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Shou S, Li Y, Chen J, Zhang X, Zhang C, Jiang X, Liu F, Yi L, Zhang X, Geer E, Pu Z, Pang B. Understanding, diagnosing, and treating pancreatic cancer from the perspective of telomeres and telomerase. Cancer Gene Ther 2024:10.1038/s41417-024-00768-6. [PMID: 38594465 DOI: 10.1038/s41417-024-00768-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 04/11/2024]
Abstract
Telomerase is associated with cellular aging, and its presence limits cellular lifespan. Telomerase by preventing telomere shortening can extend the number of cell divisions for cancer cells. In adult pancreatic cells, telomeres gradually shorten, while in precancerous lesions of cancer, telomeres in cells are usually significantly shortened. At this time, telomerase is still in an inactive state, and it is not until before and after the onset of cancer that telomerase is reactivated, causing cancer cells to proliferate. Methylation of the telomerase reverse transcriptase (TERT) promoter and regulation of telomerase by lactate dehydrogenase B (LDHB) is the mechanism of telomerase reactivation in pancreatic cancer. Understanding the role of telomeres and telomerase in pancreatic cancer will help to diagnose and initiate targeted therapy as early as possible. This article reviews the role of telomeres and telomerase as biomarkers in the development of pancreatic cancer and the progress of research on telomeres and telomerase as targets for therapeutic intervention.
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Affiliation(s)
- Songting Shou
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yuanliang Li
- Department of Oncology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jiaqin Chen
- Department of Gastroenterology, Dongzhimen Hospital, Beijing, China
| | - Xing Zhang
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Chuanlong Zhang
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xiaochen Jiang
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Fudong Liu
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Li Yi
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xiyuan Zhang
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - En Geer
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Zhenqing Pu
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Bo Pang
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China.
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2
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Figueiredo J, Mergny JL, Cruz C. G-quadruplex ligands in cancer therapy: Progress, challenges, and clinical perspectives. Life Sci 2024; 340:122481. [PMID: 38301873 DOI: 10.1016/j.lfs.2024.122481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 01/20/2024] [Accepted: 01/29/2024] [Indexed: 02/03/2024]
Abstract
Guanine-rich sequences can form G-quadruplexes (G4) in living cells, making these structures promising anti-cancer targets. Compounds able to recognize these structures have been investigated as potential anticancer drugs; however, no G4 binder has yet been approved in the clinic. Here, we describe G4 ligands structure-activity relationships, in vivo effects as well as clinical trials. Addressing G4 ligand characteristics, targeting challenges, and structure-activity relationships, this review provides insights into the development of potent and selective G4-targeting molecules for therapeutic applications.
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Affiliation(s)
- Joana Figueiredo
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal
| | - Jean-Louis Mergny
- Laboratoire d'Optique et Biosciences, Institut Polytechnique de Paris, CNRS, INSERM, Université Paris-Saclay, 91128 Palaiseau cedex, France; Institute of Biophysics of the CAS, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic.
| | - Carla Cruz
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal; Departamento de Química, Faculdade de Ciências, Universidade da Beira Interior, Rua Marquês de Ávila e Bolama, 6201-001 Covilhã, Portugal.
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3
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Ahmed AA, Chen S, Roman-Escorza M, Angell R, Oxenford S, McConville M, Barton N, Sunose M, Neidle D, Haider S, Arshad T, Neidle S. Structure-activity relationships for the G-quadruplex-targeting experimental drug QN-302 and two analogues probed with comparative transcriptome profiling and molecular modeling. Sci Rep 2024; 14:3447. [PMID: 38342953 PMCID: PMC10859377 DOI: 10.1038/s41598-024-54080-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 02/08/2024] [Indexed: 02/13/2024] Open
Abstract
The tetrasubstituted naphthalene diimide compound QN-302 binds to G-quadruplex (G4) DNA structures. It shows high potency in pancreatic ductal adenocarcinoma (PDAC) cells and inhibits the transcription of cancer-related genes in these cells and in PDAC animal models. It is currently in Phase 1a clinical evaluation as an anticancer drug. A study of structure-activity relationships of QN-302 and two related analogues (CM03 and SOP1247) is reported here. These have been probed using comparisons of transcriptional profiles from whole-genome RNA-seq analyses, together with molecular modelling and molecular dynamics simulations. Compounds CM03 and SOP1247 differ by the presence of a methoxy substituent in the latter: these two compounds have closely similar transcriptional profiles. Whereas QN-302 (with an additional benzyl-pyrrolidine group), although also showing down-regulatory effects in the same cancer-related pathways, has effects on distinct genes, for example in the hedgehog pathway. This distinctive pattern of genes affected by QN-302 is hypothesized to contribute to its superior potency compared to CM03 and SOP1247. Its enhanced ability to stabilize G4 structures has been attributed to its benzyl-pyrrolidine substituent fitting into and filling most of the space in a G4 groove compared to the hydrogen atom in CM03 or the methoxy group substituent in SOP1247.
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Affiliation(s)
- Ahmed Abdullah Ahmed
- The School of Pharmacy, University College London, London, WC1N 1AX, UK
- Now at Guy's Cancer Centre, Guy's Hospital, London, SE1 9RT, UK
| | - Shuang Chen
- The School of Pharmacy, University College London, London, WC1N 1AX, UK
| | | | - Richard Angell
- The School of Pharmacy, University College London, London, WC1N 1AX, UK
- Now at Medicines Discovery Institute, Cardiff University, Cardiff, CF10 3AT, UK
| | - Sally Oxenford
- The School of Pharmacy, University College London, London, WC1N 1AX, UK
- Now at Artios Ltd, Cambridge, CB22 3FH, UK
| | | | | | - Mihiro Sunose
- Sygnature Discovery Ltd, BioCity, Nottingham, NG1 1GR, UK
| | - Dan Neidle
- Tax Policy Associates, London, EC1R 0ET, UK
| | - Shozeb Haider
- The School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Tariq Arshad
- Qualigen Therapeutics Inc, Carlsbad, CA, 92011, USA
| | - Stephen Neidle
- The School of Pharmacy, University College London, London, WC1N 1AX, UK.
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Han ZQ, Wen LN. Application of G-quadruplex targets in gastrointestinal cancers: Advancements, challenges and prospects. World J Gastrointest Oncol 2023; 15:1149-1173. [PMID: 37546556 PMCID: PMC10401460 DOI: 10.4251/wjgo.v15.i7.1149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 04/11/2023] [Accepted: 05/08/2023] [Indexed: 07/12/2023] Open
Abstract
Genomic instability and inflammation are considered to be two enabling characteristics that support cancer development and progression. G-quadruplex structure is a key element that contributes to genomic instability and inflammation. G-quadruplexes were once regarded as simply an obstacle that can block the transcription of oncogenes. A ligand targeting G-quadruplexes was found to have anticancer activity, making G-quadruplexes potential anticancer targets. However, further investigation has revealed that G-quadruplexes are widely distributed throughout the human genome and have many functions, such as regulating DNA replication, DNA repair, transcription, translation, epigenetics, and inflammatory response. G-quadruplexes play double regulatory roles in transcription and translation. In this review, we focus on G-quadruplexes as novel targets for the treatment of gastrointestinal cancers. We summarize the application basis of G-quadruplexes in gastrointestinal cancers, including their distribution sites, structural characteristics, and physiological functions. We describe the current status of applications for the treatment of esophageal cancer, pancreatic cancer, hepatocellular carcinoma, gastric cancer, colorectal cancer, and gastrointestinal stromal tumors, as well as the associated challenges. Finally, we review the prospective clinical applications of G-quadruplex targets, providing references for targeted treatment strategies in gastrointestinal cancers.
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Affiliation(s)
- Zong-Qiang Han
- Department of Laboratory Medicine, Beijing Xiaotangshan Hospital, Beijing 102211, China
| | - Li-Na Wen
- Department of Clinical Nutrition, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China
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5
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Wang Z, Liu W, Li G, Wang J, Zhao B, Huang P, Mei W. Ruthenium(II) Complexes Coupled by Erianin via a Flexible Carbon Chain as a Potential Stabilizer of c-myc G-Quadruplex DNA. Molecules 2023; 28:molecules28041529. [PMID: 36838516 PMCID: PMC9958891 DOI: 10.3390/molecules28041529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/08/2023] Open
Abstract
Herein, two novel ruthenium(II) complexes coupled by erianin via a flexible carbon chain, [Ru(phen)2(L1-(CH2)4-erianin)](ClO4)2 (L1 = 2-(2-(tri-fluoromethyphenyl))-imidazo [4,5f][1-10]phenanthroline (1) and [Ru(phen)2(L2-(CH2)4-eria)](ClO4)2 (L2 = 2-(4-(tri-fluoromethyphenyl))-imidazo [4,5f][1,10]phenanthroline (2), have been synthesized and investigated as a potential G-quadruplex(G4) DNA stabilizer. Both complexes, especially 2, can bind to c-myc G4 DNA with high affinity by electronic spectra, and the binding constant calculated for 1 and 2 is about 15.1 and 2.05 × 107 M-1, respectively. This was further confirmed by the increase in fluorescence intensity for both complexes. Moreover, the positive band at 265 nm in the CD spectra of c-myc G4 DNA decreased treated with 2, indicating that 2 may bind to c-myc G4 DNA through extern groove binding mode. Furthermore, fluorescence resonance energy transfer (FRET) assay indicated that the melting point of c-myc G4 DNA treated with 1 and 2 increased 15.5 and 16.5 °C, respectively. Finally, molecular docking showed that 1 can bind to c-myc G4 DNA in the extern groove formed by base pairs G7-G9 and G22-A24, and 2 inserts into the small groove of c-myc G4 DNA formed by base pairs T19-A24. In summary, these ruthenium(II) complexes, especially 2, can be developed as potential c-myc G4 DNA stabilizers and will be exploited as potential anticancer agents in the future.
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Affiliation(s)
- Zhixiang Wang
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Wentao Liu
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Guohu Li
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Jiacheng Wang
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Bin Zhao
- Department of Southern Pharmacy, Guangdong Jiangmen Chinese Medical, Jiangmen 510047, China
- Correspondence: (B.Z.); (W.M.)
| | - Peishan Huang
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Wenjie Mei
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
- Guangdong Province Engineering Technology Centre for Molecular Probe and Bio-Medical Imaging, Guangzhou 510006, China
- Correspondence: (B.Z.); (W.M.)
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Yousaf M, Fatima D, Amin J, Noureen A, Fatmi MQ. Discovering potential stabilizers for KRAS22RT G-quadruplex DNA: an alternative next generation approach to treat pancreatic cancer. J Biomol Struct Dyn 2023; 41:11957-11968. [PMID: 36729158 DOI: 10.1080/07391102.2023.2174188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 12/25/2022] [Indexed: 02/03/2023]
Abstract
KRAS is the signature gene responsible for the occurrence of pancreatic cancer, which is a complex, multifactorial and intractable lethal malignancy. Prevention and treatment of the ailment have always been a key motivation behind the search for new therapeutic drug molecules. G-quadruplexes are non-canonical guanine-rich secondary structures, commonly formed at eukaryotic telomeric ends, oncogenic promotors and G-rich regions of the DNA. These G-quadruplexes play a crucial role in the regulation of gene expression and maintenance of genome integrity, therefore, they are considered as emerging potential therapeutic drug targets. The present study is concerned with the discovery of a potential stabilizer for KRAS22RT G-quadruplex DNA, located in the NHE region of the promotor, while inhibiting the upregulation of KRAS proto-oncogene, as an alternative approach for the treatment of pancreatic cancer. Various chemical libraries have been virtually screened against the targeted G4 structure and 143 compounds showed promising results. However, molecular dynamic studies, ADME and toxicity analyses predicted that three compounds belonging to the class of tetra-substituted phenanthrolines (i.e., 7i, 7j and 7k) can not only effectively stabilize KRAS22RT G4 structure but also have least toxic effects in the in vivo system. Therefore, it is highly recommended to further investigate their effectiveness and efficacy through experimental analysis in laboratory.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Maha Yousaf
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Dua Fatima
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Javaria Amin
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Aqsa Noureen
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
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7
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Saleh MM, Abuarqoub DA, Hammad AM, Hossan MS, Ahmed N, Aslam N, Naser AY, Moody CJ, Laughton CA, Bradshaw TD. In Vitro Anticancer Properties of Novel Bis-Triazoles. Curr Issues Mol Biol 2022; 45:175-96. [PMID: 36661500 DOI: 10.3390/cimb45010014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/01/2022] [Accepted: 12/08/2022] [Indexed: 12/30/2022] Open
Abstract
Here, we describe the anticancer activity of our novel bis-triazoles MS47 and MS49, developed previously as G-quadruplex stabilizers, focusing specifically upon the human melanoma MDA-MB-435 cell line. At the National Cancer Institute (NCI), USA, bis-triazole MS47 (NCS 778438) was evaluated against a panel of sixty human cancer cell lines, and showed selective, distinct multi-log differential patterns of activity, with GI50 and LC50 values in the sub-micromolar range against human cancer cells. MS47 showed highly selective cytotoxicity towards human melanoma, ovarian, CNS and colon cancer cell lines; in contrast, the leukemia cell lines interestingly showed resistance to MS47 cytotoxic activity. Further studies revealed the potent cell growth inhibiting properties of MS47 and MS49 against the human melanoma MDA-MB-435 cell line, as verified by MTT assays; both ligands were more potent against cancer cells than MRC-5 fetal lung fibroblasts (SI > 9). Melanoma colony formation was significantly suppressed by MS47 and MS49, and time- and dose-dependent apoptosis induction was also observed. Furthermore, MS47 significantly arrested melanoma cells at the G0/G1 cell cycle phase. While the expression levels of Hsp90 protein in melanoma cells were significantly decreased by MS49, corroborating its binding to the G4-DNA promoter of the Hsp90 gene. Both ligands failed to induce senescence in the human melanoma cells after 72 h of treatment, corroborating their weak stabilization of the telomeric G4-DNA.
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8
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Neidle S. Structured Waters Mediate Small Molecule Binding to G-Quadruplex Nucleic Acids. Pharmaceuticals (Basel) 2021; 15:7. [PMID: 35056064 DOI: 10.3390/ph15010007] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/19/2021] [Accepted: 12/20/2021] [Indexed: 01/24/2023] Open
Abstract
The role of G-quadruplexes in human cancers is increasingly well-defined. Accordingly, G-quadruplexes can be suitable drug targets and many small molecules have been identified to date as G-quadruplex binders, some using computer-based design methods and co-crystal structures. The role of bound water molecules in the crystal structures of G-quadruplex-small molecule complexes has been analyzed in this study, focusing on the water arrangements in several G-quadruplex ligand complexes. One is the complex between the tetrasubstituted naphthalene diimide compound MM41 and a human intramolecular telomeric DNA G-quadruplex, and the others are in substituted acridine bimolecular G-quadruplex complexes. Bridging water molecules form most of the hydrogen-bond contacts between ligands and DNA in the parallel G-quadruplex structures examined here. Clusters of structured water molecules play essential roles in mediating between ligand side chain groups/chromophore core and G-quadruplex. These clusters tend to be conserved between complex and native G-quadruplex structures, suggesting that they more generally serve as platforms for ligand binding, and should be taken into account in docking and in silico studies.
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Manoli F, Doria F, Colombo G, Zambelli B, Freccero M, Manet I. The Binding Pocket at the Interface of Multimeric Telomere G-quadruplexes: Myth or Reality? Chemistry 2021; 27:11707-11720. [PMID: 34152657 PMCID: PMC8456957 DOI: 10.1002/chem.202101486] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Indexed: 01/23/2023]
Abstract
Human telomeric DNA with hundreds of repeats of the 5'-TTAGGG-3' motif plays a crucial role in several biological processes. It folds into G-quadruplex (G4) structures and features a pocket at the interface of two contiguous G4 blocks. Up to now no structural NMR and crystallographic data are available for ligands interacting with contiguous G4s. Naphthalene diimide monomers and dyads were investigated as ligands of a dimeric G4 of human telomeric DNA comparing the results with those of the model monomeric G4. Time-resolved fluorescence, circular dichroism, isothermal titration calorimetry and molecular modeling were used to elucidate binding features. Ligand fluorescence lifetime and induced circular dichroism unveiled occupancy of the binding site at the interface. Thermodynamic parameters confirmed the hypothesis as they remarkably change for the dyad complexes of the monomeric and dimeric telomeric G4. The bi-functional ligand structure of the dyads is a fundamental requisite for binding at the G4 interface as only the dyads engage in complexes with 1 : 1 stoichiometry, lodging in the pocket at the interface and establishing multiple interactions with the DNA skeleton. In the absence of NMR and crystallographic data, our study affords important proofs of binding at the interface pocket and clues on the role played by the ligand structure.
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Affiliation(s)
- Francesco Manoli
- Institute for Organic Synthesis and Photoreactivity (ISOF)National Research Council (CNR)Via P. Gobetti 10140129BolognaItaly
| | - Filippo Doria
- Department of ChemistryUniversity of PaviaV. le Taramelli 1027100PaviaItaly
| | - Giorgio Colombo
- Department of ChemistryUniversity of PaviaV. le Taramelli 1027100PaviaItaly
| | - Barbara Zambelli
- Department of Pharmacy and BiotechnologyUniversity of BolognaV. le Fanin 4040127BolognaItaly
| | - Mauro Freccero
- Department of ChemistryUniversity of PaviaV. le Taramelli 1027100PaviaItaly
| | - Ilse Manet
- Institute for Organic Synthesis and Photoreactivity (ISOF)National Research Council (CNR)Via P. Gobetti 10140129BolognaItaly
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Chaudhuri R, Fatma K, Dash J. Regulation of gene expression by targeting DNA secondary structures. J CHEM SCI 2021. [DOI: 10.1007/s12039-021-01898-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Platella C, Napolitano E, Riccardi C, Musumeci D, Montesarchio D. Disentangling the Structure-Activity Relationships of Naphthalene Diimides as Anticancer G-Quadruplex-Targeting Drugs. J Med Chem 2021; 64:3578-3603. [PMID: 33751881 PMCID: PMC8041303 DOI: 10.1021/acs.jmedchem.1c00125] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
![]()
In the context of
developing efficient anticancer therapies aimed
at eradicating any sort of tumors, G-quadruplexes represent excellent
targets. Small molecules able to interact with G-quadruplexes can
interfere with cell pathways specific of tumors and common to all
cancers. Naphthalene diimides
(NDIs) are among the most promising, putative anticancer G-quadruplex-targeting
drugs, due to their ability to simultaneously target multiple G-quadruplexes
and their strong, selective in vitro and in vivo anticancer activity.
Here, all the available biophysical, biological, and structural data
concerning NDIs targeting G-quadruplexes were systematically analyzed.
Structure–activity correlations were obtained by analyzing
biophysical data of their interactions with G-quadruplex targets and
control duplex structures, in parallel to biological data concerning
the antiproliferative activity of NDIs on cancer and normal cells.
In addition, NDI binding modes to G-quadruplexes were discussed in
consideration of the structures and properties of NDIs by in-depth
analysis of the available structural models of G-quadruplex/NDI complexes.
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Affiliation(s)
- Chiara Platella
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy
| | - Ettore Napolitano
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy
| | - Claudia Riccardi
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy
| | - Domenica Musumeci
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy.,Institute of Biostructures and Bioimages, CNR, via Mezzocannone 16, I-80134 Naples, Italy
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy
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Kosiol N, Juranek S, Brossart P, Heine A, Paeschke K. G-quadruplexes: a promising target for cancer therapy. Mol Cancer 2021; 20:40. [PMID: 33632214 PMCID: PMC7905668 DOI: 10.1186/s12943-021-01328-4] [Citation(s) in RCA: 198] [Impact Index Per Article: 66.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 02/01/2021] [Indexed: 12/13/2022] Open
Abstract
DNA and RNA can fold into a variety of alternative conformations. In recent years, a particular nucleic acid structure was discussed to play a role in malignant transformation and cancer development. This structure is called a G-quadruplex (G4). G4 structure formation can drive genome instability by creating mutations, deletions and stimulating recombination events. The importance of G4 structures in the characterization of malignant cells was currently demonstrated in breast cancer samples. In this analysis a correlation between G4 structure formation and an increased intratumor heterogeneity was identified. This suggests that G4 structures might allow breast cancer stratification and supports the identification of new personalized treatment options. Because of the stability of G4 structures and their presence within most human oncogenic promoters and at telomeres, G4 structures are currently tested as a therapeutic target to downregulate transcription or to block telomere elongation in cancer cells. To date, different chemical molecules (G4 ligands) have been developed that aim to target G4 structures. In this review we discuss and compare G4 function and relevance for therapeutic approaches and their impact on cancer development for three cancer entities, which differ significantly in their amount and type of mutations: pancreatic cancer, leukemia and malignant melanoma. G4 structures might present a promising new strategy to individually target tumor cells and could support personalized treatment approaches in the future.
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Affiliation(s)
- Nils Kosiol
- Department of Oncology, Hematology, Rheumatology and Immune-Oncology, University Hospital Bonn, 53127, Bonn, Germany
| | - Stefan Juranek
- Department of Oncology, Hematology, Rheumatology and Immune-Oncology, University Hospital Bonn, 53127, Bonn, Germany
| | - Peter Brossart
- Department of Oncology, Hematology, Rheumatology and Immune-Oncology, University Hospital Bonn, 53127, Bonn, Germany
| | - Annkristin Heine
- Department of Oncology, Hematology, Rheumatology and Immune-Oncology, University Hospital Bonn, 53127, Bonn, Germany
| | - Katrin Paeschke
- Department of Oncology, Hematology, Rheumatology and Immune-Oncology, University Hospital Bonn, 53127, Bonn, Germany.
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Chaudhuri R, Bhattacharya S, Dash J, Bhattacharya S. Recent Update on Targeting c-MYC G-Quadruplexes by Small Molecules for Anticancer Therapeutics. J Med Chem 2020; 64:42-70. [PMID: 33355454 DOI: 10.1021/acs.jmedchem.0c01145] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Guanine-rich DNA sequences have the propensity to adopt four-stranded tetrahelical G-quadruplex (G4) structures that are overrepresented in gene promoters. The structural polymorphism and physicochemical properties of these non-Watson-Crick G4 structures make them important targets for drug development. The guanine-rich nuclease hypersensitivity element III1 present in the upstream of P1 promoter of c-MYC oncogene has the ability to form an intramolecular parallel G4 structure. The G4 structure that forms transiently in the c-MYC promoter functions as a transcriptional repressor element. The c-MYC oncogene is overexpressed in a wide variety of cancers and plays a key role in cancer progression. Till now, a large number of compounds that are capable of interacting and stabilizing thec-MYC G4 have been reported. In this review, we summarize various c-MYC G4 specific molecules and discuss their effects on c-MYC gene expression in vitro and in vivo.
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Affiliation(s)
- Ritapa Chaudhuri
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Semantee Bhattacharya
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Jyotirmayee Dash
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Santanu Bhattacharya
- School of Applied & Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India.,Department of Organic Chemistry, Indian Institute of Science, Bangalore 560012, India
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14
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Platella C, Trajkovski M, Doria F, Freccero M, Plavec J, Montesarchio D. On the interaction of an anticancer trisubstituted naphthalene diimide with G-quadruplexes of different topologies: a structural insight. Nucleic Acids Res 2020; 48:12380-12393. [PMID: 33170272 PMCID: PMC7708068 DOI: 10.1093/nar/gkaa1001] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/29/2020] [Accepted: 10/22/2020] [Indexed: 12/12/2022] Open
Abstract
Naphthalene diimides showed significant anticancer activity in animal models, with therapeutic potential related to their ability to strongly interact with G-quadruplexes. Recently, a trifunctionalized naphthalene diimide, named NDI-5, was identified as the best analogue of a mini-library of novel naphthalene diimides for its high G-quadruplex binding affinity along with marked, selective anticancer activity, emerging as promising candidate drug for in vivo studies. Here we used NMR, dynamic light scattering, circular dichroism and fluorescence analyses to investigate the interactions of NDI-5 with G-quadruplexes featuring either parallel or hybrid topology. Interplay of different binding modes of NDI-5 to G-quadruplexes was observed for both parallel and hybrid topologies, with end-stacking always operative as the predominant binding event. While NDI-5 primarily targets the 5'-end quartet of the hybrid G-quadruplex model (m-tel24), the binding to a parallel G-quadruplex model (M2) occurs seemingly simultaneously at the 5'- and 3'-end quartets. With parallel G-quadruplex M2, NDI-5 formed stable complexes with 1:3 DNA:ligand binding stoichiometry. Conversely, when interacting with hybrid G-quadruplex m-tel24, NDI-5 showed multiple binding poses on a single G-quadruplex unit and/or formed different complexes comprising two or more G-quadruplex units. NDI-5 produced stabilizing effects on both G-quadruplexes, forming complexes with dissociation constants in the nM range.
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Affiliation(s)
- Chiara Platella
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy
| | - Marko Trajkovski
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Filippo Doria
- Department of Chemistry, University of Pavia, Viale Taramelli 10, I-27100 Pavia, Italy
| | - Mauro Freccero
- Department of Chemistry, University of Pavia, Viale Taramelli 10, I-27100 Pavia, Italy
| | - Janez Plavec
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
- EN→FIST Centre of Excellence, Trg OF 13, SI-1000 Ljubljana, Slovenia
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy
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15
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Zhirov AM, Kovalev DA, Ulshina DV, Pisarenko SV, Demidov OP, Borovlev IV. Diazapyrenes: interaction with nucleic acids and biological activity. Chem Heterocycl Compd (N Y) 2020; 56:674-693. [PMID: 32836316 PMCID: PMC7366485 DOI: 10.1007/s10593-020-02717-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 11/26/2019] [Indexed: 12/22/2022]
Abstract
The review summarizes data on the practical aspects of the interaction of nucleic acids with diazapyrene derivatives. The information on biological activity is given and the probable mechanisms underlying the action of diazapyrenes are analyzed. It contains 119 references.
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Affiliation(s)
- Andrey M. Zhirov
- Stavropol Research Anti-Plague Institute, 13-15 Sovetskaya St, Stavropol, 355035 Russia
| | - Dmitry A. Kovalev
- Stavropol Research Anti-Plague Institute, 13-15 Sovetskaya St, Stavropol, 355035 Russia
| | - Diana V. Ulshina
- Stavropol Research Anti-Plague Institute, 13-15 Sovetskaya St, Stavropol, 355035 Russia
| | - Sergey V. Pisarenko
- Stavropol Research Anti-Plague Institute, 13-15 Sovetskaya St, Stavropol, 355035 Russia
| | - Oleg P. Demidov
- North Caucasus Federal University, 1a Pushkina St, Stavropol, 355017 Russia
| | - Ivan V. Borovlev
- North Caucasus Federal University, 1a Pushkina St, Stavropol, 355017 Russia
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16
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Ma Y, Iida K, Nagasawa K. Topologies of G-quadruplex: Biological functions and regulation by ligands. Biochem Biophys Res Commun 2020; 531:3-17. [PMID: 31948752 DOI: 10.1016/j.bbrc.2019.12.103] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 12/20/2019] [Accepted: 12/28/2019] [Indexed: 01/06/2023]
Abstract
G-Quadruplex (G4) is one of the higher-order structures occurring in guanine-rich sequences of nucleic acids, and plays critical roles in biological processes. The G4-forming sequences can generate three kinds of topologies, i.e., parallel, anti-parallel, and hybrid, and these polymorphic structures have an important influence on G4-related biological functions. In this review, we highlight variety of structures generated by G4s containing various sequences and under diverse conditions. We also discuss the G4 ligands which induce specific topologies and/or conversion between different topologies.
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Affiliation(s)
- Yue Ma
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Japan.
| | - Keisuke Iida
- Department of Chemistry, Chiba University, Japan
| | - Kazuo Nagasawa
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Japan.
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17
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Doria F, Salvati E, Pompili L, Pirota V, D'Angelo C, Manoli F, Nadai M, Richter SN, Biroccio A, Manet I, Freccero M. Dyads of G‐Quadruplex Ligands Triggering DNA Damage Response and Tumour Cell Growth Inhibition at Subnanomolar Concentration. Chemistry 2019; 25:11085-11097. [DOI: 10.1002/chem.201900766] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 06/18/2019] [Indexed: 02/05/2023]
Affiliation(s)
- Filippo Doria
- Department of ChemistryUniversity of Pavia V. le Taramelli 10 27100 Pavia Italy
| | - Erica Salvati
- Oncogenomic and Epigenetic UnitIRCCS Regina Elena National Cancer Institute Via Elio Chianes 53 00144 Rome Italy
- Present address: Institute of Molecular Biology and Pathology (IBPM)National Research Council (CNR) Via degli Apuli 4 00185 Rome Italy
| | - Luca Pompili
- Oncogenomic and Epigenetic UnitIRCCS Regina Elena National Cancer Institute Via Elio Chianes 53 00144 Rome Italy
| | - Valentina Pirota
- Department of ChemistryUniversity of Pavia V. le Taramelli 10 27100 Pavia Italy
| | - Carmen D'Angelo
- Oncogenomic and Epigenetic UnitIRCCS Regina Elena National Cancer Institute Via Elio Chianes 53 00144 Rome Italy
| | - Francesco Manoli
- Institute for Organic Synthesis and Photoreactivity (ISOF)National Research Council (CNR) Via P. Gobetti 101 40129 Bologna Italy
| | - Matteo Nadai
- Department of Molecular MedicineUniversity of Padua Via Gabelli 63 35121 Padua Italy
| | - Sara N. Richter
- Department of Molecular MedicineUniversity of Padua Via Gabelli 63 35121 Padua Italy
| | - Annamaria Biroccio
- Oncogenomic and Epigenetic UnitIRCCS Regina Elena National Cancer Institute Via Elio Chianes 53 00144 Rome Italy
| | - Ilse Manet
- Institute for Organic Synthesis and Photoreactivity (ISOF)National Research Council (CNR) Via P. Gobetti 101 40129 Bologna Italy
| | - Mauro Freccero
- Department of ChemistryUniversity of Pavia V. le Taramelli 10 27100 Pavia Italy
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18
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Gurung SK, Dana S, Mandal K, Mukhopadhyay P, Mondal N. Downregulation of c-Myc and p21 expression and induction of S phase arrest by naphthalene diimide derivative in gastric adenocarcinoma cells. Chem Biol Interact 2019; 304:106-23. [PMID: 30840857 DOI: 10.1016/j.cbi.2019.02.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 01/23/2019] [Accepted: 02/14/2019] [Indexed: 12/13/2022]
Abstract
Naphthalene diimide (NDI) derivatives have been shown to exhibit promising antineoplastic properties. In the current study, we assessed the anticancer and anti-bacterial properties of di-substituted NDI derivative. The naphthalene-bis-hydrazimide, 1, negatively affected the cell viability of three cancer cell lines (AGS, HeLa and PC3) and induced S phase cell cycle arrest along with SubG0/G1 accumulation. Amongst three cell lines, gastric cancer cell line, AGS, showed the highest sensitivity towards the NDI derivative 1. Compound 1 induced extensive DNA double strand breaks causing p53 activation leading to transcription of p53 target gene p21 in AGS cells. Reduction in protein levels of p21 and BRCA1 suggested that 1 treated AGS cells underwent cell death due to accumulation of DNA damage as a result of impaired DNA damage repair. β-catenin downregulation and consequently decrease in levels of c-Myc may have led to 1 induced AGS cell proliferation inhibition.1 induced AGS cell S phase arrest was mediated through CylinA/CDK2 downregulation. The possible mechanisms involved in anticancer activity of 1 includes ROS upregulation, induction of DNA damage, disruption of mitochondrial membrane potential causing ATP depletion, inhibition of cell proliferation and downregulation of antiapoptotic factors ultimately leading to mitochondria mediated apoptosis. Further compound 1 also inhibited H. pylori proliferation as well as H. pylori induced morphological changes in AGS cells. These findings suggest that NDI derivative 1 exhibits two-pronged anticancer activity, one by directly inhibiting cancer cell growth and inducing apoptosis and the other by inhibiting H. pylori.
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19
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Marchetti C, Zyner KG, Ohnmacht SA, Robson M, Haider SM, Morton JP, Marsico G, Vo T, Laughlin-Toth S, Ahmed AA, Di Vita G, Pazitna I, Gunaratnam M, Besser RJ, Andrade ACG, Diocou S, Pike JA, Tannahill D, Pedley RB, Evans TRJ, Wilson WD, Balasubramanian S, Neidle S. Targeting Multiple Effector Pathways in Pancreatic Ductal Adenocarcinoma with a G-Quadruplex-Binding Small Molecule. J Med Chem 2018; 61:2500-2517. [PMID: 29356532 PMCID: PMC5867665 DOI: 10.1021/acs.jmedchem.7b01781] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Indexed: 12/11/2022]
Abstract
Human pancreatic ductal adenocarcinoma (PDAC) involves the dysregulation of multiple signaling pathways. A novel approach to the treatment of PDAC is described, involving the targeting of cancer genes in PDAC pathways having over-representation of G-quadruplexes, using the trisubstituted naphthalene diimide quadruplex-binding compound 2,7-bis(3-morpholinopropyl)-4-((2-(pyrrolidin-1-yl)ethyl)amino)benzo[ lmn][3,8]phenanthroline-1,3,6,8(2 H,7 H)-tetraone (CM03). This compound has been designed by computer modeling, is a potent inhibitor of cell growth in PDAC cell lines, and has anticancer activity in PDAC models, with a superior profile compared to gemcitabine, a commonly used therapy. Whole-transcriptome RNA-seq methodology has been used to analyze the effects of this quadruplex-binding small molecule on global gene expression. This has revealed the down-regulation of a large number of genes, rich in putative quadruplex elements and involved in essential pathways of PDAC survival, metastasis, and drug resistance. The changes produced by CM03 represent a global response to the complexity of human PDAC and may be applicable to other currently hard-to-treat cancers.
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Affiliation(s)
- Chiara Marchetti
- UCL
School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, U.K.
| | - Katherine G. Zyner
- Cancer
Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, U.K.
| | - Stephan A. Ohnmacht
- UCL
School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, U.K.
| | - Mathew Robson
- Cancer
Research UK Cancer Centre, UCL Cancer Institute, University College London, London WC1E 6BT, U.K.
| | - Shozeb M. Haider
- UCL
School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, U.K.
| | - Jennifer P. Morton
- Cancer
Research UK, Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD U.K.
- Institute
of Cancer Sciences. University of Glasgow, Glasgow G12 8QQ, U.K.
| | - Giovanni Marsico
- Cancer
Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, U.K.
| | - Tam Vo
- Department
of Chemistry and Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30303-3083, United States
| | - Sarah Laughlin-Toth
- Department
of Chemistry and Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30303-3083, United States
| | - Ahmed A. Ahmed
- UCL
School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, U.K.
| | - Gloria Di Vita
- UCL
School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, U.K.
| | - Ingrida Pazitna
- UCL
School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, U.K.
| | - Mekala Gunaratnam
- UCL
School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, U.K.
| | - Rachael J. Besser
- UCL
School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, U.K.
| | - Ana C. G. Andrade
- UCL
School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, U.K.
| | - Seckou Diocou
- UCL
Cancer Institute, University College London, London WC1E 6BT, U.K.
| | - Jeremy A. Pike
- Cancer
Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, U.K.
| | - David Tannahill
- Cancer
Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, U.K.
| | - R. Barbara Pedley
- UCL
Cancer Institute, University College London, London WC1E 6BT, U.K.
| | - T. R. Jeffry Evans
- Cancer
Research UK, Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD U.K.
- Institute
of Cancer Sciences. University of Glasgow, Glasgow G12 8QQ, U.K.
| | - W. David Wilson
- Department
of Chemistry and Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30303-3083, United States
| | - Shankar Balasubramanian
- Cancer
Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, U.K.
- Department
of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
- The
School of Clinical Medicine, University
of Cambridge, Cambridge CB2 0SP, U.K.
| | - Stephen Neidle
- UCL
School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, U.K.
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20
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Lopergolo A, Perrone R, Tortoreto M, Doria F, Beretta GL, Zuco V, Freccero M, Borrello MG, Lanzi C, Richter SN, Zaffaroni N, Folini M. Targeting of RET oncogene by naphthalene diimide-mediated gene promoter G-quadruplex stabilization exerts anti-tumor activity in oncogene-addicted human medullary thyroid cancer. Oncotarget 2018; 7:49649-49663. [PMID: 27351133 PMCID: PMC5226536 DOI: 10.18632/oncotarget.10105] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 05/13/2016] [Indexed: 12/21/2022] Open
Abstract
Medullary thyroid cancer (MTC) relies on the aberrant activation of RET proto-oncogene. Though targeted approaches (i.e., tyrosine kinase inhibitors) are available, the absence of complete responses and the onset of resistance mechanisms indicate the need for novel therapeutic interventions. Due to their role in regulation of gene expression, G-quadruplexes (G4) represent attractive targets amenable to be recognized or stabilized by small molecules. Here, we report that exposure of MTC cells to a tri-substituted naphthalene diimide (NDI) resulted in a significant antiproliferative activity paralleled by inhibition of RET expression. Biophysical analysis and gene reporter assays showed that impairment of RET expression was consequent to the NDI-mediated stabilization of the G4 forming within the gene promoter. We also showed for the first time that systemic administration of the NDI in mice xenotransplanted with MTC cells resulted in a remarkable inhibition of tumor growth in vivo. Overall, our findings indicate that NDI-dependent RET G4 stabilization represents a suitable approach to control RET transcription and delineate the rationale for the development of G4 stabilizing-based treatments for MTC as well as for other tumors in which RET may have functional and therapeutic implications.
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Affiliation(s)
- Alessia Lopergolo
- Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133, Milano, Italy
| | - Rosalba Perrone
- Department of Molecular Medicine, University of Padua, 35121, Padova, Italy
| | - Monica Tortoreto
- Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133, Milano, Italy
| | - Filippo Doria
- Department of Chemistry, University of Pavia, 27100, Pavia, Italy
| | - Giovanni L Beretta
- Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133, Milano, Italy
| | - Valentina Zuco
- Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133, Milano, Italy
| | - Mauro Freccero
- Department of Chemistry, University of Pavia, 27100, Pavia, Italy
| | - Maria Grazia Borrello
- Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133, Milano, Italy
| | - Cinzia Lanzi
- Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133, Milano, Italy
| | - Sara N Richter
- Department of Molecular Medicine, University of Padua, 35121, Padova, Italy
| | - Nadia Zaffaroni
- Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133, Milano, Italy
| | - Marco Folini
- Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133, Milano, Italy
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21
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Arévalo-Ruiz M, Doria F, Belmonte-Reche E, De Rache A, Campos-Salinas J, Lucas R, Falomir E, Carda M, Pérez-Victoria JM, Mergny JL, Freccero M, Morales JC. Synthesis, Binding Properties, and Differences in Cell Uptake of G-Quadruplex Ligands Based on Carbohydrate Naphthalene Diimide Conjugates. Chemistry 2017; 23:2157-2164. [PMID: 27925323 DOI: 10.1002/chem.201604886] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Indexed: 11/06/2022]
Abstract
The G-quadruplexes (G4s) are currently being explored as therapeutic targets in cancer and other pathologies. Six carbohydrate naphthalene diimide conjugates (carb-NDIs) have been synthesized as G4 ligands to investigate their potential selectivity in G4 binding and cell penetration. Carb-NDIs have shown certain selectivity for G4 structures against DNA duplexes, but different sugar moieties do not induce a preference for a specific G4 topology. Interestingly, when monosaccharides were attached through a short ethylene linker to the NDI scaffold, their cellular uptake was two- to threefold more efficient than that when the sugar was directly attached through its anomeric position. Moreover, a correlation between more efficient cell uptake of these carb-NDIs and their higher toxicity in cancerous cell lines has been observed. Carb-NDIs seem to be mainly translocated into cancer cells through glucose transporters (GLUT), of which GLUT4 plays a major role.
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Affiliation(s)
- Matilde Arévalo-Ruiz
- Department of Biochemistry and Molecular Pharmacology, Instituto de Parasitología y Biomedicina, CSIC, Parque Tecnológico Ciencias de la Salud, Avenida del Conocimiento, s/n, 18016, Armilla, Granada, Spain
| | - Filippo Doria
- Department of Chemistry, University of Pavia, V.le Taramelli 10, 27100, Pavia, Italy
| | - Efres Belmonte-Reche
- Department of Biochemistry and Molecular Pharmacology, Instituto de Parasitología y Biomedicina, CSIC, Parque Tecnológico Ciencias de la Salud, Avenida del Conocimiento, s/n, 18016, Armilla, Granada, Spain
| | - Aurore De Rache
- Institut Européen de Chimie Biologie (IECB), ARNA Laboratory, Université de Bordeaux, Inserm U1212, CNRS UMR5320, 2, rue Robert Escarpit, Pessac, France
| | - Jenny Campos-Salinas
- Department of Biochemistry and Molecular Pharmacology, Instituto de Parasitología y Biomedicina, CSIC, Parque Tecnológico Ciencias de la Salud, Avenida del Conocimiento, s/n, 18016, Armilla, Granada, Spain
| | - Ricardo Lucas
- Department of Biochemistry and Molecular Pharmacology, Instituto de Parasitología y Biomedicina, CSIC, Parque Tecnológico Ciencias de la Salud, Avenida del Conocimiento, s/n, 18016, Armilla, Granada, Spain
| | - Eva Falomir
- Department of Inorganic and Organic Chemistry, University Jaume I, 12071, Castellón, Spain
| | - Miguel Carda
- Department of Inorganic and Organic Chemistry, University Jaume I, 12071, Castellón, Spain
| | - José María Pérez-Victoria
- Department of Biochemistry and Molecular Pharmacology, Instituto de Parasitología y Biomedicina, CSIC, Parque Tecnológico Ciencias de la Salud, Avenida del Conocimiento, s/n, 18016, Armilla, Granada, Spain
| | - Jean-Louis Mergny
- Institut Européen de Chimie Biologie (IECB), ARNA Laboratory, Université de Bordeaux, Inserm U1212, CNRS UMR5320, 2, rue Robert Escarpit, Pessac, France
| | - Mauro Freccero
- Department of Chemistry, University of Pavia, V.le Taramelli 10, 27100, Pavia, Italy
| | - Juan Carlos Morales
- Department of Biochemistry and Molecular Pharmacology, Instituto de Parasitología y Biomedicina, CSIC, Parque Tecnológico Ciencias de la Salud, Avenida del Conocimiento, s/n, 18016, Armilla, Granada, Spain
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22
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Abstract
Maintenance of telomeres – specialized complexes that protect the ends of chromosomes – is provided by the enzyme complex telomerase, which is a key factor that is activated in more than 80% of cancer cells, but absent in most normal cells.
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Affiliation(s)
- Maysaa M. Saleh
- School of Pharmacy
- Centre of Bimolecular Science
- University of Nottingham
- University Park
- Nottingham NG7 2RD
| | - Charles A. Laughton
- School of Pharmacy
- Centre of Bimolecular Science
- University of Nottingham
- University Park
- Nottingham NG7 2RD
| | - Tracey D. Bradshaw
- School of Pharmacy
- Centre of Bimolecular Science
- University of Nottingham
- University Park
- Nottingham NG7 2RD
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23
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Affiliation(s)
- Mohammad Al Kobaisi
- School
of Applied Sciences, RMIT University
, GPO Box 2476, Melbourne, Victoria
3001, Australia
| | - Sidhanath V. Bhosale
- Polymers
and Functional Materials Division, CSIR-Indian Institute of Chemical Technology
, Hyderabad, Telangana-500007, India
| | - Kay Latham
- School
of Applied Sciences, RMIT University
, GPO Box 2476, Melbourne, Victoria
3001, Australia
| | - Aaron M. Raynor
- School
of Applied Sciences, RMIT University
, GPO Box 2476, Melbourne, Victoria
3001, Australia
| | - Sheshanath V. Bhosale
- School
of Applied Sciences, RMIT University
, GPO Box 2476, Melbourne, Victoria
3001, Australia
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24
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Wang C, Carter-cooper B, Du Y, Zhou J, Saeed MA, Liu J, Guo M, Roembke B, Mikek C, Lewis EA, Lapidus RG, Sintim HO. Alkyne-substituted diminazene as G-quadruplex binders with anticancer activities. Eur J Med Chem 2016; 118:266-75. [DOI: 10.1016/j.ejmech.2016.04.030] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 04/11/2016] [Accepted: 04/11/2016] [Indexed: 01/18/2023]
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25
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Ghule NV, La DD, Bhosale RS, Al Kobaisi M, Raynor AM, Bhosale SV, Bhosale SV. Effect of Amide Hydrogen Bonding Interaction on Supramolecular Self-Assembly of Naphthalene Diimide Amphiphiles with Aggregation Induced Emission. ChemistryOpen 2016; 5:157-63. [PMID: 27308233 PMCID: PMC4906475 DOI: 10.1002/open.201500201] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Indexed: 11/18/2022] Open
Abstract
In the present work, two new naphthalene diimide (NDI) amphiphiles, NDI-N and NDI-NA, were successfully synthesized and employed to investigate their self-assembly and optical properties. For NDI-NA, which contains an amide group, aggregation-induced emission enhancement (AIEE) was demonstrated in the presence of various ratios of methylcyclohexane (MCH) in chloroform, which led to the visual color changes. This new amide-containing NDI-NA amphiphile formed nanobelt structures in chloroform/MCH (10:90, v/v) and microcup-like morphologies in chloroform/MCH (5:95, v/v). The closure of these microcups led to the formation of vesicles and microcapsules. The structural morphologies gained from the solvophobic control of NDI-NA were confirmed by various complementary techniques such as infrared spectroscopy, X-ray diffraction, and scanning and transmission electron microscopy. In the absence of the amide moiety in NDI-N, no self-assembly was observed, indicating the fundamental role of H-bonding in the self-association process.
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Affiliation(s)
- Namdev V. Ghule
- Polymers and Functional Materials DivisionCSIR-Indian Institute of Chemical TechnologyHyderabadTelangana500 007India
| | - Duong Duc La
- School of Applied SciencesRMIT UniversityGPO Box 2476MelbourneVIC3001Australia
| | - Rajesh S. Bhosale
- Polymers and Functional Materials DivisionCSIR-Indian Institute of Chemical TechnologyHyderabadTelangana500 007India
| | - Mohammad Al Kobaisi
- School of Applied SciencesRMIT UniversityGPO Box 2476MelbourneVIC3001Australia
| | - Aaron M. Raynor
- School of Applied SciencesRMIT UniversityGPO Box 2476MelbourneVIC3001Australia
| | | | - Sidhanath V. Bhosale
- Polymers and Functional Materials DivisionCSIR-Indian Institute of Chemical TechnologyHyderabadTelangana500 007India
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26
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Nagasawa K, Ma Y, Iida K, Nakamura T, Seimiya H, Ohtake T. Design, Synthesis and Evaluation of an L-Dopa-Derived Macrocyclic Hexaoxazole (6otd) as a G-Quadruplex-Selective Ligand. HETEROCYCLES 2016. [DOI: 10.3987/com-15-13383] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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27
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Ohnmacht SA, Marchetti C, Gunaratnam M, Besser RJ, Haider SM, Di Vita G, Lowe HL, Mellinas-Gomez M, Diocou S, Robson M, Šponer J, Islam B, Barbara Pedley R, Hartley JA, Neidle S. A G-quadruplex-binding compound showing anti-tumour activity in an in vivo model for pancreatic cancer. Sci Rep 2015; 5:11385. [PMID: 26077929 PMCID: PMC4468576 DOI: 10.1038/srep11385] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 04/22/2015] [Indexed: 01/05/2023] Open
Abstract
We report here that a tetra-substituted naphthalene-diimide derivative (MM41) has significant in vivo anti-tumour activity against the MIA PaCa-2 pancreatic cancer xenograft model. IV administration with a twice-weekly 15 mg/kg dose produces ca 80% tumour growth decrease in a group of tumour-bearing animals. Two animals survived tumour-free after 279 days. High levels of MM41 are rapidly transported into cell nuclei and were found to accumulate in the tumour. MM41 is a quadruplex-interactive compound which binds strongly to the quadruplexes encoded in the promoter sequences of the BCL-2 and k-RAS genes, both of which are dis-regulated in many human pancreatic cancers. Levels of BCL-2 were reduced by ca 40% in tumours from MM41-treated animals relative to controls, consistent with BCL-2 being a target for MM41. Molecular modelling suggests that MM41 binds to a BCL-2 quadruplex in a manner resembling that previously observed in co-crystal structures with human telomeric quadruplexes. This supports the concept that MM41 (and by implication other quadruplex-targeting small molecules) can bind to quadruplex-forming promoter regions in a number of genes and down-regulate their transcription. We suggest that quadruplexes within those master genes that are up-regulated drivers for particular cancers, may be selective targets for compounds such as MM41.
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Affiliation(s)
| | - Chiara Marchetti
- UCL School of Pharmacy, University College London, London WC1N 1AX, UK
| | - Mekala Gunaratnam
- UCL School of Pharmacy, University College London, London WC1N 1AX, UK
| | - Rachael J Besser
- UCL School of Pharmacy, University College London, London WC1N 1AX, UK
| | - Shozeb M Haider
- UCL School of Pharmacy, University College London, London WC1N 1AX, UK
| | - Gloria Di Vita
- UCL School of Pharmacy, University College London, London WC1N 1AX, UK
| | - Helen L Lowe
- UCL Cancer Institute, University College London, London WC1E 6BT, UK
| | | | - Seckou Diocou
- UCL Cancer Institute, University College London, London WC1E 6BT, UK
| | - Mathew Robson
- UCL Cancer Institute, University College London, London WC1E 6BT, UK
| | - Jiri Šponer
- Central European Institute of Technology (CEITEC), Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65, Brno, Czech Republic
| | - Barira Islam
- Central European Institute of Technology (CEITEC), Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - R Barbara Pedley
- UCL Cancer Institute, University College London, London WC1E 6BT, UK
| | - John A Hartley
- UCL Cancer Institute, University College London, London WC1E 6BT, UK
| | - Stephen Neidle
- UCL School of Pharmacy, University College London, London WC1N 1AX, UK
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28
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Housaindokht MR, Verdian-Doghaei A. Biophysical probing of the binding properties of a Cu(II) complex with G-quadruplex DNA: an experimental and computational study. LUMINESCENCE 2015; 31:22-9. [DOI: 10.1002/bio.2916] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2014] [Revised: 02/08/2015] [Accepted: 03/08/2015] [Indexed: 11/10/2022]
Affiliation(s)
| | - Asma Verdian-Doghaei
- Biophysical Chemistry Laboratory, Department of Chemistry; Ferdowsi University of Mashhad; Mashhad Iran
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29
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Prato G, Silvent S, Saka S, Lamberto M, Kosenkov D. Thermodynamics of binding of di- and tetrasubstituted naphthalene diimide ligands to DNA G-quadruplex. J Phys Chem B 2015; 119:3335-47. [PMID: 25635929 DOI: 10.1021/jp509637y] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Naphthalene diimide ligands have the potential to stabilize human telomeric G-quadruplex DNA via noncovalent interactions. Stabilization of G-quadruplex high order structures has become an important strategy to develop novel anticancer therapeutics. In this study four naphthalene diimide based ligands were analyzed in order to elucidate the principal factors determining contributions to G-quadruplex-ligand binding. Three possible modes of binding and their respective Gibbs free energies for two naphthalene diimide based di-N-alkylpyridinium substituted ligands have been determined using a molecular docking technique and compared to experimental results. The structures obtained from the molecular docking calculations, were analyzed using the ab initio based fragment molecular orbital (FMO) method in order to determine the major enthalpic contributions to the binding and types of interactions between the ligand and specific residues of the G-quadruplex. A computational methodology for the efficient and inexpensive ligand optimization as compared to fully ab initio methods based on the estimation of binding affinities of the naphthalene diimide derived ligands to G-quadruplex is proposed.
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Affiliation(s)
- Gary Prato
- Department of Chemistry and Physics, Monmouth University , 400 Cedar Avenue, West Long Branch, New Jersey 07764, United States
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30
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NADAI MATTEO, CIMINO-REALE GRAZIELLA, SATTIN GIOVANNA, DORIA FILIPPO, BUTOVSKAYA ELENA, ZAFFARONI NADIA, FRECCERO MAURO, PALUMBO MANLIO, RICHTER SARAN, FOLINI MARCO. Assessment of gene promoter G-quadruplex binding and modulation by a naphthalene diimide derivative in tumor cells. Int J Oncol 2014; 46:369-80. [DOI: 10.3892/ijo.2014.2723] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 09/03/2014] [Indexed: 11/05/2022] Open
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31
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Parrotta L, Ortuso F, Moraca F, Rocca R, Costa G, Alcaro S, Artese A. Targeting unimolecular G-quadruplex nucleic acids: a new paradigm for the drug discovery? Expert Opin Drug Discov 2014; 9:1167-87. [PMID: 25109710 DOI: 10.1517/17460441.2014.941353] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
INTRODUCTION G-quadruplexes (G4s) are targets of great interest because of their roles in crucial biological processes, such as aging and cancer. G4s are based on the formation of G-quartets, stabilised by Hoogsteen-type hydrogen bonds and by interaction with cations between the tetrads. These biologically relevant conformations were first discovered in eukaryotic chromosomal telomeric DNA, but have also been found in the proximal location of promoters in a number of human genes. Therefore, the extensive analysis of an intriguing target could move towards the rational drug design of new selective anticancer agents. AREAS COVERED The authors review G4 structural characterisation, with detailed insight related to the polymorphism issue. The authors describe the topologically distinct G4 structural forms and the factors involved in their interconversion mechanisms, such as the sequence of the oligonucleotides, the strand stoichiometry and orientation, the syn-anti conformation of the guanine glycosidic bonds and the G4 loop types and the environmental factors. Furthermore, the authors report several studies related to folding and unfolding kinetic profiles in order to understand the conformational view of monomolecular G4 formations. EXPERT OPINION G4 unimolecular nucleic acids can be considered as valid targets for the rational drug development of novel anticancer agents. Structural biology represents an essential link between the biology and medicinal chemistry knowledge in this field. In silico methods have already been demonstrated to be useful, especially if well integrated with biophysical tests. If this proves successful, the G4-targeting paradigm could also be extended to drug discovery beyond neoplastic pathologies.
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Affiliation(s)
- Lucia Parrotta
- Università degli Studi "Magna Græcia", Dipartimento di Scienze della Salute , Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro , Italy
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32
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Maji B, Kumar K, Kaulage M, Muniyappa K, Bhattacharya S. Design and Synthesis of New Benzimidazole–Carbazole Conjugates for the Stabilization of Human Telomeric DNA, Telomerase Inhibition, and Their Selective Action on Cancer Cells. J Med Chem 2014; 57:6973-88. [DOI: 10.1021/jm500427n] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Basudeb Maji
- Department of Organic
Chemistry, Indian Institute of Science, Bangalore, Karnataka 560 012, India
| | - Krishan Kumar
- Department of Organic
Chemistry, Indian Institute of Science, Bangalore, Karnataka 560 012, India
| | - Mangesh Kaulage
- Department of Organic
Chemistry, Indian Institute of Science, Bangalore, Karnataka 560 012, India
- Department
of Biochemistry, Indian Institute of Science, Bangalore, Karnataka 560 012, India
| | - K. Muniyappa
- Department
of Biochemistry, Indian Institute of Science, Bangalore, Karnataka 560 012, India
| | - Santanu Bhattacharya
- Department of Organic
Chemistry, Indian Institute of Science, Bangalore, Karnataka 560 012, India
- Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, Karnataka 560 012, India
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Ali A, Bhattacharya S. DNA binders in clinical trials and chemotherapy. Bioorg Med Chem 2014; 22:4506-21. [DOI: 10.1016/j.bmc.2014.05.030] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2014] [Revised: 05/09/2014] [Accepted: 05/14/2014] [Indexed: 01/09/2023]
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Abstract
Telomerase is an attractive drug target to develop new generation drugs against cancer.
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Affiliation(s)
- Basudeb Maji
- Department of Organic Chemistry
- Indian Institute of Science
- Bangalore-560012, India
| | - Santanu Bhattacharya
- Department of Organic Chemistry
- Indian Institute of Science
- Bangalore-560012, India
- Chemical Biology Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research
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35
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Wei H, Lv M, Duan X, Li S, Yao Y, Wang K, Zhang P, Li X, Chen H. Cytotoxicity and DNA-binding property of water-soluble naphthalene diimide derivatives bearing 2-oligoethoxy ethanamine side chain end-labeled with tertiary amino groups. Med Chem Res 2014; 23:2277-86. [DOI: 10.1007/s00044-013-0823-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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36
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Bidzinska J, Cimino-Reale G, Zaffaroni N, Folini M. G-quadruplex structures in the human genome as novel therapeutic targets. Molecules 2013; 18:12368-95. [PMID: 24108400 DOI: 10.3390/molecules181012368] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 09/24/2013] [Accepted: 09/27/2013] [Indexed: 01/07/2023] Open
Abstract
G-quadruplexes are secondary structures that may form within guanine-rich nucleic acid sequences. Telomeres have received much attention in this regard since they can fold into several distinct intramolecular G-quadruplexes, leading to the rational design and development of G-quadruplex-stabilizing molecules. These ligands were shown to selectively exert an antiproliferative and chemosensitizing activity in in vitro and in vivo tumor models, without appreciably affecting normal cells. Such findings point to them as possible drug candidates for clinical applications. Other than in telomeres, G-quadruplexes may form at additional locations in the human genome, including gene promoters and untranslated regions. For instance, stabilization of G-quadruplex structures within the promoter of MYC, KIT, or KRAS resulted in the down-regulation of the corresponding oncogene either in gene reporter assays or in selected experimental models. In addition, the alternative splicing of a number of genes may be affected for a therapeutic benefit through the stabilization of G-quadruplexes located within pre-mRNAs. It is now emerging that G-quadruplex structures may act as key regulators of several biological processes. Consequently, they are considered as attractive targets for broad-spectrum anticancer therapies, and much effort is being made to develop a variety of ligands with improved G-quadruplex recognition properties. Quarfloxin, a fluoroquinolone derivative designed to target a G-quadruplex within ribosomal DNA and disrupt protein-DNA interactions, has entered clinical trials for different malignancies. This review will provide some hints on the role of G-quadruplex structures in biological processes and will evaluate their implications as novel therapeutic targets.
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Lavrado J, Borralho PM, Ohnmacht SA, Castro RE, Rodrigues CMP, Moreira R, dos Santos DJVA, Neidle S, Paulo A. Synthesis, G-quadruplex stabilisation, docking studies, and effect on cancer cells of indolo[3,2-b]quinolines with one, two, or three basic side chains. ChemMedChem 2013; 8:1648-61. [PMID: 23960016 DOI: 10.1002/cmdc.201300288] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Indexed: 11/07/2022]
Abstract
G-quadruplex (G4) DNA structures in telomeres and oncogenic promoter regions are potential targets for cancer therapy, and G4 ligands have been shown to modulate telomerase activity and oncogene transcription. Herein we report the synthesis and G4 thermal stabilisation effects, determined by FRET melting assays, of 20 indolo[3,2-b]quinolines mono-, di-, and trisubstituted with basic side chains. Molecular modelling studies were also performed in an attempt to rationalise the ligands' binding poses with G4. Overall, the results suggest that ligand binding and G4 DNA thermal stabilisation increase with an N5-methyl or a 7-carboxylate group and propylamine side chains, whereas selectivity between G4 and duplex DNA appears to be modulated by the number and relative position of basic side chains. From all the indoloquinoline derivatives studied, the novel trisubstituted compounds 3 d and 4 d, bearing a 7-(aminoalkyl)carboxylate side chain, stand out as the most promising compounds; they show high G4 thermal stabilisation (ΔTm values between 17 and 8 °C) with an inter-G4 ΔTm trend of Hsp90A>KRas21R≈F21T>c-Kit2, 10-fold selectivity for G4 over duplex DNA, and 100-fold selectivity for the HCT116 cancer cell line (IC50 and IC90: <10 μM) over primary rat hepatocytes. Compounds 3 d and 4 d also decreased protein expression levels of Hsp90 and KRas in HCT116 cancer cells.
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Affiliation(s)
- João Lavrado
- Medicinal Chemistry Group, Research Institute for Medicines and Pharmaceutical Sciences, Faculty of Pharmacy, University of Lisbon, Av. Prof. Gama Pinto, 1649-003 Lisbon (Portugal)
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38
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Mpima S, Ohnmacht SA, Barletta M, Husby J, Pett LC, Gunaratnam M, Hilton ST, Neidle S. The influence of positional isomerism on G-quadruplex binding and anti-proliferative activity of tetra-substituted naphthalene diimide compounds. Bioorg Med Chem 2013; 21:6162-70. [PMID: 23769166 DOI: 10.1016/j.bmc.2013.05.027] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 05/17/2013] [Accepted: 05/18/2013] [Indexed: 10/26/2022]
Abstract
The synthesis together with biophysical and biological evaluation of a series of tetra-substituted naphthalene diimide (ND) compounds, are presented. These compounds are positional isomers of a recently-described series of quadruplex-binding ND derivatives, in which the two N-methyl-piperidine-alkyl side-chains have now been interchanged with the positions of side-chains bearing a range of end-groups. Molecular dynamics simulations of a pair of positional isomers are in accord with the quadruplex stabilization and biological data for these compounds. Analysis of structure-activity data indicates that for compounds where the side-chains are not of equivalent length then the positional isomers described here tend to have improved cell proliferation potency and in some instances, superior quadruplex stabilization ability.
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Affiliation(s)
- Sheila Mpima
- The School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
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Micco M, Collie GW, Dale AG, Ohnmacht SA, Pazitna I, Gunaratnam M, Reszka AP, Neidle S. Structure-based design and evaluation of naphthalene diimide G-quadruplex ligands as telomere targeting agents in pancreatic cancer cells. J Med Chem 2013; 56:2959-74. [PMID: 23514618 DOI: 10.1021/jm301899y] [Citation(s) in RCA: 137] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Tetra-substituted naphthalene diimide (ND) derivatives with positively charged termini are potent stabilizers of human telomeric and gene promoter DNA quadruplexes and inhibit the growth of human cancer cells in vitro and in vivo. The present study reports the enhancement of the pharmacological properties of earlier ND compounds using structure-based design. Crystal structures of three complexes with human telomeric intramolecular quadruplexes demonstrate that two of the four strongly basic N-methyl-piperazine groups can be replaced by less basic morpholine groups with no loss of intermolecular interactions in the grooves of the quadruplex. The new compounds retain high affinity to human telomeric quadruplex DNA but are 10-fold more potent against the MIA PaCa-2 pancreatic cancer cell line, with IC50 values of ~10 nM. The lead compound induces cellular senescence but does not inhibit telomerase activity at the nanomolar dosage levels required for inhibition of cellular proliferation. Gene array qPCR analysis of MIA PaCa-2 cells treated with the lead compound revealed significant dose-dependent modulation of a distinct subset of genes, including strong induction of DNA damage responsive genes CDKN1A, DDIT3, GADD45A/G, and PPM1D, and repression of genes involved in telomere maintenance, including hPOT1 and PARP1.
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Affiliation(s)
- Marialuisa Micco
- The School of Pharmacy, University College London, London WC1N 1AX, UK
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40
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Samatanga B, Dominguez C, Jelesarov I, Allain FHT. The high kinetic stability of a G-quadruplex limits hnRNP F qRRM3 binding to G-tract RNA. Nucleic Acids Res 2012; 41:2505-16. [PMID: 23275549 PMCID: PMC3575826 DOI: 10.1093/nar/gks1289] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The RNA binding protein heterogeneous nuclear ribonucleoprotein (hnRNP) F is involved in telomeres maintenance and pre-mRNA processing, such as alternative splicing and polyadenylation. It specifically recognizes RNA containing three consecutive guanines (G-tracts) that have the potential to assemble into G-quadruplexes. We have proposed recently that hnRNP F could regulate alternative splicing by remodeling RNA structures, such as G-quadruplexes. However, the exact mechanism of hnRNP F binding to such RNA sequences remains unknown. Here, we have studied the binding of the third RNA binding domain of hnRNP F [quasi-RNA recognition motif 3 (qRRM3)] to G-tract RNA using isothermal titration calorimetry, circular dichroism and nuclear magnetic resonance spectroscopy. Our results show that qRRM3 binds specifically exclusively to single-stranded G-tracts (ssRNA), in contrast to previous reports stating that the G-quadruplex was recognized as well. Furthermore, we demonstrate that the pre-existent ssRNA/G-quadruplex equilibrium slows down the formation of the protein–ssRNA complex. Based on in vitro transcription assays, we show that the rate of the protein–RNA complex formation is faster than that of the G-quadruplex. We propose a model according to which hnRNP F could bind RNA co-transcriptionally and prevents G-quadruplex formation.
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Affiliation(s)
- Brighton Samatanga
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, CH-8093 Zurich, Switzerland
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41
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Doria F, Nadai M, Folini M, Scalabrin M, Germani L, Sattin G, Mella M, Palumbo M, Zaffaroni N, Fabris D, Freccero M, Richter SN. Targeting loop adenines in G-quadruplex by a selective oxirane. Chemistry 2012; 19:78-81. [PMID: 23212868 DOI: 10.1002/chem.201203097] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Indexed: 11/06/2022]
Abstract
Caught in the oxirane: Naphthalene diimides conjugated to a quinone methide and an oxirane have been synthesized and investigated as selective DNA G-quadruplex alkylating agents. The oxirane derivative generates a stable adduct with a G-quadruplex and shows selective alkylation of the loop adenines, as illustrated.
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Affiliation(s)
- Filippo Doria
- Dipartimento di Chimica, Università di Pavia, V.le Taramelli 10, 27100 Pavia (Italy)
| | - Matteo Nadai
- Dipartimento di Medicina Molecolare, Università di Padova, via Gabelli 63, 35121 Padua, Italy
| | - Marco Folini
- Dipartimento di Oncologia Sperimentale e Medicina Molecolare, Fondazione IRCCS Istituto Nazionale dei Tumori, Via G. Amadeo 42,20133 Milano, Italy
| | - Matteo Scalabrin
- The RNA Institute of University at Albany (SUNY), Albany, New York
| | - Luca Germani
- Dipartimento di Chimica, Università di Pavia, V.le Taramelli 10, 27100 Pavia (Italy)
| | - Giovanna Sattin
- Dipartimento di Medicina Molecolare, Università di Padova, via Gabelli 63, 35121 Padua, Italy
| | - Mariella Mella
- Dipartimento di Chimica, Università di Pavia, V.le Taramelli 10, 27100 Pavia (Italy)
| | - Manlio Palumbo
- Department of Pharmaceutical and Pharmacological Sciences, Università di Padova, Via Marzolo 5, 35131 Padova, Italy
| | - Nadia Zaffaroni
- Dipartimento di Oncologia Sperimentale e Medicina Molecolare, Fondazione IRCCS Istituto Nazionale dei Tumori, Via G. Amadeo 42,20133 Milano, Italy
| | - Daniele Fabris
- The RNA Institute of University at Albany (SUNY), Albany, New York
| | - Mauro Freccero
- Dipartimento di Chimica, Università di Pavia, V.le Taramelli 10, 27100 Pavia (Italy)
| | - Sara N Richter
- Dipartimento di Medicina Molecolare, Università di Padova, via Gabelli 63, 35121 Padua, Italy
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Hampel SM, Pepe A, Greulich-Bode KM, Malhotra SV, Reszka AP, Veith S, Boukamp P, Neidle S. Mechanism of the antiproliferative activity of some naphthalene diimide G-quadruplex ligands. Mol Pharmacol 2012. [PMID: 23188717 DOI: 10.1124/mol.112.081075] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
G-quadruplexes are higher-order nucleic acid structures that can form in G-rich telomeres and promoter regions of oncogenes. Telomeric quadruplex stabilization by small molecules can lead to telomere uncapping, followed by DNA damage response and senescence, as well as chromosomal fusions leading to deregulation of mitosis, followed by apoptosis and downregulation of oncogene expression. We report here on investigations into the mechanism of action of tetra-substituted naphthalene diimide ligands on the basis of cell biologic data together with a National Cancer Institute COMPARE study. We conclude that four principal mechanisms of action are implicated for these compounds: 1) telomere uncapping with subsequent DNA damage response and senescence; 2) inhibition of transcription/translation of oncogenes; 3) genomic instability through telomeric DNA end fusions, resulting in mitotic catastrophe and apoptosis; and 4) induction of chromosomal instability by telomere aggregate formation.
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Affiliation(s)
- Sonja M Hampel
- School of Pharmacy, University College London, London, United Kingdom
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43
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Elahi MY, Bathaie S, Mousavi M, Hoshyar R, Ghasemi S. A new DNA-nanobiosensor based on G-quadruplex immobilized on carbon nanotubes modified glassy carbon electrode. Electrochim Acta 2012. [DOI: 10.1016/j.electacta.2012.05.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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44
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Polander LE, Barlow S, Seifried BM, Marder SR. A 2,6-Diformylnaphthalene-1,8:4,5-bis(dicarboximide): Synthesis and Knoevenagel Condensation with Malononitrile. J Org Chem 2012; 77:9426-8. [DOI: 10.1021/jo301876v] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lauren E. Polander
- School of
Chemistry and Biochemistry, Center for Organic
Photonics and Electronics, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Stephen Barlow
- School of
Chemistry and Biochemistry, Center for Organic
Photonics and Electronics, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Brian M. Seifried
- School of
Chemistry and Biochemistry, Center for Organic
Photonics and Electronics, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Seth R. Marder
- School of
Chemistry and Biochemistry, Center for Organic
Photonics and Electronics, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
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45
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Ohnmacht SA, Micco M, Petrucci V, Todd AK, Reszka AP, Gunaratnam M, Carvalho MA, Zloh M, Neidle S. Sequences in the HSP90 promoter form G-quadruplex structures with selectivity for disubstituted phenyl bis-oxazole derivatives. Bioorg Med Chem Lett 2012; 22:5930-5. [DOI: 10.1016/j.bmcl.2012.07.065] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2012] [Revised: 07/11/2012] [Accepted: 07/16/2012] [Indexed: 12/11/2022]
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Polander LE, Pandey L, Romanov A, Fonari A, Barlow S, Seifried BM, Timofeeva TV, Brédas JL, Marder SR. 2,6-Diacylnaphthalene-1,8:4,5-bis(dicarboximides): synthesis, reduction potentials, and core extension. J Org Chem 2012; 77:5544-51. [PMID: 22621328 DOI: 10.1021/jo3006232] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
2,6-Diacyl derivatives of naphthalene-1,8:4,5-bis(dicarboximide)s have been synthesized via Stille coupling reactions of the corresponding 2,6-distannyl derivative with acyl halides. Reaction of these diketones with hydrazine gave phthalazino[6,7,8,1-lmna]pyridazino[5,4,3-gh][3,8]phenanthroline-5,11(4H,10H)-dione fused-ring derivatives. The products were characterized by UV-vis absorption spectroscopy and electrochemistry, modeled using density functional theory calculations, and, in some cases, studied and compared using single-crystal X-ray diffraction.
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Affiliation(s)
- Lauren E Polander
- School of Chemistry and Biochemistry, Center for Organic Photonics and Electronics, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
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Doria F, Nadai M, Sattin G, Pasotti L, Richter SN, Freccero M. Water soluble extended naphthalene diimides as pH fluorescent sensors and G-quadruplex ligands. Org Biomol Chem 2012; 10:3830-40. [PMID: 22469919 DOI: 10.1039/c2ob07006e] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Extended naphthalene diimides (NDIs) fused to 1,4-dihydropyrazine-2,3-dione, containing two solubilizing moieties, have been synthesized. Fluorescence spectra of the new NDIs were remarkably affected by pH, as the second deprotonation of the dihydropyrazinedione moiety (pK(a) 6.9) switched off the emission. Binding to a G-quadruplex folded oligonucleotide and stoichiometry were evaluated by FRET melting assay and CD analysis. G-quadruplex binding was strongly enhanced shifting from pH 7.4 to pH 6.0 as a consequence of the dihydropyrazinedione moiety protonation. Cytotoxicity studies using two human telomerase-positive cell lines (HT29 and A549) revealed that the best G-quadruplex ligand was very active against the colon cell line, with an EC(50) of 300 nM.
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Affiliation(s)
- Filippo Doria
- Dipartimento di Chimica, Università di Pavia, Pavia, Italy.
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Collie GW, Promontorio R, Hampel SM, Micco M, Neidle S, Parkinson GN. Structural Basis for Telomeric G-Quadruplex Targeting by Naphthalene Diimide Ligands. J Am Chem Soc 2012; 134:2723-31. [DOI: 10.1021/ja2102423] [Citation(s) in RCA: 186] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gavin W. Collie
- CRUK Biomolecular Structure Group, The School of Pharmacy, University of London, London, WC1N 1AX, United Kingdom
| | - Rossella Promontorio
- CRUK Biomolecular Structure Group, The School of Pharmacy, University of London, London, WC1N 1AX, United Kingdom
| | - Sonja M. Hampel
- CRUK Biomolecular Structure Group, The School of Pharmacy, University of London, London, WC1N 1AX, United Kingdom
| | - Marialuisa Micco
- CRUK Biomolecular Structure Group, The School of Pharmacy, University of London, London, WC1N 1AX, United Kingdom
| | - Stephen Neidle
- CRUK Biomolecular Structure Group, The School of Pharmacy, University of London, London, WC1N 1AX, United Kingdom
| | - Gary N. Parkinson
- CRUK Biomolecular Structure Group, The School of Pharmacy, University of London, London, WC1N 1AX, United Kingdom
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50
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Polander LE, Romanov AS, Barlow S, Hwang DK, Kippelen B, Timofeeva TV, Marder SR. Stannyl Derivatives of Naphthalene Diimides and Their Use in Oligomer Synthesis. Org Lett 2012; 14:918-21. [DOI: 10.1021/ol203432x] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lauren E. Polander
- School of Chemistry and Biochemistry, School of Electrical and Computer Engineering, Center for Organic Photonics and Electronics, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States, and Department of Chemistry, New Mexico Highlands University, Las Vegas, New Mexico 87701, United States
| | - Alexander S. Romanov
- School of Chemistry and Biochemistry, School of Electrical and Computer Engineering, Center for Organic Photonics and Electronics, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States, and Department of Chemistry, New Mexico Highlands University, Las Vegas, New Mexico 87701, United States
| | - Stephen Barlow
- School of Chemistry and Biochemistry, School of Electrical and Computer Engineering, Center for Organic Photonics and Electronics, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States, and Department of Chemistry, New Mexico Highlands University, Las Vegas, New Mexico 87701, United States
| | - Do Kyung Hwang
- School of Chemistry and Biochemistry, School of Electrical and Computer Engineering, Center for Organic Photonics and Electronics, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States, and Department of Chemistry, New Mexico Highlands University, Las Vegas, New Mexico 87701, United States
| | - Bernard Kippelen
- School of Chemistry and Biochemistry, School of Electrical and Computer Engineering, Center for Organic Photonics and Electronics, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States, and Department of Chemistry, New Mexico Highlands University, Las Vegas, New Mexico 87701, United States
| | - Tatiana V. Timofeeva
- School of Chemistry and Biochemistry, School of Electrical and Computer Engineering, Center for Organic Photonics and Electronics, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States, and Department of Chemistry, New Mexico Highlands University, Las Vegas, New Mexico 87701, United States
| | - Seth R. Marder
- School of Chemistry and Biochemistry, School of Electrical and Computer Engineering, Center for Organic Photonics and Electronics, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States, and Department of Chemistry, New Mexico Highlands University, Las Vegas, New Mexico 87701, United States
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