Acridine and quindoline oligomers linked through a 4-aminoproline backbone prefer G-quadruplex structures

Biochimica et Biophysica Acta - General Subjects

Volumn 1810, Issue 8, 2011, Pages 769-776

  Ferreira, Rubén ^a   Artali, Roberto ^b   Farrera Sinfreu, Josep ^c   Albericio, Fernando ^c   Royo, Miriam ^c   Eritja, Ramon ^a   Mazzini, Stefania ^b  

^a BIOMATERIALES Y NANOMEDICINA CIBER BBN   (Spain)

^b UNIVERSITY OF MILAN   (Italy)

^c UNIVERSITY OF BARCELONA   (Spain)

Author keywords

Acridine; DNA binding drugs; G quadruplex; NMR; Oligonucleotides; Quindoline

Indexed keywords

4 AMINOPROLINE DERIVATIVE; INTERCALATING AGENT; MYC PROTEIN; PROTEIN BCL 2; UNCLASSIFIED DRUG;

ARTICLE; BCL 2 GENE; BINDING AFFINITY; BINDING COMPETITION; DRUG DNA BINDING; DRUG STRUCTURE; MOLECULAR DYNAMICS; MOLECULAR MODEL; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; ONCOGENE; ONCOGENE C MYC; PRIORITY JOURNAL; PROMOTER REGION; TELOMERE;

ACRIDINES; ALKALOIDS; DNA; GENES, BCL-2; GENES, MYC; HUMANS; INDOLES; MODELS, MOLECULAR; MOLECULAR STRUCTURE; QUINOLINES;

EID: 79959862951     PISSN: 03044165     EISSN: 18728006     Source Type: Journal    
DOI: 10.1016/j.bbagen.2011.04.013     Document Type: Article

References (34)

1. R. Palchaudhuri, and P.J. Hergerother DNA as a target for anticancer compounds: methods to determine the mode of binding and the mechanism of action Curr. Opin. Biotechnol. 18 2007 497 503
2. B.A. Neto, and A.A. Lapis Recent developments in the chemistry of deoxyribonucleic acid (DNA) intercalators: principles, design, synthesis, applications and trends Molecules 14 2009 1725 1746
3. D.P. Arya, and B. Willis Reaching into the major groove of B-DNA: synthesis and nucleic acid binding of a neomycin-Hoechst 33258 conjugate J. Am. Chem. Soc. 125 2003 12398 12399 (Pubitemid 37254744)
4. E. Fechter, B. Olenyuk, and P.B. Dervan Design of a sequence specific DNA bis-intercalator Angew. Chem. Int. Ed. 43 2004 3591 3594 (Pubitemid 39257546)
5. D.J. Patel, A.T. Phan, and V. Kuryavyi Human telomere, oncogenic promoter and 5′-UTR G-quadruplexes: diverse higher order DNA and RNA targets for cancer therapeutics Nucleic Acids Res. 35 2007 7429 7455
6. G.N. Parkinson, M.P.H. Lee, and S. Neidle Crystal structure of parallel quadruplexes from human telomeric DNA Nature 417 2002 876 880 (Pubitemid 34670337)
7. J.L. Huppert Hunting G-quadruplexes Biochimie 90 2008 1140 1148
8. L.H. Hurley Secondary DNA structures as molecular targets for cancer therapeutics Biochem. Soc. Trans. 29 2001 692 696 (Pubitemid 33131762)
9. H. Han, and L.H. Hurley G-quadruplex DNA: a potential target for anti-cancer drug design Trends in Pharm. Sci. 21 2000 136 142 (Pubitemid 30190138)
10. D. Monchaud, and M.P. Teulade-Fichou A hitchhiker's guide to G-quadruplex ligands Org. Biomol. Chem. 6 2008 627 636 (Pubitemid 351972601)
11. N.H. Campbell, G.N. Parkinson, A.P. Reszka, and S. Neidle Structural basis of DNA quadruplex recognition by an acridine drug J. Am. Chem. Soc. 130 2008 6722 6724 (Pubitemid 351748405)
12. A. Aviñó, I. Navarro, J. Farrera-Sinfreu, M. Royo, J. Aymamí, A. Delgado, A. Llebaria, F. Albericio, and R. Eritja Solid-phase synthesis of oligomers carrying several chromophore units linked by phosphodiester backbones Bioorg. Med. Chem. Lett. 18 2008 2306 2310 (Pubitemid 351442902)
13. J. Farrera-Sinfreu, A. Aviñó, I. Navarro, J. Aymamí, N.G. Beteta, S. Varón, R. Pérez-Tomás, W. Castillo-Avila, R. Eritja, F. Albericio, and M. Royo Design, synthesis and antiproliferative properties of oligomers with chromophore units linked by amide backbones Bioorg. Med. Chem. Lett. 18 2008 2440 2444 (Pubitemid 351447285)
14. R. Ferreira, A. Aviñó, R. Pérez-Tomás, R. Gargallo, and R. Eritja Synthesis and G-quadruplex-binding properties of defined acridine oligomers J. Nucleic Acids 2010 10.4061/2010/489060 article ID 489060 10 pages
15. A. Siddiqui-Jain, C.L. Grand, D.J. Bearss, and L.H. Hurley Direct evidence for a G-quadruplex in a promoter region and its targeting with a small molecule to repress c-myc transcription Proc. Natl. Acad. Sci. USA 99 2002 11593 11598 (Pubitemid 34994444)
16. J. Dai, T.S. Dexheimer, D. Chen, M. Carver, A. Ambrus, R.A. Jones, and D. Yang An intermolecular G-quadruplex structure with mixed parallel/antiparallel G-strands formed in the BCL-2 promoter region in solution J. Am. Chem. Soc. 128 2006 1096 1098 (Pubitemid 43190620)
17. M. Del Toro, P. Puceck, A. Aviñó, J. Jaumot, C. González, R. Eritja, and R. Gargallo Targeting the G-quadruplex-forming region near the P1 promoter in the human BCL-2 gene with the cation porphyrin TMPyP4 and with the complementary C-rich strand Biochimie 91 2009 894 902
18. A. Kumar, R.R. Ernst, and K. Wüthrich A two-dimensional nuclear Overhauser enhancement (2D NOE) experiment for the elucidation of complete proton-proton cross-relaxation networks in biological macromolecules Biochem. Biophys. Res. Comm. 95 1980 1 6
19. L. Braunschweiler, and R.R. Ernst Coherence transfer by isotropic mixing. Application to proton correlation spectroscopy J. Magn. Reson. 53 1983 521 528
20. T.D. Goddard, and D.G. Kneller SPARKY 3 2004 University of California San Francisco, USA
21. Y. Wang, and D.J. Patel Guanine residues in d(T2AG3) and d(T2G4) form parallel-stranded potassium cation stabilized G-quadruplexes with anti glycosidic torsion angles in solution Biochemistry 31 1992 8112 8119
22. S. Mazzini, R. Mondelli, and E. Ragg Structure and dynamics of intercalation complexes of anthracyclines with d(CGATCG)(2) and d(CGTACG)(2). 2D-H-1 and P-31 NMR investigations J. Chem. Soc., Perkin Trans 2 1998 1983 1991 (Pubitemid 128434837)
23. G.M. Morris, D.S. Goodsell, R.S. Halliday, R. Huey, W.E. Hart, R.K. Belew, and A.J. Olson Automated docking using Lamarckian Genetic Algorithm and an empirical binding free energy function J. Comput. Chem. 19 1998 1639 1662 (Pubitemid 128590223)
24. R. Huey, G.M. Morris, A.J. Olson, and D.S. Goodsell A semiempirical free energy force field with charge-based desolvation J. Comput. Chem. 28 2007 1145 1152 (Pubitemid 46506716)
25. F.J. Solis, and J.-B. Wets Minimization by random search techniques Math. Oper. Res. 6 1981 19 30
26. M.F. Sanner Python: a programming language for software integration and development J. Mol. Graphics Modell. 17 1999 57 61 (Pubitemid 30029318)
27. J. Gasteiger, and M. Marsili Iterative partial equalization of orbital electronegativity-a rapid access to atomic charges Tetrahedron 36 1980 3219 3228
28. J. Gros, F. Rosu, S. Amrane, A. De Cian, V. Gabelica, L. Lacroix, and J.L. Mergny Guanines are a quartet's best friends: impact of base substitutions on the kinetics and stability of tetramolecular quadruplexes Nucleic Acids Res. 35 2007 3064 3075 (Pubitemid 47073644)
29. L.C. Bock, L.C. Griffin, J.A. Latham, E.H. Vermaas, and J.J. Toole Selection of single-stranded DNA molecules that bind and inhibit human thrombin Nature 355 1992 564 566
30. 3] G-tetraplex Structure 1 1993 263 282 (Pubitemid 2031126)
31. J. Ren, and J.B. Chaires Sequence and structural selectivity of nucleic acid binding ligands Biochemistry 38 1999 16067 16075 (Pubitemid 129520527)
32. P. Ragazzon, and J.B. Chaires Use of competition dialysis in the discovery of G-quadruplex selective ligands Methods 43 2007 313 323 (Pubitemid 47633211)
33. Y.J. Lu, T.M. Ou, J.H. Tan, J.Q. Hou, W.Y. Shao, D. Peng, N. Sun, X.D. Wang, W.B. Wu, X.Z. Bu, Z.S. Huang, D.L. Ma, K.Y. Wong, and L.Q. Gu 5-N-methylated quindoline derivatives as telomeric G-quadruplex stabilizing ligands: effects of 5-N positive charge on quadruplex binding affinity and cell proliferation J. Med. Chem. 51 2008 6381 6392
34. O.Y. Fedoroff, M. Salazar, H. Han, V.V. Chemeris, S.M. Kerwin, and L.H. Hurley NMR-based model of a telomerase-inhibiting compound bound to G-quadruplex DNA Biochemistry 37 1998 12367 12374 (Pubitemid 28427520)