Backpropagation neural network analysis applied to β-sheet breakers used against alzheimer's amyloid aggregation

Molecular Simulation

Volumn 28, Issue 3, 2002, Pages 239-247

  Mager, Peter P ^a  

^a UNIVERSITY OF LEIPZIG   (Germany)

Author keywords

sheet breakers; A peptide; Morbus Alzheimer; Neural networks

Indexed keywords

AGGLOMERATION; BACKPROPAGATION; COMPUTER SIMULATION; CONFORMATIONS; ELECTROSTATICS; HYDRATION; MOLECULAR DYNAMICS;

Β-SHEET BREAKERS; AΒ PEPTIDE; MORBUS ALZHEIMER; SHEET INHIBITORS;

NEURAL NETWORKS;

EID: 0010592540     PISSN: 08927022     EISSN: 10290435     Source Type: Journal    
DOI: 10.1080/08927020290014358     Document Type: Article

References (32)

1. Simmonis, L. W., Becker, G. W., Brems, D. N., Brigham, E. F., Fuson, K. S., Li, W. Y., Lieberburg, I., May, P. C., Reydel, R. E., Tomaselli, K. J. and Wright, S. (1994). Secondary structure of amyloid β peptide correlates with neurotoxic activity in vitro, Mol. Pharmacol., 45, 373-379.
2. Mager, P. P. (1998). Molecular simulation of the primary and secondary structures of the Aβ(1-42)-peptide of Alzheimer's disease, Med. Res. Rev., 18, 403-430.
3. Soto, C., Kindy, M. S., Baumann, M. and Frangione, B. (1996). Inhibition of Alzheimer's amyloidosis by peptides that prevent β-sheet conformation, Biochem. Biophys. Res. Commun., 226, 672-680.
4. Soto, C. and Frangione, B., Inhibition of Alzheimer's amyloidogenesis by anti-β-sheet peptides, In: Alzheimer's Disease: Biology, Diagnosis and Therapeutics, Iqbal, K., Winblad, B., Nishimura, T., Takeda, M. and Wisniewski, H. M. Eds., Wiley, New York, 1997, pp. 711-716.
5. Soto, C., Sigurdsson, E. M., Morelli, L., Kumar, R. A., Castano, E. M. and Frangione, B. (1998). β-Sheet breaker peptides inhibit fibrillogenesis in a rat brain model of amyloidosis: Implications for Alzheimer's therapy, Nature Med., 4, 822-826.
6. Ghanta, J., Shen, C. L., Kiessling, L. L. and Murphy, R. M. (1996). Strategy for designing inhibitors of β-amyloid toxicity, J. Biol. Chem., 22, 29525-29528.
7. Tjernberg, L. O., Näslund, J., Lindqvist, F., Johannson, J., Karlström, A. R., Thyberg, J., Terenius, L. and Nordstedt, C. (1996). Arrest of β-amyloid fibril formation by a pentapeptide ligand, J. Biol. Chem., 271, 8545-8548.
8. Tjernberg, L. O., Lilliehöök, C., Callaways, D. J. E., Näslund, J., Hahne, S., Thyberg, J., Terenius, L., and Nordstedt, C. (1997). Controlling amyloid β-peptide fibril formation with protease-stable ligands, J. Biol. Chem., 272, 12601-12605.
9. Allinger, N. L. and Yan, L. (1993). Molecular mechanics (MM3). Calculation of furan, vinyl, ethers, and related compounds, J. Am. Chem. Soc., 115, 11918-11925.
10. Tai, J. C., Yang, L. and Allinger, N. L. (1993). Molecular mechanics (MM3). Calculation on nitrogen-containing aromatic heterocyclics, J. Am. Chem. Soc., 115, 11906-11917.
11. Gasteiger, J. and Marsili, M. (1980). Iterative partial equalization of orbital electronegativity - a rapid access to atomic charges, Tetrahedron, 36, 3219-3288.
12. Frey, R. F., Coffin, J., Newton, S. Q., Ramek, M., Cheng, V. K. W., Momany, F. A. and Schäfer, L. (1992). Importance of correlation-gradient geometry optimization for molecular conformational analyses, J. Am. Chem. Soc., 114, 5369-5377.
13. Kyte, J. and Doolite, R. F. (1982). Simple method for displaying the hydrophobic character of a protein, J. Mol. Biol., 157, 105-132.
14. a for organic oxyacids using calculated atomic charges, J. Comput. Chem., 14, 1460-1467.
15. Meylan, W. M. and Howard, P. H. (1995). Atom/fragment contribution method for estimating octanol-water partition coefficients, J. Pharm. Sci., 84, 83-92.
16. Eisenhaber, F., Argos, P., Lijnzaad, P., Sander, C. and Scharf, M. (1995). The double cubic lattice method: efficient approaches to numerical integration of surface area and volume and to dot surface contouring of molecular assemblies, J. Comput. Chem., 16, 273-284.
17. Stout, J. M. and Dykstra, C. E. (1995). Static dipole polarizabilities and a predictive model, J. Am. Chem. Soc., 117, 5127-5132.
18. Manallack, D. T. and Livingstone, D. J. (1999). Neural networks in drug discovery: have they lived up to their promise?, Eur. J. Med. Chem., 34, 195-208.
19. Mager, P. P., Design Statistics in Pharmacochemistry, Wiley, New York, 1991.
20. Jiang, H., Burdick, D., Glabe, C. G., Cotman, C. W., Tenner, A. J. (1994). β-amyloid activates complement by binding to a specific region of the collagen-like domain of the Clq A chain, J. Immunol., 152, 5050-5059.
21. Terzi, E., Holzemann, G. and Seelig, J. (1994), Alzheimer β-amyloid peptide 25-35: electrostatic interactions with phospholipid membranes, Biochemistry, 33, 7431-7441.
22. Mason, R. P., Estermeier, J. D., Kelley, J. S. and Mason, P. E. (1996). Alzheimer's disease amyloid β-peptide 25-35 is localized in the membrane hydrocarbon core: X-ray diffraction analysis, Biochem. Biophys. Res. Commun., 222, 78-82.
23. Mager, P. P. and Fischer, K., Simulation of the lipophilic and antigenic cores of the Aβ(1-42) peptide of Alzheimer's disease, Mol. Simul., in press.
24. Hilbich, C., Kisters-Wolke, B., Masters, C. L. and Reed, J. (1991). Aggregation and secondary structure of synthetic amyloid βA4 peptide of Alzheimer's disease, J. Mol. Biol., 218, 149-163.
25. Hilbich, C., Kisters-Woike, B., Reed, J., Masters, C. L. and Beyreuther, K. (1992). Substitutions of hydrophobic amino acids reduce the amyloidgenicity of Alzheimer's disease βA4 peptides, J. Mol. Biol., 228, 460-473.
26. Barrow, C. J., Kenny, P. T. M., Ykikazu, A. and Zagorski, M. G. (1992). Solution conformations and aggregational properties of synthetic amyloid β-peptides of Alzheimer's disease, J. Mol. Biol., 225, 1075-1093.
27. Chaney, M. O., Webster, S. D., Kuo, Y.-M. and Roher, A. E. (1998). Molecular modeling of the Aβ1-42 peptide from Alzheimer's disease, Protein Engineering, 11, 761-767.
28. Benzinger, T. L. S., Gregory, D. M., Burkoth, T. S., Miller-Auer, H., Lynn, D. G., Botto, R. E. and Meredith, S. C. (1998). Propagating structure of Alzheimer's β-amyloid (10-35) is parallel β-sheet with residues in exact register, Proc. Natl. Acad. Sci. USA, 95, 13407-13412.
29. 2a adenosine receptor agonists, Med. Chem. Res., 8, 277-290.
30. Mager, P. P. and Reinhardt, R. (1999). A comparison of backpropagation and generalized-regression genetic-neural network models, Drug Design and Discovery, 16, 49-53.
31. Salomon, A. R., Marcinowski, K. J., Friedland, R. P. and Zagorski, M. G. (1996). Nicotine inhibits amyloid formation by the β-peptide, J. Am. Chem. Soc., 35, 13568-13578.
32. Fujita, T., The Extrathermodynamic Approach to Drug Design, In: Comprehensive Medicinal Chemistry, Hansch, C. and Taylor, J. B. Eds., Pergamon, Oxford, 1990, pp. 497-560.