Ligand binding to the voltage-gated Kv1.5 potassium channel in the open state - Docking and computer simulations of a homology model

Biophysical Journal

Volumn 94, Issue 3, 2008, Pages 820-831

  Andér, Martin ^a   Luzhkov, Victor B ^a   Åqvist, Johan ^a  

^a UPPSALA UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

DOCKING PROTEIN; VOLTAGE GATED POTASSIUM CHANNEL;

ARTICLE; BINDING AFFINITY; COMPUTER SIMULATION; CONFORMATION; CRYSTAL STRUCTURE; GEOMETRY; LIGAND BINDING; MOLECULAR DOCKING; MOLECULAR DYNAMICS; PROTEIN INTERACTION;

EID: 38549144657     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.107.112045     Document Type: Article

References (61)

1. Hille, B. 1992. Ionic Channels of Excitable Membranes. Sinauer Associates, Sunderland, MA.
2. Gerlach, U. 2001. IKs channel blockers: potential antiarrhythmic agents. Drugs Future. 26:473-484.
3. Kannel, W. B., P. A. Wolf, E. J. Benjamin, and D. Levy. 1998. Prevalence, incidence, prognosis, and predisposing conditions for atrial fibrillation: population-based estimates. Am. J. Cardiol. 82:2N-8N.
4. Hart, R. G., and J. L. Halperin. 2001. Atrial fibrillation and stroke: concepts and controversies. Stroke. 32:803-808.
5. Camm, A. J., and I. Savelieva. 2004. Advances in antiarrhythmic drug treatment of atrial fibrillation: where do we stand now? Heart Rhythm. 1:244-246.
6. Choudhury, A., and G. Y. H. Lip. 2004. Antiarrhythmic drugs in atrial fibrillation: an overview of new agents, their mechanisms of action and potential clinical utility. Expert Opin. Investig. Drugs. 13:841-855.
7. Waldo, A. L., A. J. Camm, H. deRuyter, P. L. Friedman, D. J. MacNeil, J. F. Pauls, B. Pitt, C. M. Pratt, P. J. Schwartz, and E. P. Veltri. 1996. Effect of d-sotalol on mortality in patients with left ventricular dysfunction after recent and remote myocardial infarction. Lancet. 348:7-12.
8. Pratt, C. M., and L. A. Moye. 1990. The cardiac arrhythmia suppression trial: background, interim results and implications. Am. J. Cardiol. 65:B20-B29.
9. + current in human ventricular myocytes. Circ. Res. 78:689-696.
10. Amos, G. J., E. Wettwer, F. Metzger, Q. Li, H. M. Himmel, and U. Ravens. 1996. Differences between outward currents of human atrial, and subepicardial ventricular myocytes. J. Physiol. 491:31-50.
11. + current in cultured adult human atrial myocytes. Circ. Res. 80:572-579.
12. + channel current. Circ. Res. 73:210-216.
13. Snyders, D. J., M. M. Tamkun, and P. B. Bennett. 1993. A rapidly activating and slowly inactivating potassium channel cloned from human heart: functional analysis after stable mammalian cell culture expression. J. Gen. Physiol. 101:513-543.
14. + current similar to Kv1.5 cloned channel currents. Circ. Res. 73:1061-1076.
15. Mackinnon, R. 1991. Determination of the subunit stoichiometry of a voltage-activated potassium channel. Nature. 350:232-235.
16. + channel. Nature. 423:42-48.
17. + channel voltage sensor measured with luminescence energy transfer. Nature. 436:848-851.
18. + channel. Cell. 123:463-475.
19. + conduction and selectivity. Science. 280:69-77.
20. Snyders, D. J., K. M. Knoth, S. L. Roberds, and M. M. Tamkun. 1992. Time-dependent, voltage-dependent, and state-dependent block by quinidine of a cloned human cardiac potassium channel. Mol. Pharmacol. 41:322-330.
21. Snyders, D. J., and S. W. Yeola. 1995. Determinants of antiarrhythmic drug action: electrostatic and hydrophobic components of block of the human cardiac hKv1.5 channel. Circ. Res. 77:575-583.
22. + channel: role of S6 in antiarrhythmic drug binding. Circ. Res. 78:1105-1114.
23. Franqueza, L., M. Longobardo, J. Vicente, E. Delpon, M. M. Tamkun, J. Tamargo, D. J. Snyders, and C. Valenzuela. 1997. Molecular determinants of stereoselective bupivacaine block of hKv1.5 channels. Circ. Res. 81:1053-1064.
24. Caballero, R., I. Moreno, T. Gonzalez, C. Valenzuela, J. Tamargo, and E. Delpon. 2002. Putative binding sites for benzocaine on a human cardiac cloned channel (Kv1.5). Cardiovasc. Res. 56:104-117.
25. + channels. J. Biol. Chem. 279:394-400.
26. Decher, N., P. Kumar, T. Gonzalez, B. Pirard, and M. C. Sanguinetti. 2006. Binding site of a novel Kv1.5 blocker: a "foot in the door" against atrial fibrillation. Mol. Pharmacol. 70:1204-1211.
27. Decher, N., P. Kumar, T. Gonzalez, V. Renigunta, and M. C. Sanguinetti. 2005. Structural basis for competition between drug binding and Kvβ1.3 accessory subunit-induced N-type inactivation of Kv1.5 channels. Mol. Pharmacol. 68:995-1005.
28. + channel. Science. 309:897-903.
29. Luzhkov, V. B., J. Nilsson, P. Århem, and J. Åqvist. 2003. Computational modelling of the open-state Kv1.5 ion channel block by bupivacaine. Biochim. Biophys. Acta. 1652:35-51.
30. + channel using docking and molecular dynamics methods. FEBS Lett. 579:2939-2944.
31. Peukert, S., J. Brendel, B. Pirard, A. Bruggemann, P. Below, H. W. Kleemann, H. Hemmerle, and W. Schmidt. 2003. Identification, synthesis, and activity of novel blockers of the voltage-gated potassium channel Kv1.5. J. Med. Chem. 46:486-498.
32. Alonso, H., A. A. Bliznyuk, and J. E. Gready. 2006. Combining docking and molecular dynamics simulations in drug design. Med. Res. Rev. 26:531-568.
33. Marti-Renom, M. A., A. C. Stuart, A. Fiser, R. Sanchez, F. Melo, and A. Sali. 2000. Comparative protein structure modeling of genes and genomes. Annu. Rev. Biophys. Biomol. Struct. 29:291-325.
34. Sali, A., and T. L. Blundell. 1993. Comparative protein modeling by satisfaction of spatial restraints. J. Mol. Biol. 234:779-815.
35. Fiser, A., R. K. G. Do, and A. Sali. 2000. Modeling of loops in protein structures. Protein Sci. 9:1753-1773.
36. Luzhkov, V. B., M. Almlöf, M. Nervall, and J. Åqvist. 2006. Computational study of the binding affinity and selectivity of the bacterial ammonium transporter AmtB. Biochemistry. 45:10807-10814.
37. Martinez, J. M., and L. Martinez. 2003. Packing optimization for automated generation of complex system's initial configurations for molecular dynamics and docking. J. Comput. Chem. 24:819-825.
38. Jorgensen, W. L., J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein. 1983. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79:926-935.
39. Jorgensen, W. L., D. S. Maxwell, and J. Tirado-Rives. 1996. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J. Am. Chem. Soc. 118:11225-11236.
40. Verdonk, M. L., J. C. Cole, M. J. Hartshorn, C. W. Murray, and R. D. Taylor. 2003. Improved protein-ligand docking using GOLD. Proteins. 52:609-623.
41. Jones, G., P. Willett, R. C. Glen, A. R. Leach, and R. Taylor. 1997. Development and validation of a genetic algorithm for flexible docking. J. Mol. Biol. 267:727-748.
42. Eldridge, M. D., C. W. Murray, T. R. Auton, G. V. Paolini, and R. P. Mee. 1997. Empirical scoring functions. I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes. J. Comput. Aided Mol. Des. 11:425-445.
43. Åqvist, J., C. Medina, and J. E. Samuelsson. 1994. New method for predicting binding affinity in computer-aided drug design. Protein Eng. 7:385-391.
44. Hansson, T., J. Marelius, and J. Åqvist. 1998. Ligand binding affinity prediction by linear interaction energy methods. J. Comput. Aided Mol. Des. 12:27-35.
45. Almlöf, M., B. O. Brandsdal, and J. Åqvist. 2004. Binding affinity prediction with different force fields: examination of the linear interaction energy method. J. Comput. Chem. 25:1242-1254.
46. Marelius, J., K. Kolmodin, I. Feierberg, and J. Åqvist. 1998. Q: a molecular dynamics program for free energy calculations and empirical valence bond simulations in biomolecular systems. J. Mol. Graph. Model. 16:213-225, 261.
47. Åqvist, J., and V. B. Luzhkov. 2000. Ion permeation mechanism of the potassium channel. Nature. 404:881-884.
48. Luzhkov, V. B., and J. Åqvist. 2005. Ions and blockers in potassium channels: insights from free energy calculations. Biochim. Biophys. Acta. 1747:109-120.
49. + selectivity filter. Nature. 414:37-42.
50. King, G., and A. Warshel. 1989. A surface constrained all-atom solvent model for effective simulations of polar solutions. J. Chem. Phys. 91:3647-3661.
51. Ryckaert, J.-P., G. Ciccotti, and H. J. C. Berendsen. 1977. Numerical integration of the Cartesian equations ofmotion of a systemwith constraints: molecular dynamics of n-alkanes. J. Comput. Phys. 23:327-341.
52. Lee, F. S., and A. Warshel. 1992. A local reaction field method for fast evaluation of long-range electrostatic interactions in molecular simulations. J. Chem. Phys. 97:3100-3107.
53. Almlöf, M., J. Carlsson, and J. Åqvist. 2007. Improving the accuracy of the linear interaction energy method for solvation free energies. J. Chem. Theor. Comput. 3:2162-2175.
54. + channel-Fab complex at 2.0 Å resolution. Nature. 414:43-48.
55. Carlsson, J., M. Andér, M. Nervall, and J. Åqvist. 2006. Continuum solvation models in the linear interaction energy method. J. Phys. Chem. B. 110:12034-12041.
56. Carlsson, J., and J. Åqvist. 2006. Calculations of solute and solvent entropies from molecular dynamics simulations. Phys. Chem. Chem. Phys. 8:5385-5395.
57. Su, Y., E. Gallicchio, K. Das, E. Arnold, and R. M. Levy. 2007. Linear interaction energy (LIE) models for ligand binding in implicit solvent: theory and application to the binding of NNRTIs to HIV-1 reverse transcriptase. J. Chem. Theory Comput. 3:256-277.
58. Mobley, D. L., A. P. Graves, J. D. Chodera, A. C. McReynolds, B. K. Shoichet, and K. A. Dill. 2007. Predicting absolute binding free energies to a simple model site. J. Mol. Biol. 371:1118-1134.
59. Wang, J., Y. Deng, and B. Roux. 2006. Absolute binding free energy calculations using molecular dynamics simulations with restraining potentials. Biophys. J. 91:2798-2814.
60. Fujitani, H., Y. Tanida, M. Ito, G. Jayachandran, C. D. Snow, M. R. Shirts, E. J. Sorin, and V. S. Pande. 2005. Direct calculation of the binding free energies of FKBP ligands. J. Chem. Phys. 123:084108.
61. Peukert, S., J. Brendel, B. Pirard, C. Strubing, H. W. Kleemann, T. Bohme, and H. Hemmerle. 2004. Pharmacophore-based search, synthesis, and biological evaluation of anthranilic amides as novel blockers of the Kv1.5 channel. Bioorg. Med. Chem. Lett. 14:2823-2827.