A more detailed picture of the interactions between virtual screening-derived hits and the DNA G-quadruplex: NMR, molecular modelling and ITC studies

Biochimie

Volumn 93, Issue 8, 2011, Pages 1280-1287

  Trotta, Roberta ^a   De Tito, Stefano ^a   Lauri, Ilaria ^a   La Pietra, Valeria ^a   Marinelli, Luciana ^a   Cosconati, Sandro ^a   Martino, Luigi ^b   Conte, Maria R ^b   Mayol, Luciano ^a   Novellino, Ettore ^a   Randazzo, Antonio ^a  

^a UNIVERSITY OF NAPLES FEDERICO II   (Italy)

^b KING'S COLLEGE LONDON   (United Kingdom)

Author keywords

Brominated G quadruplex; Isothermal titration calorimetry; NMR titration; Virtual screening

Indexed keywords

DISTAMYCIN A; GUANINE QUADRUPLEX; MOLECULAR SCAFFOLD;

ARTICLE; BINDING AFFINITY; DNA STRUCTURE; DRUG DNA INTERACTION; DRUG SCREENING; DRUG STRUCTURE; ISOTHERMAL TITRATION CALORIMETRY; MOLECULAR MODEL; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; VIRTUAL REALITY;

BINDING SITES; CALORIMETRY; DISTAMYCINS; DRUG EVALUATION, PRECLINICAL; G-QUADRUPLEXES; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR;

EID: 79960697708     PISSN: 03009084     EISSN: 61831638     Source Type: Journal    
DOI: 10.1016/j.biochi.2011.05.021     Document Type: Article

References (30)

1. T. de Lange Shelterin: the protein complex that shapes and safeguards human telomeres Genes Dev. 19 2005 2100 2110 (Pubitemid 41330312)
2. C. Autexier, and N.F. Lue The structure and function of telomerase reverse transcriptase Annu. Rev. Biochem. 75 2006 493 517 (Pubitemid 44118041)
3. W.C. Hahn, S.A. Stewart, M.W. Brooks, S.G. York, E. Eaton, A. Kurachi, R.L. Beijersbergen, J.H. Knoll, M. Meyerson, and R.A. Weinberg Inhibition of telomerase limits the growth of human cancer cells Nat. Med. 5 1999 1164 1170 (Pubitemid 29474421)
4. D. Sun, B. Thompson, B.E. Cathers, M. Salazar, S.M. Kerwin, J.O. Trent, T.C. Jenkins, S. Neidle, and L.H. Hurley Inhibition of human telomerase by a G-quadruplex-interactive compound J. Med. Chem. 40 1997 2113 2116 (Pubitemid 27284346)
5. D. Ma, C. Che, and S. Yan Platinum(II) complexes with dipyridophenazine ligands as human telomerase inhibitors and luminescent probes for G-quadruplex DNA J. Am. Chem. Soc. 131 2009 1835 1846
6. T. Lai Discovery of a drug-like G-quadruplex binding ligand by high-throughput docking ChemMedChem 3 2008 881 884
7. S.E. Burge, G.N. Parkinson, P. Hazel, A.K. Todd, and S. Neidle Quadruplex DNA: sequence, topology and structure Nucleic Acids Res. 34 2006 5402 5415 (Pubitemid 44742430)
8. R. Rodriquez, S. Muller, J.A. Yeoman, C. Trentesaux, J.-F. Riou, and S. Balasubramanian A novel small molecule that alters shelterin integrity and triggers a DNA-damage response at telomeres J. Am. Chem. Soc. 130 2008 15758 15759
9. A. de Cian, L. Lacroix, C. Douarre, N. Temime-Smaali, C. Trentesaux, J.-F. Riou, and J.-L. Mergny Targeting telomeres and telomerase Biochimie 90 2008 131 155 (Pubitemid 350245369)
10. T. Ou, Y. Lu, J. Tan, Z. Huang, K. Wong, and L. Gu G-quadruplexes: targets in anticancer drug design ChemMedChem 3 2008 690 713
11. 4 Chem. Commun. 11 2001 1030 1031 (Pubitemid 32521850)
12. 1H-NMR study Nucleosides Nucleotides Nucleic Acids 21 2002 535 545 (Pubitemid 35417090)
13. L. Martino, A. Virno, B. Pagano, A. Virgilio, S. Di Micco, A. Galeone, C. Giancola, G. Bifulco, L. Mayol, and A. Randazzo J. Am. Chem. Soc. 129 2007 15950 15956
14. S. Cosconati, L. Marinelli, R. Trotta, A. Virno, S. De Tito, R. Romagnoli, B. Pagano, V. Limongelli, C. Giancola, P.G. Baraldi, L. Mayol, E. Novellino, and A. Randazzo Structural and conformational requisites in DNA quadruplex groove binding: another piece to the puzzle J. Am. Chem. Soc. 132 18 2010 6425 6433
15. B. Pagano, A. Virno, C.A. Mattia, L. Mayol, A. Randazzo, and C. Giancola Targeting DNA quadruplexes with distamycin A and its derivatives: an ITC and NMR study Biochimie 90 8 2008 1224 1232
16. S. Cosconati, L. Marinelli, R. Trotta, A. Virno, L. Mayol, E. Novellino, A.J. Olson, and A. Randazzo Tandem application of virtual screening and NMR experiments in the discovery of brand new DNA quadruplex groove binders J. Am. Chem. Soc. 131 2009 16336 16337
17. T.L. Hwang, and A.J. Shaka Water suppression that works. Excitation sculpting using arbitrary waveforms and pulsed field gradients J. Magn. Reson. A112 1995 275 279
18. C. Dalvit Efficient multiple-solvent suppression for the study of the interactions of organic solvents with biomolecules J. Biomol. NMR 11 1998 437 444 (Pubitemid 128512224)
19. J. Jeener, B. Meier, H.P. Bachmann, and R.R. Ernst Investigation of exchange processes by two-dimensional NMR spectroscopy J. Chem. Phys. 71 1979 4546 4553
20. D. Marion, M. Ikura, R. Tschudin, and A. Bax Rapid recording of 2D NMR spectra without phase cycling: application to the study of hydrogen exchange in proteins J. Magn. Reson. 85 1989 393 399
21. 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)
22. S. Cosconati, J.A. Hong, E. Novellino, K.S. Carroll, D.S. Goodsell, and A.J. Olson Structure-based virtual screening and biological evaluation of Mycobacterium tuberculosis adenosine 5′-phosphosulfate reductase inhibitors J. Med. Chem. 51 2008 6627 6630
23. Maestro, Version 9.0.211 2009 Schrodinger, L.L.C. New York, NY
24. E.F. Pettersen, T.D. Goddard, C.C. Huang, G.S. Couch, D.M. Greenblatt, E.C. Meng, and T.E. Ferrin UCSF chimera - a visualization system for exploratory research and analysis J. Comput. Chem. 25 13 2004 1605 1612
25. C.R. Cantor, R.R. Warshaw, and H. Shapiro Oligonucleotide interactions. 3. Circular dichroism studies of the conformation of deoxyoligonucleotides Biopolymers 9 1970 1059 1077
26. A. Virgilio, V. Esposito, A. Randazzo, L. Mayol, and A. Galeone 8-Methyl-2′-deoxyguanosine incorporation into parallel DNA quadruplex structures Nucleic Acids Res. 33 19 2005 6188 6195 (Pubitemid 41742556)
27. L. Petraccone, E. Erra, V. Esposito, A. Randazzo, A. Galeone, G. Barone, and C. Giancola Biophysical properties of quadruple helices of modified human telomeric DNA Biopolymers 77 2 2005 75 85 (Pubitemid 40269318)
28. B. Pagano, C.A. Mattia, and C. Giancola Applications of isothermal titration calorimetry in biophysical studies of G-quadruplexes Int. J. Mol. Sci. 10 2009 2935 2957
29. S.W. Sigurskjold Exact analysis of competition ligand binding by displacement isothermal titration calorimetry Anal. Biochem. 277 2000 260 266
30. Y.L. Zhang, and Z.Y. Zhang Low-affinity binding determined by titration calorimetry using a high-affinity coupling ligand: a thermodynamic study of ligand binding to protein tyrosine phosphatase 1B Anal. Biochem. 261 1998 139 148