Therapeutic Targeting Group, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Portugal, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - Stephan A Ohnmacht
- The School of Pharmacy, University College London. 29/39 Brunswick Square, London WC1N 1AX, United Kingdom
| | - Nam-Soon Kim
- Medical Genomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-333, Republic of Korea
| | - Clara Leitão
- The School of Pharmacy, University College London. 29/39 Brunswick Square, London WC1N 1AX, United Kingdom
| | - Sílvia Pisco
- The School of Pharmacy, University College London. 29/39 Brunswick Square, London WC1N 1AX, United Kingdom
| | - Mekala Gunaratnam
- The School of Pharmacy, University College London. 29/39 Brunswick Square, London WC1N 1AX, United Kingdom
| | - Cecília M P Rodrigues
- Cell Function and Therapeutic Targeting Group, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Portugal, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - Rui Moreira
- Medicinal Chemistry Group, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Portugal, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - Stephen Neidle
- The School of Pharmacy, University College London. 29/39 Brunswick Square, London WC1N 1AX, United Kingdom
| | - Alexandra Paulo
- Medicinal Chemistry Group, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Portugal, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| |
Collapse
|
139
|
Lavrado J, Ohnmacht SA, Correia I, Leitão C, Pisco S, Gunaratnam M, Moreira R, Neidle S, Santos DJVAD, Paulo A. Indolo[3,2-c]quinoline G-quadruplex stabilizers: a structural analysis of binding to the human telomeric G-quadruplex. ChemMedChem 2015; 10:836-49. [PMID: 25820698 DOI: 10.1002/cmdc.201500067] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 03/04/2015] [Indexed: 12/22/2022]
Abstract
A library of 5-methylindolo[3,2-c]quinolones (IQc) with various substitution patterns of alkyldiamine side chains were evaluated for G-quadruplex (G4) binding mode and efficiency. Fluorescence resonance energy transfer melting assays showed that IQcs with a positive charge in the heteroaromatic nucleus and two weakly basic side chains are potent and selective human telomeric (HT) and gene promoter G4 stabilizers. Spectroscopic studies with HT G4 as a model showed that an IQc stabilizing complex involves the binding of two IQc molecules (2,9-bis{[3-(diethylamino)propyl]amino}-5-methyl-11H-indolo[3,2-c]quinolin-5-ium chloride, 3 d) per G4 unit, in two non-independent but equivalent binding sites. Molecular dynamics studies suggest that end-stacking of 3 d induces a conformational rearrangement in the G4 structure, driving the binding of a second 3 d ligand to a G4 groove. Modeling studies also suggest that 3 d, with two three-carbon side chains, has the appropriate geometry to participate in direct or water-mediated hydrogen bonding to the phosphate backbone and/or G4 loops, assisted by the terminal nitrogen atoms of the side chains. Additionally, antiproliferative studies showed that IQc compounds 2 d (2-{[3-(diethylamino)propyl]amino}-5-methyl-11H-indolo[3,2-c]quinolin-5-ium chloride) and 3 d are 7- to 12-fold more selective for human malignant cell lines than for nonmalignant fibroblasts.
Collapse
Affiliation(s)
- João Lavrado
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisbon (Portugal).
| | | | | | | | | | | | | | | | | | | |
Collapse
|
140
|
Hou JQ, Chen SB, Zan LP, Ou TM, Tan JH, Luyt LG, Huang ZS. Identification of a selective G-quadruplex DNA binder using a multistep virtual screening approach. Chem Commun (Camb) 2015; 51:198-201. [DOI: 10.1039/c4cc06951j] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A selective G-quadruplex binder was identified using a multistep virtual screening approach by simultaneously taking into account G-quadruplex and duplex DNA.
Collapse
Affiliation(s)
- Jin-Qiang Hou
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou 510006
- China
- London Regional Cancer Program
| | - Shuo-Bin Chen
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou 510006
- China
| | - Li-Peng Zan
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou 510006
- China
| | - Tian-Miao Ou
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou 510006
- China
| | - Jia-Heng Tan
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou 510006
- China
| | - Leonard G. Luyt
- London Regional Cancer Program
- Ontario N6A 4L6
- Canada
- Depts. Oncology, Chemistry, Medical Imaging
- The University of Western Ontario
| | - Zhi-Shu Huang
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou 510006
- China
| |
Collapse
|
141
|
Pagano B, Margarucci L, Zizza P, Amato J, Iaccarino N, Cassiano C, Salvati E, Novellino E, Biroccio A, Casapullo A, Randazzo A. Identification of novel interactors of human telomeric G-quadruplex DNA. Chem Commun (Camb) 2015; 51:2964-7. [DOI: 10.1039/c4cc07231f] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Starting from a chemoproteomic-driven approach, novel human telomeric G-quadruplex binding proteins were identified that directly bind the DNA structure in vitro and colocalize with such structures in cells.
Collapse
Affiliation(s)
- Bruno Pagano
- Department of Pharmacy
- University of Naples “Federico II”
- 80131 Napoli
- Italy
| | | | - Pasquale Zizza
- Experimental Chemotherapy Laboratory
- Regina Elena National Cancer Institute
- 00158 Rome
- Italy
| | - Jussara Amato
- Department of Pharmacy
- University of Naples “Federico II”
- 80131 Napoli
- Italy
| | - Nunzia Iaccarino
- Department of Pharmacy
- University of Naples “Federico II”
- 80131 Napoli
- Italy
| | - Chiara Cassiano
- Department of Pharmacy
- University of Salerno
- 84084 Fisciano
- Italy
| | - Erica Salvati
- Experimental Chemotherapy Laboratory
- Regina Elena National Cancer Institute
- 00158 Rome
- Italy
| | - Ettore Novellino
- Department of Pharmacy
- University of Naples “Federico II”
- 80131 Napoli
- Italy
| | - Annamaria Biroccio
- Experimental Chemotherapy Laboratory
- Regina Elena National Cancer Institute
- 00158 Rome
- Italy
| | | | - Antonio Randazzo
- Department of Pharmacy
- University of Naples “Federico II”
- 80131 Napoli
- Italy
| |
Collapse
|
142
|
Bonnet R, Lavergne T, Gennaro B, Spinelli N, Defrancq E. Construction of anti-parallel G-quadruplexes through sequential templated click. Chem Commun (Camb) 2015; 51:4850-3. [DOI: 10.1039/c4cc09744k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Biologically relevant anti-parallel DNA G-quadruplexes were constrained and stabilised onto addressable cyclopeptide scaffolds through sequential oxime and CuAAc reactions.
Collapse
Affiliation(s)
- Romaric Bonnet
- Université Grenoble Alpes
- Département de Chimie Moléculaire
- F-38000 Grenoble
- France
| | - Thomas Lavergne
- Université Grenoble Alpes
- Département de Chimie Moléculaire
- F-38000 Grenoble
- France
| | - Béatrice Gennaro
- Université Grenoble Alpes
- Département de Chimie Moléculaire
- F-38000 Grenoble
- France
| | - Nicolas Spinelli
- Université Grenoble Alpes
- Département de Chimie Moléculaire
- F-38000 Grenoble
- France
| | - Eric Defrancq
- Université Grenoble Alpes
- Département de Chimie Moléculaire
- F-38000 Grenoble
- France
| |
Collapse
|
143
|
Laguerre A, Chang Y, Pirrotta M, Desbois N, Gros CP, Lesniewska E, Monchaud D. Surface-promoted aggregation of amphiphilic quadruplex ligands drives their selectivity for alternative DNA structures. Org Biomol Chem 2015; 13:7034-9. [DOI: 10.1039/c5ob00692a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The surface-promoted aggregation of a structurally fine-tuned TMPyP4 derivative allows for the straightforward visualization of the quadruplex/ligand interactionsviahigh-speed AFM.
Collapse
Affiliation(s)
| | - Yi Chang
- Institute of Molecular Chemistry
- Dijon
- France
| | | | | | | | | | | |
Collapse
|
144
|
Diveshkumar KV, Sakrikar S, Harikrishna S, Dhamodharan V, Pradeepkumar PI. Targeting promoter G-quadruplex DNAs by indenopyrimidine-based ligands. ChemMedChem 2014; 9:2754-65. [PMID: 25359695 DOI: 10.1002/cmdc.201402394] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Indexed: 11/07/2022]
Abstract
The formation of G-quadruplex structures can regulate telomerase activity and the expression of oncogenes at the transcriptional and translational levels. Therefore, stabilization of G-quadruplex DNA structures by small molecules has been recognized as a promising strategy for anticancer drug therapy. One of the major challenges in this field is to impart stabilizing molecules with selectivity toward quadruplex structures over duplex DNAs, and to maintain specificity toward a particular quadruplex topology. Herein we report the synthesis and binding interactions of indenopyrimidine derivatives, endowed with drug-like properties, with oncogenic promoters of c-myc and c-kit, telomeric and duplex DNAs. The results show specific stabilization of promoter over telomeric quadruplexes and duplex DNAs. Molecular modeling studies support the experimental observations by unraveling the dual binding mode of ligands by exploiting the top and bottom quartets of a G-quadruplex structure. This study underscores the potential of the indenopyrimidine scaffold, which can be used to achieve specific G-quadruplex-mediated anticancer activity.
Collapse
Affiliation(s)
- K V Diveshkumar
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076 (India)
| | | | | | | | | |
Collapse
|
145
|
Rizzo A, Iachettini S, Zizza P, Cingolani C, Porru M, Artuso S, Stevens M, Hummersone M, Biroccio A, Salvati E, Leonetti C. Identification of novel RHPS4-derivative ligands with improved toxicological profiles and telomere-targeting activities. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2014; 33:81. [PMID: 25288403 PMCID: PMC4193996 DOI: 10.1186/s13046-014-0081-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 09/22/2014] [Indexed: 02/07/2023]
Abstract
The pentacyclic acridinium salt RHPS4 (3,11-difluoro-6,8,13-trimethyl-8H-quino [4,3,2-kl] acridinium methosulfate, compound 1) is one of the most interesting DNA G-quadruplex binding molecules due to its high efficacy in tumor cell growth inhibition both in in vitro models and in vivo against human tumor xenografts in combination with conventional chemotherapeutics. Despite compound 1 having desirable chemical and pharmaceutical properties, its potential as a therapeutic agent is compromised by off-target effects on cardiovascular physiology. In this paper we report a new series of structurally-related compounds which were developed in an attempt to minimize its off-target profile, but maintaining the same favorable chemical and pharmacological features of the lead compound. By performing a comparative analysis it was possible to identify which derivatives had the following properties: (i) to show a reduced capacity in respect to compound 1 to inhibit the hERG tail current tested in a patch clamp assay and/or to interact with the human recombinant β2 receptor; (ii) to maintain both a good G4-binding affinity and cancer cell selectivity; and (iii) to trigger DNA damage with specific telomere uncapping. These studies allowed us to identify a novel G4-stabilizing molecule, compound 8, being characterized by reduced off-target effects and potent telomere on-target properties compared to the prototypic compound 1. Moreover, compound 8 shares with compound 1 the same molecular mode of action and an anti-tumour activity specifically restricted to replicating cells, as evident with its particularly efficient activity in combination therapy with a topoisomerase I inhibitor. In conclusion, we have identified a new pentacyclic derivative 8 having suitable properties to be the focus of further investigations as a clinical candidate for cancer therapy.
Collapse
Affiliation(s)
- Angela Rizzo
- Experimental Chemotherapy Laboratory, Regina Elena National Cancer Institute, via delle Messi d'Oro 156, 00158, Rome, Italy.
| | - Sara Iachettini
- Experimental Chemotherapy Laboratory, Regina Elena National Cancer Institute, via delle Messi d'Oro 156, 00158, Rome, Italy.
| | - Pasquale Zizza
- Experimental Chemotherapy Laboratory, Regina Elena National Cancer Institute, via delle Messi d'Oro 156, 00158, Rome, Italy.
| | - Chiara Cingolani
- Experimental Chemotherapy Laboratory, Regina Elena National Cancer Institute, via delle Messi d'Oro 156, 00158, Rome, Italy.
| | - Manuela Porru
- Experimental Chemotherapy Laboratory, Regina Elena National Cancer Institute, via delle Messi d'Oro 156, 00158, Rome, Italy.
| | - Simona Artuso
- Experimental Chemotherapy Laboratory, Regina Elena National Cancer Institute, via delle Messi d'Oro 156, 00158, Rome, Italy.
| | - Malcolm Stevens
- School of Pharmacy, University of Nottingham, Nottingham, NG7 2RD, UK.
| | - Marc Hummersone
- Pharminox Ltd, Biocity, Pennyfoot St, Nottingham, NG1 1GF, UK.
| | - Annamaria Biroccio
- Experimental Chemotherapy Laboratory, Regina Elena National Cancer Institute, via delle Messi d'Oro 156, 00158, Rome, Italy.
| | - Erica Salvati
- Experimental Chemotherapy Laboratory, Regina Elena National Cancer Institute, via delle Messi d'Oro 156, 00158, Rome, Italy.
| | - Carlo Leonetti
- Experimental Chemotherapy Laboratory, Regina Elena National Cancer Institute, via delle Messi d'Oro 156, 00158, Rome, Italy.
| |
Collapse
|
146
|
Laguerre A, Stefan L, Larrouy M, Genest D, Novotna J, Pirrotta M, Monchaud D. A twice-as-smart synthetic G-quartet: PyroTASQ is both a smart quadruplex ligand and a smart fluorescent probe. J Am Chem Soc 2014; 136:12406-14. [PMID: 25101894 DOI: 10.1021/ja506331x] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Recent and unambiguous evidences of the formation of DNA and RNA G-quadruplexes in cells has provided solid support for these structures to be considered as valuable targets in oncology. Beyond this, they have lent further credence to the anticancer strategies relying on small molecules that selectively target these higher-order DNA/RNA architectures, referred to as G-quadruplex ligands. They have also shed bright light on the necessity of designing multitasking ligands, displaying not only enticing quadruplex interacting properties (affinity, structural selectivity) but also additional features that make them usable for detecting quadruplexes in living cells, notably for determining whether, when, and where these structures fold and unfold during the cell cycle and also for better assessing the consequences of their stabilization by external agents. Herein, we report a brand new design of such multitasking ligands, whose structure experiences a quadruplex-promoted conformational switch that triggers not only its quadruplex affinity (i.e., smart ligands, which display high affinity and selectivity for DNA/RNA quadruplexes) but also its fluorescence (i.e., smart probes, which behave as selective light-up fluorescent reporters on the basis of a fluorogenic electron redistribution). The first prototype of such multifunctional ligands, termed PyroTASQ, represents a brand new generation of quadruplex ligands that can be referred to as "twice-as-smart" quadruplex ligands.
Collapse
Affiliation(s)
- Aurélien Laguerre
- Institute of Molecular Chemistry, University of Dijon, ICMUB CNRS UMR6302 , 21078 Dijon, France
| | | | | | | | | | | | | |
Collapse
|
147
|
Amato J, Iaccarino N, Pagano B, Morigi R, Locatelli A, Leoni A, Rambaldi M, Zizza P, Biroccio A, Novellino E, Randazzo A. Bis-indole derivatives with antitumor activity turn out to be specific ligands of human telomeric G-quadruplex. Front Chem 2014; 2:54. [PMID: 25105115 PMCID: PMC4109613 DOI: 10.3389/fchem.2014.00054] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 07/04/2014] [Indexed: 01/04/2023] Open
Abstract
Bis-indolinone derivatives having either 2,6-disubstituted pyridine core (1a and 1b) or 1,10-disubstituted phenanthroline core (2a and 2b), already known to have antitumor activity, have been tested as potential G-quadruplex binders. Compounds 2a and 2b are able to selectively stabilize G-quadruplex over duplex DNA, and also to discriminate among different G-quadruplex structures, having a particular affinity for the parallel form of the human telomeric G-quadruplex. Both compounds are also able to induce telomeric DNA damage that may explain the activity of these compounds.
Collapse
Affiliation(s)
- Jussara Amato
- Department of Pharmacy, University of Naples "Federico II" Naples, Italy
| | - Nunzia Iaccarino
- Department of Pharmacy, University of Naples "Federico II" Naples, Italy
| | - Bruno Pagano
- Department of Pharmacy, University of Naples "Federico II" Naples, Italy
| | - Rita Morigi
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna Bologna, Italy
| | - Alessandra Locatelli
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna Bologna, Italy
| | - Alberto Leoni
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna Bologna, Italy
| | - Mirella Rambaldi
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna Bologna, Italy
| | - Pasquale Zizza
- Experimental Chemotherapy Laboratory, Regina Elena National Cancer Institute Rome, Italy
| | - Annamaria Biroccio
- Experimental Chemotherapy Laboratory, Regina Elena National Cancer Institute Rome, Italy
| | - Ettore Novellino
- Department of Pharmacy, University of Naples "Federico II" Naples, Italy
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples "Federico II" Naples, Italy
| |
Collapse
|