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Original Article

Structural Bioinformatics and QSAR Analysis Applied to the Acetylcholinesterase and Bispyridinium Aldoximes

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Pages 127-150 | Published online: 04 Dec 2011

References

  • Ashani, Y., Radic, Z., Tsigelny, D. C., Vellmom, D. C., Pickering, N. A., Quinn, D. M., Doctor, B. P., and Taylor, P. (1995). Amino acid residues controlling reactivation of organophosphonyl conjugates of acetylcholinesterase by mono- and bisquaternary oximes. J. Biol. Chem., 270, 6370- 6380.
  • Grosfeld, H., Barak, D., Ordentlich, A., Velan, B., and Shafferman, A. (1996). Interactions of oxime reactivators with diethylphosphoryl adducts of human acetylcholinesterase and its mutant derivatives. Mol. Pharmacol., 50, 639–649.
  • Wong, L., Radic, Z., Brüggemann, R. J. M., Hosea, N., Berman, H. A., and Taylor, P. (2000). Mechanism of oxime reactivation of acetylcholinesterase analyzed by chirality and mutagenesis. Biochemistry, 39, 5750–5757.
  • Luo, C., Leader, H., Radic, Z., Maxwell, D. M., Taylor, P., Doctor, B. P., and Saxena, A. (2003). Two possible orientations of the HI-6 molecule in the reactivation of organophosphate-inhibited acetylcholinesterase. Biochem. Pharmacology, 66, 387–392.
  • Hammond, P. I., Kern, C., Hong, F., Kollmeyer, T. M., Pang, Y.-P., and Brimijoin, S. (2003). Cholinesterase reactivation in vivo with a novel bis-oxime optimized by computer-aided design. J. Pharmacol. Exp. Ther., 307, 190–196.
  • Pang, Y.-P., Kollmeyer, T. M., Hong, F., Lee, J.-C., Hammond, P. I., Haugabouk, S. P., and Brimijoin, S. (2003). Rational design of alkylene-linked bis-pyridiniumoximes as improved acetylcholinesterase reactivators. Chem. Biol., 10, 491- 502.
  • Mager, P. P. (1981). Quantitative structure-reactivity and structure-toxicity relationships of reactivators of phosphylated acetylcholinesterase. Pharmazie, 36, 450–451.
  • Mager, P. P. (1982). Quantitative structure-activity relationships of reactivators of phosphylated acetylcholinesterase. Pharmazie, 37, 800–801
  • Mager, P. P., and Das Gupta, S. (1982). Quantitative structure-activity relationships of reactivators of phosphylated acetylcholinesterase. Pharmazie, 37, 607–608.
  • Mager, P. P., and Seese, A. (1982). Organophosphorus pesticides and mammalicides: A mathematical study on chemical structure and biological activity applied to parameters of inhibition of myoneuronal junctions, axon demyelination, and reactivation of poisoned acetylcholinesterase. Zool. Jahrb. Anat., 107,46-70.
  • Mager, P. P. (1994). The oxime problem can be solved by molecular simulation, Sci. Conf. Chem. Biol. Defense Res., Comput. Chem. Sect., 15-18 Nov. 1994, U.S. Army Edgewood Area Conf. Center: Aberdeen Proving Ground, MD, p. 166.
  • Dayhoff, M. O., Barker, W. C., and Hunt, L. T. (1983). Establishing homology in protein sequence. Meth. Enzymol., 91, 524–545.
  • Corpet, F. (1988). Multiple alignment analysis with hierarchical clustering. Nucl. Acids Res., 16, 10881–10890.
  • Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994). ClustalW: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucl. Acids Res., 22, 4673–4680.
  • Bairoch, A. (1996). The PROSITE database. Nucleic Acid Res., 24, 189–196.
  • Corpet, F., Gouzy, J., and Kahn, D. (1999). Recent improvements of the ProDom database of protein domain families. Nucleic Acids Res., 27, 263–267.
  • Attwood, T. K., Croning, M. D. R., Flower, D. R., Lewis, A. P., Mabey, J. E., Scordis, P., Selley, J. N., and Right, W. (2000). PRINT-S: The database formerly known as PRINTS. Nucl. Acids Res., 28, 225–227.
  • Attwood, T. K., Blythe, M., Flower, D. R., Gaulton, A., Mabey, J. E., Maudling, N., McGregor, L., Mitchell, A., Moulton, G., Paine, K., and Scordis, P. (2002). PRINTS and PRINT-S shed light on protein ancestry. Nucl. Acids Res., 30, 239–241.
  • Bateman, A., Birney, E., Cerruti, L., Durbin, R., Etwiller, L., Eddy, S. R., Griffiths-Jones, S., Howe, K. L., Marshall, M., and Sonnhammer, E. L. (2002). The PFAM protein families database. Nucl. Acids Res., 30, 276–280.
  • Falquet, L., Pagni, M., Bucher, P., Hulo, N., Sigrist, C. J., Hofmann, K., and Bairoch, A. (2002). The PROSITE database, its status in 2002. Nucl. Acids Res., 30, 235–238. MODELLING OF AChE AND ALDOXIMES 149
  • Chen, C. P., Kernytsky, A., and Rost, B. (2002). Transmembrane helix predictions revisited. Protein Sci., 11, 2774–2791.
  • Ryde, U., Olsen, L., and Nilsson, K. (2002). Quantum chemical geometry optimizations in proteins using crystallographic raw data. J. Comput. Chem., 23, 1058–1070.
  • Taylor, R. (2002). Life-science applications of the cambridge structural database. Acta Cryst., D58, 879–888.
  • Mager, P. P. (1984). Multidimensional Pharmacochemistry, Academic Press, New York, pp. 51, 355, 356, 365–367.
  • Glick, M., Grant, G. H., and Richards, W. G. (2002). Docking of flexible molecules using multiscale ligand representations. J. Med. Chem., 45, 4639–4646.
  • Hansch, C., and Leo, A. (1979). Substituent Constants for Correlation Analysis in Chemistry and Biology, Wiley, New York.
  • Hansch, C., and Leo, A. (1995). Exploring QSAR: Fundamentals and Applications in Chemistry and Biology, Am. Chem. Soc., Washington, DC.
  • Fujita, T. (1990). The extrathermodynamic approach to drug design. Compr. Med. Chem., 4, 497–560.
  • Walters, D. E., and Hopfinger, A. J. (1984). Application of molecular shape analysis in QSAR, In QSAR in Design of Bioactive Compounds, edited by M. Kuchar, Proc. 1st Telesymp. Med. Chem. 1984, J. R. Prous Sci. Publ., Barcelona, pp. 279–286.
  • Remko, M., Scheiner, S., and Van Duijnen, P. T. (1992). Ab initio investigations of interactions between models of local anesthetics and polar groups of membranes. In QSAR in Design of Bioactive Compounds, edited by M. Kuchar, Proc. 2nd Telesymp. Med. Chem. 1992, J. R. Prous Sci. Publ., Barcelona, pp. 83–95.
  • Free, S. M., and Wilson, J. W. (1964). A mathematical contribution to structure-activity studies. J. Med. Chem., 7, 395–399.
  • Hall, L. H., and Kier, L. B. (1976). Molecular Connectivity in Chemistry and Drug Research. New York: Academic Press.
  • Verloop, A., Hoogenstraaten, W., and Tipker, J. (1976). Development and application of new steric substituent parameters in drug design, in: Ariens, E. J. (Ed.). Drug Design. New York: Academic Press, Vol. 7, pp. 165–207.
  • Dixon, S. L., and Jurs, P. C. (1993). Estimation of pKa for organic oxyacids using calculated atomic charges. J. Comput. Chem., 14, 1460–1467.
  • Meylan, W. M., and Howard, P. H. (1995). Atom/fragment contribution method for estimating octanol-water partition coefficients. J. Pharmaceut. Sci., 84,83-92.
  • Oldiges. K., and Schoene, K. (1970). Pyridinium and imidazolium salts as antidotes for soman and paraoxon poisoning in mice. Arch. Toxicol., 26, 293–305.
  • Schoene, K., and Oldiges, K. (1973). Efficacy of pyridinium salts in tabun and sarin poisoning in vivo and in vitro. Arch. Int. Pharmacodyn. Ther., 204, 110–123.
  • Schoene, K. (1980). Pyridinium salts as organophosphate antagonists, Monogr. Neural. Sci., 7,85-98.
  • Mager, P. P. (1988). Multivariate Chemometrics in QSAR: A Dialogue. New York: Wiley.
  • Mager, P. P. (1991). Design Statistics in Pharmacochemistry. New York: John Wiley.
  • Schneider, G. (2000). Neural networks are useful tools for drug design. Neural Netw., 13,15-60.
  • Mager, P. P., and Reinhardt, R. (2000). Comparison of neural network and regression models in molecular simulation of relationships between chemical structure and biological activity. Mol. Simul., 28, 287–294.
  • Radic, Z., Gibney, G., Kawamoto, S., MacPhee-Quigley, K., Bongiorno, C., and Taylor, P. (1993). Three distinct domains in the cholinesterase molecule confer selectivity for acetyland butyrylcholinesterase inhibitors. Biochemistry, 32, 12074- 12084.
  • Radic, Z., Pickering, N. A., Vellom, D. C., Camp, S., and Taylor, P. (1993). Expression of recombinant acetylcholinesterase in a baculovirus system: Kinetic properties of glutamate 199 mutants. Biochemistry, 31, 9760–9767.
  • Harel, M., Sussman, J. L., Krejci, E., Bon, S., Chanal, P., Massoulie, J., and Silman, I. (1992). Conversion of acetylcholinesterase to butylcholinesterase: modeling and mutagenesis. Proc. Natl. Acad. Sci. USA, 89, 10827–10831.
  • Ordentlich, A., Barak, D., Kronman, C., Flashner, Y., Leitner, M., Segall, Y., Ariel, N., Cohen, S., Velan, B., and Shafferman, A. (1993). Dissection of the human acetylcholinesterase active center determinants of substrate specificity. Identification of residues constituting the anionic site, the hydrophobic site, and the acyl pocket. J. Biol. Chem., 268, 17083–17095.
  • Masson, P., Froment, M.-T., Bartels, C., and Lockridge, O. (1997). Importance of aspartate-70 in organophasphate inhibition, oxime re-activation and aging of human acetylcholinesterase. Biochem. J., 325,53-61.
  • Massoulie, J., Pezzementi, L., Bon, S., Krejci, E., and Vallette, F.-M. (1993). Molecular and cellular biology of cholinesterases. Prog. Neurobiol., 41,31-91.
  • Taylor, P., and Radic, Z. (1994). The cholinesterases: From genes to proteins. Annu. Rev. Pharmacol. Toxicol., 34, 281- 320.
  • Sussman, J. L., Harel, M., Frolow, F., Oefner, C., Goldman, A., Toker, L., and Silman, I. (1991). Atomic structure of acetylcholinesterase from Torpedo california: A prototypic acetylcholine-binding protein. Science, 253, 872–879.
  • Bernard, P. P., Kireev, D. B., Pintore, M., Chretien, J. R., Fortier, P.-L., and Froment, D. (2000). A CoMFA study of enantiomeric organophosphorus inhibitors of acetylcholinesterase. J. Mol. Model., 6, 618–629.
  • Kua, J., Zhang, Y., and McCammon, J. A. (2002). Studying enzyme binding specificity in acetylcholinesterase using a combined molecular dynamics and multiple docking approach. J. Am. Chem. Soc., 124, 8260–8267.
  • Harel, M., Quinn, D. M., Nair, H. K., Silman, I., and Sussman, J. L. (1996). The X-ray structure of a transition state analog complex reveals the molecular origins on the catalytic power and substrate specificity of acetylcholinesterase. J. Am. Chem. Soc., 118, 2340–2346.
  • Shi, J., Tai, K., McCammon, A., Taylor, P., and Johnson, D. A. (2003). Nanosecond dynamics of the mouse acetylcholinesterase Cys69-Cys95 omega loop. J. Biol. Chem., 278, 30905–30911.
  • Chen, J. W., Luo, Y. L., Hwang, M. J., Peng, P. C., and Ling, K. H. (1999). Territrem B, a tremorgenic mycotoxin that inhibits acetylcholinesterase with a noncovalent yet irreversible binding mechanism. J. Biol. Chem., 274, 34916–34923.
  • Shen, T., Tai, K., Henchman, R. H., and McCammon, J. A. (2002). Molecular dynamics of acetylcholinesterase. Acc. Chem. Res., 35, 332–340.
  • Davies, H., Richter, R., Keifer, M., Broomfield, C., Sowalla, J., and Furlong, C. (1996). The effect of human serum paraoxonase polymorphism is reversed with diazoxon, soman and sarin. Nat. Genet., 14, 334–336.
  • Boström, J. (2001). Reproducing the conformations of protein-bound ligands: A critical evaluation of several popular conformational searching tools. J. Comput.-Aided Mol. Des., 15, 1137–1152.
  • Boström, J., Greenwood, J. R., and Gottfries, J. (2003). Assessing the performance of OMEGA with respect to retrieving bioactive conformations. J. Mol. Graphics Model., 21, 449- 462.
  • Clark, R. D., Strizhev, A., Leonard, J. M., Blake, J. F., and Matthew, J. B. (2002). Consensus scoring for ligand/protein interactions. J. Mol. Graphics Model., 20, 281–295.
  • Glick, M., Grant, G. H., and Richards, W. G. (2002). Docking of flexible molecules using multiscale ligand representations. J. Med. Chem., 45, 4639–4646.
  • Palm, V. A. (1991). Grundlagen der quantitativen Theorie organischer Reaktionen. Berlin: Akademie-Verlag, pp. 220- 221.
  • Schwetlick, K. (1991). Kinetische Methoden zur Untersuchung von Reaktionsmechanismen, Berlin: Akademie-Verlag, p. 177.
  • Mager, P. P. (1997). How design statistics concepts can improve experimentation in medicinal chemistry. Med. Res. Rev., 17, 453–475.
  • De Jong, L. P., Verhagen, M. A., Langenberg, J. P., Hagedorn, I., and Loffler, M. (1989). The bispyridinium-dioxime HLo-7. A potent reactivator for acetylcholinesterase inhibited by stereoisomers of tabun and soman. Biochem. Pharmacol., 38, 633–640.
  • Worek, F., Kirchner, T., Bäcker, M., and Szinics, L. (1996). Reactivation by various aldoximes of human erythrocyte acetylcholinesterase inhibited by different organophosphorus compounds. Arch. Toxicol., 70, 497–503.
  • Worek, F., Kirchner, T., and Szinics, L. (1995). Effect of atropine, HLö 7, and HI 6 on respiratory and circulatory function in sarin poisoned guinea-pigs. Toxicology, 95, 123–133.
  • Worek, F., Widmann, R., Knopff, O., and Szinics, L. (1998). Reactivating potency of obidoxime, pralidoxime, HI 6 and HLo 7 in human erythrocyte acetylcholinesterase inhibited by highly toxic organophosphorus compounds. Arch. Toxicol., 72, 237- 243.
  • Worek, F., Reiter, G., Eyer, P., and Szinics, L. (2002). Reactivation kinetics of acetylcholinesterase from different species inhibited by highly toxic organophosphates. Arch. Toxicol., 76, 523–529.
  • Polyzou, A., Froment, M.-T., Masson, P., and Belzunces, L. P. (1998). Absence of a protective effect of the oxime 2-PAM toward paraoxon-poisoned honey bees: Acetylcholinesterase reactivation not a fault. Toxicol. Appl. Pharmacol., 152, 184–192.

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