Possible drug candidates for Alzheimer's disease deduced from studying their binding interactions with α7 nicotinic acetylcholine receptor

Medicinal Chemistry

Volumn 5, Issue 3, 2009, Pages 250-262

  Gu, Ruo Xu ^a   Gu, Hui ^a   Xie, Zhi Yuan ^a   Wang, Jing Fang ^b   Arias, Hugo R ^c   Wei, Dong Qing ^a,d   Chou, Kuo Chen ^a,d  

^a SHANGHAI JIAO TONG UNIVERSITY   (China)

^b Shanghai Jiao Tong University Affiliated Sixth People s Hospital   (China)

^c MIDWESTERN UNIVERSITY   (United States)

^d GORDON LIFE SCIENCE INSTITUTE   (United States)

Author keywords

7 nAChR; Chemical modification; DMXBA; Docking; MD simulation

Indexed keywords

BUNGAROTOXIN RECEPTOR; GX 180; GX 50; GX 51; GX 52; NOOTROPIC AGENT; UNCLASSIFIED DRUG; 3 (2,4 DIMETHOXYBENZYLIDENE)ANABASEINE; 3-(2,4-DIMETHOXYBENZYLIDENE)ANABASEINE; ALPHA-BUNGAROTOXIN RECEPTOR; BENZYLIDENE DERIVATIVE; NICOTINIC RECEPTOR; PYRIDINE DERIVATIVE;

ALZHEIMER DISEASE; ARTICLE; CHEMICAL MODIFICATION; DRUG RECEPTOR BINDING; DRUG SCREENING; DRUG STRUCTURE; HYDROGEN BOND; HYDROPHILICITY; HYDROPHOBICITY; MOLECULAR DOCKING; MOLECULAR DYNAMICS; PRIORITY JOURNAL; SIMULATION; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; DRUG DESIGN; METABOLISM; PROTEIN BINDING; THERMODYNAMICS;

ALZHEIMER DISEASE; BENZYLIDENE COMPOUNDS; BINDING SITES; DRUG DESIGN; DRUG EVALUATION, PRECLINICAL; HYDROGEN BONDING; MODELS, MOLECULAR; PROTEIN BINDING; PYRIDINES; RECEPTORS, NICOTINIC; THERMODYNAMICS;

EID: 67651180849     PISSN: 15734064     EISSN: None     Source Type: Journal    
DOI: 10.2174/157340609788185909     Document Type: Article

References (70)

1. Carter, D. B.; Chou, K. C. A model for structure dependent binding of Congo Red to Alzeheimer beta-amyloid fibrils. Neurobiol. Aging, 1998, 19, 37-40.
2. Wang, J. F.; Wei, D. Q.; Lin, Y.; Wang, Y. H.; Du, H. L.; Li, Y. X.; Chou, K. C. Insights from modeling the 3D structure of NAD(P)H-dependent D-xylose reductase of Pichia stipitis and its binding interactions with NAD and NADP. Biochem. Biophys. Res. Commun., 2007, 359, 323-329.
3. Kem, W. R. The brain alpha7 nicotinic receptor may be an important therapeutic target for the treatment of Alzheimer's disease: studies with DMXBA (GTS-21). Behav. Brain. Res., 2000, 113, 169-181.
4. Chou, K. C.; Howe, W. J. Prediction of the tertiary structure of the beta-secretase zymogen. Biochem. Biophys. Res. Commun., 2002, 292, 702-708.
5. Meyer, E. M.; Tay, E. T.; Papke, R. L.; Meyers, C.; Huang, G. L.; de Fiebre, C. M. 3-[2,4-Dimethoxybenzylidene]anabaseine (DMXB) selectively activates rat alpha7 receptors and improves memory-related behaviors in a mecamylamine-sensitive manner. Brain Res., 1997, 768, 49-56.
6. Kem, W. R.; Mahnir, V. M.; Prokai, L.; Papke, R. L.; Cao, X.; Le-Francois, S.; Wildeboer, K.; Prokai-Tatrai, K.; Porter-Papke, J.; Soti, F. Hydroxy metabolites of the Alzheimer's drug candidate 3-[(2,4-dimethoxy)benzylidene]-anabaseine dihydrochloride (GTS-21): their molecular properties, interactions with brain nicotinic receptors, and brain penetration. Mol. Pharmacol., 2004, 65, 56-67.
7. Wei, D. Q.; Sirois, S.; Du, Q. S.; Arias, H. R.; Chou, K. C. Theoretical studies of Alzheimer's disease drug candidate [(2,4-dimethoxy) benzylidene]- anabaseine dihydrochloride (GTS-21) and its derivatives. Biochem. Biophys. Res. Commun., 2005, 338, 1059-1064.
8. Kem, W.; Soti, F.; LeFrancois, S.; Wildeboer, K.; MacDougall, K.; Wei, D. Q.; Chou, K. C.; Arias, H. R. Review: The nemertine toxin anabaseine and its derivative DMXBA (GTS-21): chemical and pharmacological properties. Marine Drugs, 2006, 4, 255-273.
9. Miller, C. Ion channels: coughing up flu's proton channels. Nature, 2008, 451, 532-533.
10. Borman, S. Flu virus proton channel analyzed: Structures of key surface protein suggest different drug mechanisms. Chem. Eng. News, 2008, 86, 53-54.
11. Schnell, J. R.; Chou, J. J. Structure and mechanism of the M2 proton channel of influenza A virus. Nature, 2008, 451, 591-595.
12. Oxenoid, K.; Chou, J. J. The structure of phospholamban pentamer reveals a channel-like architecture in membranes. Proc. Natl. Acad. Sci. U S A, 2005, 102, 10870-10875.
13. Call, M. E.; Schnell, J. R.; Xu, C.; Lutz, R. A.; Chou, J. J.; Wucherpfennig, K. W. The structure of the zetazeta transmembrane dimer reveals features essential for its assembly with the T cell receptor. Cell, 2006, 127, 355-368.
14. Chou, K. C. A vectorized sequence-coupling model for predicting HIV protease cleavage sites in proteins. J. Biol. Chem., 1993, 268, 16938-16948.
15. Chou, K. C. Review: Prediction of HIV protease cleavage sites in proteins. Anal. Biochem., 1996, 233, 1-14.
16. Sirois, S.; Wei, D. Q.; Du, Q. S.; Chou, K. C. Virtual Screening for SARS-CoV Protease Based on KZ7088 Pharmacophore Points. J. Chem. Inf. Comput. Sci., 2004, 44, 1111-1122.
17. Chou, K. C.; Shen, H. B. Signal-CF: a subsite-coupled and window-fusing approach for predicting signal peptides. Biochem. Biophys. Res. Commun., 2007, 357, 633-640.
18. Sirois, S.; Hatzakis, G. E.; Wei, D. Q.; Du, Q. S.; Chou, K. C. Assessment of chemical libraries for their druggability. Comput. Biol. Chem., 2005, 29, 55-67.
19. Chou, K. C.; Shen, H. B. MemType-2L: A web server for predicting membrane proteins and their types by incorporating evolution information through Pse-PSSM. Biochem. Biophys. Res. Commun., 2007, 360, 339-345.
20. Sirois, S.; Tsoukas, C. M.; Chou, K. C.; Wei, D. Q.; Boucher, C.; Hatzakis, G. E. Selection of molecular descriptors with artificial intelligence for the understanding of HIV-1 protease peptidomimetic inhibitors-activity. Med. Chem., 2005, 1, 173-184.
21. Shen, H. B.; Chou, K. C. Signal-3L: a 3-layer approach for predicting signal peptide. Biochem. Biophys. Res. Commun., 2007, 363, 297-303.
22. Sirois, S.; Sing, T.; Chou, K. C. Review: HIV-1 gp120 V3 loop for structure-based drug design. Curr. Protein Pept. Sci., 2005, 6, 413-422.
23. Shen, H. B.; Chou, K. C. EzyPred: A top-down approach for predicting enzyme functional classes and subclasses. Biochem. Biophys. Res. Commun., 2007, 364, 53-59.
24. Sirois, S.; Touaibia, M.; Chou, K. C.; Roy, R. Glycosylation of HIV-1gp120 V3 loop: towards the rational design of a synthetic carbohydrate vaccine. Curr. Med. Chem., 2007, 14, 3232-42.
25. Chou, K. C.; Shen, H. B. Review: Recent progresses in protein subcellular location prediction. Anal. Biochem., 2007, 370, 1-16.
26. Emanuelsson, O.; Brunak, S.; von Heijne, G.; Nielsen, H. Locating proteins in the cell using TargetP, SignalP and related tools. Nat. Protoc., 2007, 2, 953-971.
27. Chou, K. C.; Shen, H. B. Cell-PLoc: A package of web-servers for predicting subcellular localization of proteins in various organisms. Nat. Protoc., 2008, 3, 153-162.
28. Chou, K. C.; Shen, H. B. HIVcleave: a web-server for predicting human immunodeficiency virus protease cleavage sites in proteins. Anal. Biochem., 2008, 375, 388-390.
29. Chou, K.C. Structural bioinformatics and its impact to biomedical science. Curr. Med. Chem., 2004, 11, 2105-2134.
30. Chou, K. C.; Wei, D. Q.; Du, Q. S.; Sirois, S.; Zhong, W. Z. Review: Progress in computational approach to drug development against SARS. Curr. Med. Chem., 2006, 13, 3263-3270.
31. Althaus, I. W.; Chou, J. J.; Gonzales, A. J.; Diebel, M. R.; Chou, K.C.; Kezdy, F. J.; Romero, D. L.; Aristoff, P. A.; Tarpley, W. G.; Reusser, F. Steady-state kinetic studies with the non-nucleoside HIV-1 reverse transcriptase inhibitor U-87201E. J.Biol.Chem., 1993, 268, 6119-6124.
32. Althaus, I. W.; Gonzales, A. J.; Chou, J. J.; Diebel, M. R.; Chou, K. C.; Kezdy, F. J.; Romero, D. L.; Aristoff, P. A.; Tarpley, W. G.;Reusser, F. The quinoline U-78036 is a potent inhibitor of HIV-1 reverse transcriptase. J. Biol. Chem., 1993, 268, 14875-14880.
33. Althaus, I. W.; Chou, J. J.; Gonzales, A. J.; Diebel, M. R.; Chou, K. C.; Kezdy, F. J.; Romero, D. L.; Aristoff, P. A.; Tarpley, W. G.; Reusser, F. Kinetic studies with the nonnucleoside HIV-1 reverse transcriptase inhibitor U-88204E. Biochem., 1993, 32, 6548-54.
34. Chou, K. C.; Kezdy, F. J.; Reusser, F. Review: Steady-state inhibition kinetics of processive nucleic acid polymerases and nucleases. Anal. Biochem., 1994, 221, 217-230.
35. Chou, K. C.; Wei, D. Q.; Zhong, W. Z. Binding mechanism of coronavirus main proteinase with ligands and its implication to drug design against SARS. Biochem. Biophys. Res. Commun., 2003, 308, 148-151. (Erratum: ibid., 2003, 310, 675).
36. Chou, K. C. Modelling extracellular domains of GABA-A receptors: subtypes 1, 2, 3, and 5. Biochem. Biophys. Res. Commun., 2004, 316, 636-642.
37. Chou, K. C. Insights from modelling the 3D structure of the extracellular domain of alpha7 nicotinic acetylcholine receptor. Biochem. Biophys. Res. Commun., 2004, 319, 433-438.
38. Chou, K. C. Molecular therapeutic target for type-2 diabetes. J. Proteome Res., 2004, 3, 1284-1288.
39. Chou, K. C. Modeling the tertiary structure of human cathepsin-E. Biochem. Biophys. Res. Commun., 2005, 331, 56-60.
40. Chou, K. C. Insights from modeling the 3D structure of DNACBF3b complex. J. Proteome Res., 2005, 4, 1657-1660.
41. Chou, K. C. Coupling interaction between thromboxane A2 receptor and alpha-13 subunit of guanine nucleotide-binding protein. J. Proteome Res., 2005, 4, 1681-1686.
42. Wei, D. Q.; Zhang, R.; Du, Q. S.; Gao, W. N.; Li, Y.; Gao, H.; Wang,S. Q.; Zhang, X.; Li, A. X.; Sirois, S.; Chou, K. C. Anti-SARS drug screening by molecular docking. Amino Acids, 2006, 31, 73-80.
43. Wang, S. Q.; Du, Q. S.; Zhao, K.; Li, A. X.; Wei, D. Q.; Chou, K. C. Virtual screening for finding natural inhibitor against cathepsin-L for SARS therapy. Amino Acids, 2007, 33, 129-135.
44. Du, Q. S.; Wang, S. Q.; Jiang, Z. Q.; Gao, W. N.; Li, Y. D.; Wei, D. Q.; Chou, K. C. Application of bioinformatics in search for cleavable peptides of SARS-CoV Mpro and chemical modification of octapeptides. Med. Chem., 2005, 1, 209-213.
45. Zhang, R.; Wei, D. Q.; Du, Q. S.; Chou, K. C. Molecular modeling studies of peptide drug candidates against SARS. Med. Chem., 2006, 2, 309-314.
46. Gao, W. N.; Wei, D. Q.; Li, Y.; Gao, H.; Xu, W. R.; Li, A. X.; Chou, K. C. Agaritine and its derivatives are potential inhibitors against HIV proteases. Med. Chem., 2007, 3, 221-226.
47. Zheng, H.; Wei, D. Q.; Zhang, R.; Wang, C.; Wei, H.; Chou, K. C. Screening for New Agonists against Alzheimer's Disease. Med. Chem., 2007, 3, 488-493.
48. Li, Y.; Wei, D. Q.; Gao, W. N.; Gao, H.; Liu, B. N.; Huang, C. J.;Xu, W. R.; Liu, D. K.; Chen, H. F.; Chou, K. C. Computational approach to drug design for oxazolidinones as antibacterial agents. Med. Chem., 2007, 3, 576-582.
49. Lipinski, C. A.; Lombardo, F.; Dominy, B. W.; Feeney, P. J. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv. Drug Deliv. Rev., 2001, 46, 3-26.
50. MacKerell Jr., A. D.; Bashford, D.; M. Bellott, M.; Dunbrack Jr.,R. L.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.;Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T.K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.;Reiher, I., W.E.; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.;Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem., 1998, 102, 3586-3616.
51. Du, Q. S.; Wang, S.; Wei, D. Q.; Sirois, S.; Chou, K. C. Molecular modeling and chemical modification for finding peptide inhibitor against SARS CoV Mpro. Anal. Biochem., 2005, 337, 262-270.
52. Zhou, G. P.; Troy, F. A. 2nd NMR study of the preferred membrane orientation of polyisoprenols (dolichol) and the impact of their complex with polyisoprenyl recognition sequence peptides on membrane structure. Glycobiol., 2005, 15, 347-359.
53. Zhou, G. P.; Troy, F. A. NMR studies on how the binding complex of polyisoprenol recognition sequence peptides and polyisoprenols can modulate membrane structure. Curr. Protein Pept. Sci., 2005, 6, 399-411.
54. Wei, H.; Zhang, R.; Wang, C.; Zheng, H.; Chou, K. C.; Wei, D. Q. Molecular insights of SAH enzyme catalysis and their implication for inhibitor design. J.Theor. Biol., 2007, 244, 692-702.
55. Li, L.; Wei, D. Q.; Wang, J. F.; Chou, K. C. Computational studies of the binding mechanism of calmodulin with chrysin. Biochem. Biophys. Res. Commun., 2007, 358, 1102-1107.
56. Du, Q. S.; Wang, S. Q.; Chou, K. C. Analogue inhibitors by modifying oseltamivir based on the crystal neuraminidase structure for treating drug-resistant H5N1 virus. Biochem. Biophys. Res. Commun., 2007, 362, 525-531.
57. Guo, X. L.; Li, L.; Wei, D. Q.; Zhu, Y. S.; Chou, K. C. Cleavage mechanism of the H5N1 hemagglutinin by trypsin and furin. Amino Acids, 2008, 35, 375-382.
58. Du, Q. S.; Sun, H.; Chou, K. C. Inhibitor design for SARS coronavirus main protease based on "distorted key theory". Med. Chem., 2007, 3, 1-6.
59. 2A adenosine receptor antagonists. Amino Acids, 2008, 35, 389-396.
60. 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 empirical binding free energy function. J. Comput. Chem., 1998, 19, 1639-1662.
61. Kuntz, I. D.; Meng, E. C.; Shoichet, B. K. Structure-based strategies for drug design and discovery. Acc. Chem. Res., 1994, 27, 117-123.
62. Glover, F. Tabu search: a tutorial. Interfaces, 1990, 20, 74-94.
63. Battiti, R.; Tecchiolli, G. Simulated annealing and tabu search in the long run: a comparison on qap tasks. Comp. Math. Appl., 1994, 28, 1-8.
64. Wang, J. F.; Wei, D. Q.; Li, L.; Zheng, S. Y.; Li, Y. X.; Chou, K. C. 3D structure modeling of cytochrome P450 2C19 and its implication for personalized drug design. Biochem. Biophys. Res. Commun., 2007, 355, 513-519. (Corrigendum: ibid, 2007, 357, 330).
65. Chou, K. C. Energy-optimized structure of antifreeze protein and its binding mechanism. J. Mol. Biol., 1992, 223, 509-517.
66. Chou, K. C. Insights from modelling the tertiary structure of BACE2. J. Proteome Res., 2004, 3, 1069-1072.
67. Connolly, M. L. Solvent-accessible surfaces of proteins and nucleic acids. Science, 1983, 221, 709-713.
68. Wang, S. Q.; Du, Q. S.; Chou, K. C. Study of drug resistance of chicken influenza A virus (H5N1) from homology-modeled 3D structures of neuraminidases. Biochem. Biophys. Res. Commun., 2007, 354, 634-640.
69. Wei, D. Q.; Du, Q. S.; Sun, H.; Chou, K. C. Insights from modeling the 3D structure of H5N1 influenza virus neuraminidase and its binding interactions with ligands. Biochem. Biophys. Res. Commun., 2006, 344, 1048-1055.
70. Lee, W. Y.; Sine, S. M. Principal pathway coupling agonist binding to channel gating in nicotinic receptors. Nature, 2005, 438, 243-247.