A selective G-quadruplex DNA-stabilizing ligand based on a cyclic naphthalene diimide derivative

Molecules

Volumn 20, Issue 6, 2015, Pages 10963-10979

  Islam, Md Monirul ^a   Fujii, Satoshi ^a   Sato, Shinobu ^a   Okauchi, Tatsuo ^a   Takenaka, Shigeori ^a  

^a KYUSHU INSTITUTE OF TECHNOLOGY   (Japan)

Author keywords

Cyclic naphthalene diimide; G quartet; Human telomeric DNA; Promoter region; Thrombin binding aptamer

Indexed keywords

GUANINE QUADRUPLEX; IMIDE; LIGAND; NAPHTHALENE DERIVATIVE; NAPHTHALENEDIIMIDE; PROTEIN BINDING;

CHEMICAL STRUCTURE; CHEMISTRY; CIRCULAR DICHROISM; CONFORMATION; DRUG EFFECTS; TRANSITION TEMPERATURE;

CIRCULAR DICHROISM; G-QUADRUPLEXES; IMIDES; LIGANDS; MODELS, MOLECULAR; MOLECULAR CONFORMATION; MOLECULAR STRUCTURE; NAPHTHALENES; PROTEIN BINDING; TRANSITION TEMPERATURE;

EID: 84938241127     PISSN: None     EISSN: 14203049     Source Type: Journal    
DOI: 10.3390/molecules200610963     Document Type: Article

References (44)

1. Neidle, S. Therapeutic Applications of Quadruplex Nucleic Acid, 1st ed.; Academic Press: London, UK, 2012; pp. 1-15.
2. Avino, A.; Fabrega, C.; Tintore, M.; Eritja, R. Thrombin binding aptamer, more than a simple aptamer: Chemically modified derivatives and biomedical applications. Curr. Pharm. Des. 2012, 18, 2036-2047.
3. Ou, T.; Lu, Y.; Tan, J.; Huang, Z.; Wong, K.; Gu, L. G-Quadruplexes: Targets in Anticancer Drug Design. Chem. Med. Chem. 2008, 3, 690-713.
4. Dai, J.; Carver, M.; Yang, D. Polymorphism of human telomeric quadruplex structures. Biochimie 2008, 90, 1172-1183.
5. Huppert, J.L. Four-stranded nucleic acids: Structure, function and targeting of G-quadruplexes. Chem. Soc. Rev. 2008, 37, 1375-1384.
6. Haider, S.M.; Neidle, S.; Parkinson, G.N. A structural analysis of G-quadruplex/ligand interactions. Biochimie 2011, 93, 1239-1251.
7. Monchaud, D.; Teulade-Fichou, M.P. A hitchhiker's guide to G-quadruplex ligands. Org. Biomol. Chem. 2008, 6, 627-636.
8. Davis, J.T. G-Quartets 40 Years Later: From 5?-GMP to Molecular Biology and Supramolecular Chemistry. Angew. Chem. Int. Ed. Engl. 2004, 43, 668-698.
9. Nielsen, M.C.; Ulven, T. Macrocyclic G-Quadruplex Ligands. Curr. Med. Chem. 2010, 17, 3438-3448.
10. Czerwinska, I.; Sato, S.; Juskowiak, B.; Takenaka, S. Interactions of cyclic and non-cyclic naphthalene diimide derivatives with different nucleic acids. Bioorg. Med. Chem. 2014, 22, 2593-2601.
11. Hampel, S.M.; Sidibe, A.; Gunaratnam, M.; Riou, J.; Neidle, S. Tetrasubstituted naphthalene diimide ligands with selectivity for telomeric G-quadruplexes and cancer cells. Bioorganic Med. Chem. Lett. 2010, 20, 6459-6463.
12. Marchetti, C.; Minarini, A.; Tumiatti, V.; Moraca, F.; Parrotta, L.; Alcaro, S.; Rigo, R.; Sissi, C.; Gunaratnam, M.; Ohnmacht, S.A.; et al. Macrocyclic naphthalene diimides as G-quadruplex binders. Bioorg. Med. Chem. 2015, in press.
13. 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, 3335-3347.
14. Collie, G.W.; Promontorio, R.; Hampel, S.M.; Micco, M.; Neidle, S.; Parkinson, G.N. Structural Basis for Telomeric G-Quadruplex Targeting by Naphthalene Diimide Ligands. J. Am. Chem. Soc. 2012, 134, 2723-2731.
15. Micco, M.; Collie, G.W.; Dale, A.G.; Ohnmacht, S.A.; Pazitna, I.; Gunaratnam, M.; Reszka, A.P.; 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, 2959-2974.
16. Nadai, M.; Doria, F.; Antonio, M.D.; Sattin, G.; Germani, L.; Percivalle, C.; Palumbo, M.; Richter, S.N.; Freccero, M. Naphthalene diimide scaffolds with dual reversible and covalent interaction properties towards G-quadruplex. Biochimie 2011, 93, 1328-1340.
17. Doria, F.; Oppi, A.; Manoli, F.; Botti, S.; Kandoth, N.; Grande, V.; Manet, I.; Freccero, M. A naphthalene diimide dyad for fluorescence switch-on detection of G-quadruplexes. Chem. Commun. 2015, 51, 9105-9108.
18. Doria, F.; Nadai, M.; Folini, M.; Scalabrin, M.; Germani, L.; Sattin, G.; Mella, M.; Palumbo, M.; Zaffaroni, N.; Fabris, D.; et al. Targeting Loop Adenines in G-Quadruplex by a Selective Oxirane. Chem. Eur. J. 2013, 19, 78-81.
19. Doria, F.; Nadai, M.; Folini, M.; Antonio, M.D.; Germani, L.; Percivalle, C.; Sissi, C.; Zaffaroni, N.; Alcaro, S.; Artese, A.; et al. Hybrid ligand-alkylating agents targeting telomeric G-quadruplex Structures. Org. Biomol. Chem. 2012, 10, 2798-2806.
20. Antonio, M.D.; Folini, M.; Richter, S.N.; Bertipaglia, C.; Mella, M.; Sissi, C.; Manlio Palumbo, M.; Freccero, M. Quinone Methides Tethered to Naphthalene Diimides as Selective G-Quadruplex Alkylating Agents. J. Am. Chem. Soc. 2009, 131, 13132-13141.
21. Nadai, M.; Doria, F.; Germani, L.; Richter, S.N.; Freccero, M. A Photoreactive G-Quadruplex Ligand Triggered by Green Light. Chem. Eur. J. 2015, 21, 2330-2334.
22. Esaki, Y.; Islam, M.M.; Fujii, S.; Sato, S.; Takenaka, S. Design of tetraplex specific ligands: Cyclic naphthalene diimide. Chem. Commun. 2014, 50, 5967-5969.
23. Cian, A.D.; Guittat, L.; Kaiser, M.; Sacca, B.; Amrane, S.; Bourdoncle, A.; Teulade-Fichou, M.P.; Alberti, P.; Lacroix, L.; Mergny, J.L. Fluorescence-based melting assays for studying quadruplex ligands. Methods 2007, 42, 183-195.
24. Ambrus, A.; Chen, D.; Dai, J.; Bialis, T.; Jones, R.A.; Yang, D. Human telomeric sequence forms a hybrid-type intramolecular G-quadruplex structure with mixed parallel/antiparallel strands in potassium solution. Nucleic Acids Res. 2006, 34, 2723-2735.
25. Hansel, R.; Lohr, F.; Trantirkova, S.F.; Bamberg, E.; Trantirek, L.; Dotsch, V. The parallel G-quadruplex structure of vertebrate telomeric repeat sequences is not the preferred folding topology under physiological conditions. Nucleic Acids Res. 2011, 39, 5768-5775.
26. Dai, J.X.; Carver, M.; Hurley, L.H.; Yang, D.Z. Solution structure of a 2:1 quindoline-c-MYC G-quadruplex: Insights into G-quadruplex-interactive small molecule drug design. J. Am. Chem. Soc. 2011, 133, 17673-17680.
27. Phan, A.T.; Kuryavyi, V.; Burge, S.; Neidle, S.; Patel, D.J. Structure of an Unprecedented G-Quadruplex Scaffold in the Human c-kit Promoter. J. Am. Chem. Soc. 2007, 129, 4386-4392.
28. Arora, A.; Maiti, S. Effect of Loop Orientation on Quadruplex-TMPyP4 Interaction. J. Phys. Chem. B 2008, 112, 8151-8159.
29. Macaya, R.F.; Schultze, P.; Smith, F.W.; Roet, J.A.; Feigon, J. Thrombin-binding DNA aptamer forms a unimolecular quadruplex structure in solution. Proc. Natl. Acad. Sci. USA 1993, 90, 3745-3749.
30. Toro, M.; Gargallo, R.; Eritja, R.; Jaumot, J. Study of the interaction between the G-quadruplex-forming thrombin-binding aptamer and the porphyrin 5,10,15,20-tetrakis-(N-methyl-4-pyridyl)-21,23H-porphyrin tetratosylate. Anal. Biochem. 2008, 379, 8-15.
31. McGhee, J.D.; vonHippel, P.H. Theoretical aspects of DNA-protein interactions: Co-operative and non-co-operative binding of large ligands to a one-dimensional homogeneous lattice. J. Mol. Biol. 1974, 86, 469-489.
32. Benesi, H.A.; Hildebrand, J.H. A Spectrophotometric Investigation of the Interaction of Iodine with Aromatic Hydrocarbons. J. Am. Chem. Soc. 1949, 71, 2703-2707.
33. Islam, M.M.; Fujii, S.; Sato, S.; Okauchi, T.; Takenaka, S. Thermodynamics and Kinetic Studies in the Binding Interaction of Cyclic Naphthalene Diimide Derivatives with Double Stranded DNAs. Bioorganic Med. Chem. 2015, in press.
34. Phan, A.T.; Kuryavyi, V.; Luu, K.N.; Patel, D.J. Structure of two intramolecular G-quadruplexes formed by natural human telomere sequences in K+ solution. Nucleic Acids Res. 2007, 35, 6517-6525.
35. Luu, K.N.; Phan, A.T.; Kuryavyi, V.; Lacroix, L.; Patel, D.J. Structure of the Human Telomere in K+ Solution: An Intramolecular (3 + 1) G-Quadruplex Scaffold. J. Am. Chem. Soc. 2006, 128, 9963-9970.
36. Du, Y.; Zhang, D.; Chen, W.; Zhang, M.; Zhou, Y.; Zhou, X. Cationic N-confused porphyrin derivative as a better molecule scaffold for G-quadruplex recognition. Bioorganic Med. Chem. 2010, 18, 1111-1116.
37. Nagatoishi, S.; Tanaka, Y.; Tsumoto, K. Circular dichroism spectra demonstrate formation of the thrombin-binding DNA aptamer G-quadruplex under stabilizing-cation-deficient conditions. Biochem. Biophys. Res. Commun. 2007, 352, 812-817.
38. Dash, J.; Shirude, P.S.; Hsu, S.D.; Balasubramanian, S. Diarylethynyl Amides That Recognize the Parallel Conformation of Genomic Promoter DNA G-Quadruplexes. J. Am. Chem. Soc. 2008, 130, 15950-15956.
39. Wei, C.; Wang, Y.; Zhang, M. Synthesis and binding studies of novel di-substituted phenanthroline compounds with genomic promoter and human telomeric DNA G-quadruplexes. Org. Biomol. Chem. 2013, 11, 2355-2364.
40. Dhamodharan, V.; Harikrishna, S.; Jagadeeswaran, C.; Halder, K.; Pradeepkumar, P.I. Selective G-quadruplex DNA Stabilizing Agents Based on Bisquinolinium and Bispyridinium Derivatives of 1,8-Naphthyridine. J. Org. Chem. 2012, 77, 229-242.
41. Hayden, K.L.; Graves, D.E. Addition of Bases to the 5?-end of Human Telomeric DNA: Influences on Thermal Stability and Energetics of Unfolding. Molecules 2014, 19, 2286-2298.
42. Ragazzon, P.; Chaires, J.B. Use of competition dialysis in the discovery of G-quadruplex selective ligands. Methods 2007, 43, 313-323.
43. Fichou, M.P.T.; Carrasco, C.; Guittat, L.; Bailly, C.; Alberti, P.; Mergny, J.L.; David, A.; Lehn, J.M.; Wilson, W.D. Selective Recognition of G-Quadruplex Telomeric DNA by a Bis(quinacridine) Macrocycle. J. Am. Chem. Soc. 2003, 125, 4732-4740.
44. Tanious, F.A.; Yen, S.F.; Wilson, W.D. Kinetic and Equilibrium Analysis of a Threading Intercalation Mode: DNA Sequence and Ion Effects. Biochemistry 1991, 30, 1813-1819.