Structure-based discovery of potassium channel blockers from natural products: Virtual screening and electrophysiological assay testing

Chemistry and Biology

Volumn 10, Issue 11, 2003, Pages 1103-1113

  Liu, Hong ^a   Li, Yang ^a   Song, Mingke ^a   Tan, Xiaojian ^a   Cheng, Feng ^a   Zheng, Suxin ^a   Shen, Jianhua ^a   Luo, Xiaomin ^a   Ji, Ruyun ^a   Yue, Jianmin ^a   Hu, Guoyuan ^a   Jiang, Hualiang ^a   Chen, Kaixian ^a  

^a SHANGHAI INSTITUTE OF MATERIA MEDICA   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMALIA; EUKARYOTA;

EID: 0345099649     PISSN: 10745521     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.chembiol.2003.10.011     Document Type: Article

References (64)

1. Kaczorowski G.J., Garcia M. Pharmacology of voltage-gated and calcium-activated potassium channels. Curr. Opin. Chem. Biol. 3:1999;448-458.
2. Garcia M.L., Hanner M., Knaus H.G., Koch R., Schmalhofer W., Slaughter R.S., Kaczorowski G.J. Pharmacology of potassium channels. Adv. Pharmacol. 39:1997;425-471.
3. Clare J.J., Tate S.N., Nobbs M., Romanos M.A. Voltage-gated sodium channels as therapeutic targets. Drug Discov. Today. 5:2000;506-520.
4. Biggin P.C., Roosild T., Choe S. Potassium channel structure. domain by domain Curr. Opin. Struct. Biol. 10:2000;456-461.
5. + channel-Fab complex at 2.0 Å resolution. Nature. 414:2001;43-48.
6. + channels. more than model behavior Trends Pharmacol. Sci. 18:1997;474-483.
7. Lu Z., Klem A.M., Ramu Y. Ion conduction pore is conserved among potassium channels. Nature. 413:2001;809-813.
8. + conduction and selectivity Science. 280:1998;69-77.
9. Harvey A. Strategies for discovering drugs from previously unexplored natural products. Drug Discov. Today. 5:2000;294-300.
10. Hopkins A.L., Groom C.R. The druggable genome. Nat. Rev. Drug Discov. 1:2002;727-730.
11. Dean P.M., Zanders E.D., Bailey D.S. Industrial-scale, genomics-based drug design and discovery. Trends Biotechnol. 19:2001;228-292.
12. Shoichet B.K., McGovern S.L., Wei B., Irwin J.J. Lead discovery using molecular docking. Curr. Opin. Chem. Biol. 6:2002;439-446.
13. Schneider G., Böhm H.J. Virtual screening and fast automated docking methods. Drug Discov. Today. 7:2002;64-70.
14. Waszkowycz B., Perkins T.D.J., Sykes R.A., Li J. Large-scale virtual screening for discovering leads in the postgenomic era. IBM Systems J. 40:2001;360-376.
15. Richards W.G. Virtual screening using grid computing. the screensaver project Nat. Rev. Drug Discov. 1:2002;551-555.
16. Doman T.N., McGovern S.L., Witherbee B.J., Kasten T.P., Kurumbail R., Stallings W.C., Connolly D.T., Shoichet B.K. Molecular docking and high-throughput screening for novel inhibitors of protein tyrosine phosphatase-1B. J. Med. Chem. 45:2002;2213-2221.
17. Lind K.E., Du Z., Fujinaga K., Peterlin B.M., James T.L. Structure-based computational database screening, in vitro assay, and NMR assessment of compounds that target TAR RNA. Chem. Biol. 9:2002;185-193.
18. Grüneberg S., Stubbs M.T., Klebe G. Successful virtual screening for novel inhibitors of human carbonic anhydrase. strategy and experimental confirmation J. Med. Chem. 45:2002;3588-3602.
19. Kuntz I.D., Meng E.C., Shoichet B.K. Structure-based molecular design. Acc. Chem. Res. 27:1994;117-123.
20. Wang J.L., Liu D.X., Zhang Z.J., Shan S., Han X.B., Srinivasula S.M., Croce C.M., Alnemri E.S., Huang Z.W. Structure-based discovery of an organic compound that binds Bcl-2 protein and induces apoptosis of tumor cells. Proc. Natl. Acad. Sci. USA. 97:2000;7124-7129.
21. + channel. Neuron. 16:1996;123-130.
22. Carmeliet E.M.K. Antiarrhythmic drugs and cardiac ion channels. mechanisms of action Prog. Biophys. Mol. Biol. 70:1998;1-72.
23. + channels. Neuron. 11:1993;353-358.
24. Shanghai Institute of Materia Medica, Chinese Academy of Sciences and Neotrident Systems Pte Ltd. (2000). China Natural Products Database (http://www.neotrident.com).
25. Ewing T., Kuntz I.D. Critical evaluation of search algorithms for automated molecular docking and database screening. J. Comput. Chem. 18:1997;1175-1189.
26. Kuntz I.D. Structure-based strategies for drug design and discovery. Science. 257:1992;1078-1082.
27. MacKinnon R., Cohen L., Kuo A., Lee A., Chait B.T. Structural conservation in prokaryotic and eukaryotic potassium channels. Science. 280:1998;106-109.
28. Tripos Associates, St. Louis, MO. (2000). Sybyl, Version 6.7.
29. Morris G.M., Goodsell D.S., Huey R., Olson A.J. Distributed automated docking of flexible ligands to protein. parallel application of AutoDock 2.4 J. Comput. Aided Mol. Des. 10:1996;293-304.
30. Morris G.M., Goodsell D.S., Halliday R.S., Huey R., Hart W.E., Belew R.K., Olson A.J. Automated docking using Lamarckian genetic algorithm and empirical binding free energy function. J. Comput. Chem. 19:1998;1639-1662.
31. MDL Information Systems, Inc. (2001). MDL Drug Data Report (MDDR) database (http://www.prous.com/product/electron/mddr.html
32. Wang R.X., Lai L.H. Calculating partition coefficients of peptides by the addition method. J. Chem. Inf. Comput. Sci. 37:1997;615-621.
33. Klee R., Ficker E., Heinemann U. Comparison of voltage-dependent potassium currents in rat pyramidal neurons acutely isolated from hippocampal regions CA1 and CA3. J. Neurophysiol. 74:1995;1982-1995.
34. Numann R.E., Wadman W.J., Wong R.K.S. Outward currents of single hippocampal cells obtained from the adult guinea-pig. J. Physiol. 393:1987;331-353.
35. Storm J.F. Functional diversity of K currents in hippocampal pyramidal neurons. Semin. Neurosci. 5:1993;79-92.
36. Santos A.I., Wadman W.J., Costa P.F. Sustained potassium currents in maturing CA1 hippocampal neurons. Brain Res. Dev. Brain Res. 108:1998;13-21.
37. Rauer H., Grissmer S. Evidence for an internal phenylalkylamine action on the voltage-gated potassium channel KV1.3. Mol. Pharmacol. 50:1996;1625-1634.
38. Rauer H., Grissmer S. The effect of deep pore mutations on the action of phenylalkylamines on the Kv1.3 potassium channel. Br. J. Pharmacol. 127:1999;1065-1074.
39. Hu G.Y., Biro Z., Hill R.H., Grillner S. Intracellular QX-314 causes depression of membrane potential oscillations in lamprey spinal neurons during fictive locomotion. J. Neurophysiol. 87:2002;2676-2883.
40. Wallace A.C., Laskowski R.A., Thornton J.M. Ligplot. A program to generate schematic diagrams of protein-ligand interactions Protein Eng. 8:1995;127-134.
41. + channels. Science. 258:1992;1152-1155.
42. + channels. J. Membr. Biol. 109:1989;269-281.
43. Escobar L., Root M.J., MacKinnon R. Influence of protein surface charge on the bimolecular kinetics of a potassium channel peptide inhibitor. Biochemistry. 32:1993;6982-6987.
44. + channel inhibitor from scorpion venom. Biochemistry. 36:1997;6936-6940.
45. Cui M., Shen J.H., Briggs J.M., Luo X.M., Tan X.J., Jiang H.L., Chen K.X., Ji R.Y. Brownian dynamics simulations of interaction between scorpion toxin Lq2 and potassium ion channel. Biophys. J. 80:2001;1659-1669.
46. Cui M., Shen J.H., Briggs J.M., Fu W., Wu J., Zhang Y., Luo X., Chi Z., Ji R., Jiang H., et al. Brownian dynamics simulations of the recognition of the scorpion toxin P05 with the small conductance calcium-activated potassium channels. J. Mol. Biol. 318:2002;417-428.
47. GCG Wisconsin Package Version. 10:2000;0.
48. Bernstein F.C., Koetzle T.F., Williams G.J., Meyer E.E. Jr., Brice M.D., Rodgers J.R., Kennard O., Shimanouchi T., Tasumi M. The protein data bank. a computer-based archival file for macromolecular structures J. Mol. Biol. 112:1977;535-542.
49. Weiner S.J., Kollman P.A., Nguyen D.T., Case D.A. An all-atom force field for simulations of proteins and nucleic acids. J. Comput. Chem. 7:1986;230-252.
50. Accelrys Molecular Simulations Inc., San Diego, CA. (2000). InsightII, Version 2000.
51. Muegge I., Rarey M. Small molecule docking and scoring. Lipkowitz K.B., Boyd D.B. Reviews in Computational Chemistry. 2001;1-60 John Wiley & Sons, New York.
52. Charifson P.S., Corkery J.J., Murcko M.A., Walters W.P. Consensus scoring. a method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins J. Med. Chem. 42:1999;5100-5109.
53. Kavanaugh M.P., Varnum M.D., Osborne P.B., Christie M.J., Busch A.E., Adelman J.P., North R.A. Interaction between tertaethylammonium and amino acid residues in the pore of cloned voltage dependent potassium channels. J. Biol. Chem. 266:1991;7583-7587.
54. Kavanaugh M.P., Hurst R.S., Yakel J., Varnum M.D., Adelman J.P., North R.A. Multiple subunits of a voltage-dependent potassium channel contribute to the binding site for tetraethylammonium. Neuron. 8:1992;493-497.
55. + channels. Science. 250:1990;276-279.
56. Gasteiger J., Marsili M. Iterative partial equalization of orbital electronegativity-A rapid access to atomic charges. Tetrahedron. 36:1980;3219-3228.
57. Marsili M., Gasteriger J. π charge distribution from molecular topology and π orbital electronegativity. Croat. Chem. Acta. 53:1980;601-614.
58. Purcell W.P., Singer J.A. Brief review and table of semiempirical parameters used in the Hückel molecular orbital method. J. Chem. Eng. Data. 12:1967;235-246.
59. Solis F.J., Wets R.J.B. Minimization by random search techniques. Math. Oper. Res. 6:1981;19-30.
60. Mannhold R., Waterbeemd H. Substructure and whole molecule approaches for calculating log P. J. Comput. Aided Mol. Des. 15:2001;337-354.
61. Yue J.M., Xu J., Zhao Q.S., Sun H.D. Diterpenoid alkaloids from Aconitum Leucostomum. J. Nat. Prod. 59:1996;277-279.
62. Yue J.M., Jun X., Chen Y.Z. C19-Diterpenoid alkaloids of Aconitum Kongboense. Phytochemistry. 35:1994;829-831.
63. Li Y., Hu G.Y. Huperzine A, a nootropic agent, inhibits fast transient potassium current in rat dissociated hippocampal neurons. Neurosci. Lett. 324:2002;25-28.
64. Microcal Software, Inc. (1999). Origin Version 6.0 (http://www. originlab.com/