Thermodynamics of binding of Di- and tetrasubstituted naphthalene diimide ligands to DNA G-quadruplex

Journal of Physical Chemistry B

Volumn 119, Issue 8, 2015, Pages 3335-3347

  Prato, Gary ^a   Silvent, Samantha ^a   Saka, Sammy ^a   Lamberto, Massimiliano ^a   Kosenkov, Dmytro ^a  

^a MONMOUTH UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; CALCULATIONS; GIBBS FREE ENERGY; IONS; MOLECULAR MODELING; MOLECULAR ORBITALS; NAPHTHALENE; THERMODYNAMICS;

ANTI-CANCER THERAPEUTICS; BINDING AFFINITIES; COMPUTATIONAL METHODOLOGY; FRAGMENT MOLECULAR ORBITAL METHODS; HIGH-ORDER STRUCTURE; NAPHTHALENE DIIMIDE; NON-COVALENT INTERACTION; THERMODYNAMICS OF BINDINGS;

LIGANDS;

GAS; GUANINE QUADRUPLEX; IMIDE; LIGAND; NAPHTHALENE DERIVATIVE; NAPHTHALENEDIIMIDE;

BIOLOGICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; FREEZING; GAS; HUMAN; MOLECULAR DOCKING; THERMODYNAMICS;

FREEZING; G-QUADRUPLEXES; GASES; HUMANS; IMIDES; LIGANDS; MODELS, GENETIC; MOLECULAR DOCKING SIMULATION; MOLECULAR STRUCTURE; NAPHTHALENES; THERMODYNAMICS;

EID: 84923863074     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp509637y     Document Type: Article

References (50)

1. Stegle, O.; Payet, L.; Mergny, J. L.; Mackay, J. C.; Huppert, J. L. Predicting and Understanding the Stability of G-Quadruplexes Bioinformatics 2009, 25, 374-382
2. Neidle, S. Human Telomeric G-Quadruplex: The Current Status of Telomeric G-Quadruplexes as Therapeutic Targets in Human Cancer FEBS J. 2010, 277, 1118-1125
3. Collie, G. W.; Promontorio, R.; Hampel, S. M.; Micco, M.; Neidle, S. Structural Basis for Telomeric G-Quadruplex Targeting by Naphthalene Diimide Ligands J. Am. Chem. Soc. 2012, 134, 2723-2731
4. Giancola, C.; Pagano, B. Energetics of Ligand Binding to G-Quadruplexes Top. Curr. Chem. 2012, 330, 211-242
5. Reed, J. E.; Arnal, A. A.; Neidle, S.; Vilar, R. Stabilization of G-Quadruplex DNA and Inhibition of Telomerase Activity by Square-Planar Nickel(II) Complexes J. Am. Chem. Soc. 2006, 128, 5992-5993
6. Gunaratnam, M.; De La Fuente, M.; Hampel, S. M.; Todd, A. K.; Reszka, A. P.; Schatzlein, A.; Neidle, S. Targeting Pancreatic Cancer with a G-Quadruplex Ligand J. Bioorg. Med. Chem. 2011, 19, 7151-7157
7. Gunaratnam, M.; Beltran, M.; Galesa, K.; Haider, S. M.; Reszka, A. P.; Cuenca, F.; Fletcher, J. A.; Neidle, S. Targeting Human Gastrointestinal Stromal Tumour Cells with a Quadruplex-Binding Small Molecule J. Med. Chem. 2009, 52, 2774-2783
8. Ginnari-Satriani, L.; Casagrande, V.; Bianco, A.; Ortaggi, G.; Franceschin, M. A. Hydrophilic Three Side-Chained Triazatruxene as a New Strong and Selective G-Quadruplex Ligand Org. Biomol. Chem. 2009, 7, 2513-2516
9. Doria, F.; Nadai, M.; Folini, M.; Di Antonio, M.; Germani, L.; Percivalle, C.; Sissi, C.; Zaffaroni, N.; Alcaro, S.; Artese, A.; Richter, S. N.; Freccero, M. Hybrid Ligand-Alkylating Agents Targeting Telomeric G-Quadruplex Structures Org. Biomol. Chem. 2012, 10, 2798-2806
10. Di Antonio, M.; Doria, F.; Richter, S. N.; Bertipaglia, C.; Mella, M.; Sissi, C.; Palumbo, M.; Freccero, M. Quinone Methides Tethered to Naphthalene Diimides as Selective G-Quadruplex Alkylating Agents J. Am. Chem. Soc. 2009, 131, 13132-13141
11. Doria, F.; Nadai, M.; Folini, M.; Scalabrin, M.; Germani, L.; Sattin, G.; Mella, M.; Palumbo, M.; Zaffaroni, N.; Fabris, D.; Freccero, M.; Richter, S. N. Targeting Loop Adenines in G-Quadruplex by a Selective Oxirane Chem. -Eur. J. 2013, 19, 78-81
12. Nadai, M.; Doria, F.; Di Antonio, M.; 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
13. Doria, F.; Manet, I.; Grande, V.; Monti, S.; Freccero, M. Water-Soluble Naphthalene Diimides as Singlet Oxygen Sensitizers J. Org. Chem. 2013, 78, 8065-8073
14. Doria, F.; Nadai, M.; Sattin, G.; Pasotti, L.; Richter, S. N.; Freccero, M. Water Soluble Extended Naphthalene Diimides as pH Fluorescent Sensors and G-Quadruplex Ligands Org. Biomol. Chem. 2012, 10, 3830-3840
15. Steullet, V.; Dixon, D. W. Self-Stacking of Naphthalene Bis(dicarboximide)s Probed by NMR J. Chem. Soc., Perkin Trans. 2 1999, 7, 1547-1558
16. Hehre, W.; Ohlinger, S. Spartan Tutorial and User's Guide; Wavefunction, Inc.: Irvine, CA, 2010.
17. Shao, Y.; Molnar, L. F.; Jung, Y.; Kussmann, J.; Ochsenfeld, C.; Brown, S. T.; Gilbert, A. T. B.; Slipchenko, L. V.; Levchenko, S. V.; O'Neill, D. P. Advances in Methods and Algorithms in a Modern Quantum Chemistry Program Package Phys. Chem. Chem. Phys. 2006, 8, 3172-3191
18. 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
19. Hertwig, R. H.; Koch, W. On the Parameterization of the Local Correlation Functional: What is Becke-3-LYP? Chem. Phys. Lett. 1997, 268, 345-351
20. Ditchfield, R.; Hehre, W. J.; Pople, J. A. Self-Consistent Molecular-Orbital Methods. IX. An Extended Gaussian-Type Basis for Molecular-Orbital Studies of Organic Molecules Chem. Phys. 1971, 54, 724-728
21. Hehre, W. J.; Ditchfield, R.; Pople, J. A. Self-Consistent Molecular Orbital Methods. XII. Further Extensions of Gaussian-Type Basis Sets for Use in Molecular Orbital Studies of Organic Molecules Chem. Phys. 1972, 56, 2257-2261
22. Rassolov, V. A.; Ratner, M. A.; Pople, J. A.; Redfern, P. C.; Curtiss, L. A. 6-31G∗ Basis Set for Third-Row Atoms J. Comput. Chem. 2001, 22, 976-984
23. Hariharan, P. C.; Pople, J. A. The Influence of Polarization Functions on Molecular Orbital Hydrogenation Energies Theoret. Chim. Acta 1973, 28, 213-222
24. Gaussian 09, Revision D.01, Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G. A. Gaussian, Inc.: Wallingford, CT, 2009.
25. Morris, G. M.; Huey, R.; Lindstrom, W.; Sanner, M. F.; Belew, R. K.; Goodsell, D. S.; Olson, A. J. Autodock4 and AutoDockTools4: Automated Docking with Selective Receptor Flexiblity J. Comput. Chem. 2009, 16, 2785-2791
26. Alcaro, S.; Musetti, C. Identification and Characterization of New DNA G-Quadruplex Binders Selected by a Combination of Ligand and Structure-Based Virtual Screening Approaches J. Med. Chem. 2013, 56, 843-855
27. Gauto, D. F.; Petruk, A. A.; Modenutti, C. P.; Blanco, J. I.; Di Lella, S.; Marti1, M. A. Solvent Structure Improves Docking Prediction in Lectin-Carbohydrate Complexes Glycobiology 2013, 23, 241-258
28. Lindorff-Larsen, K.; Piana, S.; Palmo, K.; Maragakis, P.; Klepeis, J. L.; Dror, R. O.; Shaw, D. E. Improved Side-Chain Torsion Potentials for the Amber ff99SB Protein Force Field Proteins 2010, 78, 1950-1958
29. Gasteiger, J.; Marsili, M. Iterative Partial Equalization of Orbital Electronegativity-a Rapid Access to Atomic Charges Tetrahedron. 1980, 36, 3219-3228
30. Morris, G. M.; Goodsell, D. S.; Halliday, R. S.; Huey, R.; Hart, W. E.; Belew, R. K.; Olson, A. J. Automated Docking Using a Lamarckian Genetic Algorithm and an Empirical Binding Free Energy Function J. Comput. Chem. 1998, 19, 1639-1662
31. GaussView, Version 5, Dennington, R.; Keith, T.; Millam, J. Semichem Inc.: Shawnee Mission, KS, 2009.
32. Kitaura, K.; Ikeo, E.; Asada, T.; Nakano, T.; Uebayasi, M. Fragment Molecular Orbital Method: an Approximate Computational Method for Large Molecules Chem. Phys. Lett. 1999, 313, 701-706
33. Schmidt, M. W.; Baldridge, K. K.; Boatz, J. A.; Elbert, S. T.; Gordon, M. S.; Jensen, J. J.; Koseki, S.; Matsunaga, N.; Nguyen, K. A.; Su, S. General Atomic and Molecular Electronic Structure System J. Comput. Chem. 1993, 14, 1347-1363
34. Gordon, M. S.; Fedorov, D. G.; Pruitt, S. R.; Slipchenko, L. V. Fragmentation Methods: A Route to Accurate Calculations on Large Systems Chem. Rev. 2012, 112, 632-672
35. Maranetz, M. P.; Ichihara, O.; Law, R. J.; Whittaker, M. Prediction of Cyclin-Dependent Kinase 2 Inhibitor Potency Using the Fragment Molecular Orbital Method J. Cheminform. 2011, 3, 2-15
36. Fukuzawa, K.; Watanabe, C.; Kurisaki, I.; Taguchi, N.; Mochizuki, Y.; Nakano, T.; Tanaka, S.; Komeiji, Y. Accuracy of the Fragment Molecular Orbital (FMO) Calculations for DNA: Total Energy, Molecular Orbital, and Inter-Fragment Interaction Energy J. Comput. Theor. Chem. 2014, 1034, 7-16
37. Suenaga, M. Development of GUI for GAMESS/FMO Calculation Comput. Chem. Jpn. 2008, 7, 33-53
38. Roothaan, C. C. J. New Developments in Molecular Orbital Theory Rev. Mod. Phys. 1951, 23, 69-89
39. Møller, C.; Plesset, M. S. Note on an Approximation Treatment for Many-Electron Systems Phys. Rev. 1934, 46, 618-622
40. Pople, J. A.; Binkley, J. S.; Seeger, R. Theoretical Models Incorporating Electron Correlation Int. J. Quantum Chem. 1976, S10, 1-19
41. Mennucci, B. Polarizable Continuum Model WIREs. Comput. Mol. Sci. 2012, 2, 386-404
42. Muddana, H. S.; Neil, V. S.; Fenley, A. T.; Gilson, M. K. The Electrostatic Response of Water to Neutral Polar Solutes: Implications for Continuum Solvent Modeling J. Chem. Phys. 2013, 138, 224504-7
43. Grimme, S.; Antony, J.; Ehrlich, S.; Krieg, H. A Consistent and Accurate Ab Initio Parametrization of Density Functional Dispersion Correction (DFT-D) for the 94 Elements H-Pu J. Chem. Phys. 2010, 132, 154104-19
44. Ochterski, J. W. Thermochemistry in Gaussian; Gaussian, Inc.: Pittsburgh, PA, 2000, [Online] http://www.gaussian.com/g-whitepap/thermo.htm (Accessed Aug 20, 2014).
45. Zhao, Y.; Truhlar, D. G. The M06 Suite of Density Functionals for Main Group Thermochemistry, Thermochemical Kinetics, Noncovalent Interactions, Excited States, and Transition Elements: Two New Functionals and Systematic Testing of Four M06-Class Functionals and 12 Other Functionals Theor. Chem. Acc. 2008, 120, 215-241
46. Clark, T.; Chandrasekhar, J.; Spitznagel, G. W.; Schleyer, P.; von, R. Efficient Diffuse Function-Augmented Basis Sets for Anion Calculations. III. The 3-21+G Basis Set for First-Row Elements, Lithium to Fluorine J. Comput. Chem. 1983, 4, 294-301
47. SantaLucia, J., Jr. A Unified View of Polymer, Dumbbell, and Oligonucleotide DNA Nearest-Neighbor Thermodynamics Proc. Natl. Acad. Sci.U.S.A. 1998, 95, 1460-1465
48. Freire, E. Do Enthalpy and Entropy Distinguish First in Class From Best in Class? Drug Discovery Today 2009, 13, 869-874
49. Charles, J. B. Human Telomeric G-Quadruplex: Thermodynamic and Kinetic Studies of Telomeric Quadruplex Stability FEBS J. 2010, 227, 1098-1106
50. Thao Tran, P. L.; Mergny, J. L.; Alberti, P. Stability of Telomeric G-Quadruplexes Nucleic Acids Res. 2010, 39, 3282-3294