Structural basis of femtomolar inhibitors for acetylcholinesterase subtype selectivity: Insights from computational simulations

Journal of Molecular Graphics and Modelling

Volumn 41, Issue , 2013, Pages 55-60

  Zhu, Xiao Lei ^a   Yu, Ning Xi ^a   Hao, Ge Fei ^a   Yang, Wen Chao ^a   Yang, Guang Fu ^a  

^a CENTRAL CHINA NORMAL UNIVERSITY   (China)

Author keywords

Acetylcholinesterase; MM PBSA interaction; Molecular dynamics; Selectivity

Indexed keywords

ACETYLCHOLINESTERASE; BINDING AFFINITIES; BINDING FREE ENERGY; COMPUTATIONAL SIMULATION; DROSOPHILA MELANOGASTER; MOLECULAR DYNAMICS SIMULATIONS; ORGANIC INHIBITORS; STRUCTURAL BASIS;

BINDING ENERGY; CATALYST SELECTIVITY; ENZYMES; MOLECULAR DYNAMICS; NITROGEN COMPOUNDS;

ISOMERS;

ACETYLCHOLINESTERASE;

ARTICLE; DROSOPHILA MELANOGASTER; DRUG SELECTIVITY; HUMAN; MOLECULAR DYNAMICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN STRUCTURE; SIMULATION;

ACETYLCHOLINESTERASE; ACRIDINES; ANIMALS; BINDING SITES; CHOLINESTERASE INHIBITORS; DROSOPHILA MELANOGASTER; ISOENZYMES; MICE; MOLECULAR DYNAMICS SIMULATION; PHENANTHRIDINES; PROTEIN BINDING; STRUCTURE-ACTIVITY RELATIONSHIP; TACRINE; THERMODYNAMICS; TORPEDO; TRIAZOLES;

DROSOPHILA MELANOGASTER; TORPEDO CALIFORNICA;

EID: 84874935916     PISSN: 10933263     EISSN: 18734243     Source Type: Journal    
DOI: 10.1016/j.jmgm.2013.01.004     Document Type: Article

References (40)

1. T.L. Rosenberry, and Acetylcholinesterase Advances in Enzymology and Related Areas of Molecular Biology 43 1975 103 218
2. J.L. Sussman, M. Harel, F. Frolow, C. Oefner, A. Gpldman, L. Toker, and I. Silman Atomic structure of acetylcholinesterase from Torpedo californica: a prototypic acetylcholine-binding protein Science 253 1991 872 879
3. Y. Bourne, Z. Radic, G. Sulzenbacher, E. Kim, P. Taylor, P. Marchot, and Substrate Product trafficking through the active center gorge of acetylcholinesterase analyzed by crystallography and equilibrium binding Journal of Biological Chemistry 281 2006 29256 29267
4. J.P. Colletier, D. Bourgeois, B. Sanson, D. Fournier, J.L. Sussman, I. Silman, and M. Weik Shoot-and-trap: use of specific X-ray damage to study structural protein dynamics by temperature-controlled cryo-crystallography Proceedings of the National Academy of Sciences of the United States of America 105 2008 11742 11747
5. G. Kryger, M. Harel, K. Giles, L. Toker, B. Velan, A. Lazar, C. Kronman, D. Barak, N. Ariel, A. Shafferman, I. Silman, and J.L. Sussman Structures of recombinant native and E202Q mutant human acetylcholinesterase complexed with the snake-venom toxin fasciculin-II Acta Crystallographica. Section D: Biological Crystallography 56 2000 1385 1394
6. M. Harel, G. Kryger, T.L. Rosenberry, W.D. Mallender, T. Lewis, R.J. Fletcher, J.M. Guss, I. Silman, and J.L. Sussman Three-dimensional structures of Drosophila melanogaster acetylcholinesterase and of its complexes with two potent inhibitors Protein Science 9 2000 1063 1072
7. J.I. Kim, C.S. Jung, Y.H. Koh, and S.H. Lee Molecular, biochemical and histochemical characterization of two acetylcholinesterase cDNAs from the German cockroach Blattella germanica Insect Molecular Biology 15 2006 513 522
8. E. Huchard, M. Martinez, H. Alout, E.J. Douzery, G. Lutfalla, A. Berthomieu, C. Berticat, M. Raymond, and M. Weill Acetylcholinesterase genes within the Diptera: takeover and loss in true flies Proceedings of the Royal Society-Biological Sciences 273 2006 2595 2604
9. M. Weill, P. Fort, A. Berthomieu, M.P. Dubois, N. Pasteur, and M. Raymond A novel acetylcholinesterase gene in mosquitoes codes for the insecticide target and is nonhomologous to the ace gene Drosophila Proceedings of the Royal Society of London B 269 2002 2007 2016
10. T. Nabeshima, A. Mori, T. Kozaki, Y. Iwata, O. Hidoh, S. Harada, S. Kasai, D.W. Severson, Y. Kono, and T. Tomita An amino acid substitution attributable to insecticide insensitivity of acetylcholinesterase in a Japanese encephalitis vector mosquito, Culex tritaeniorhynchus Biochemical and Biophysical Research Communications 13 2004 794 801
11. R.H. Ffrench-Constant, and B.C. Bonning Rapid microtitre plate test distinguishes insecticide resistant acetylcholinesterase genotypes in the mosquitoes Anopheles albimanus, A. nigerrimus and Culex pipiens Medical and Veterinary Entomology 3 1989 9 16
12. G.D. Baxter, and S.C. Barker Analysis of the sequence and expression of a second putative acetylcholinesterase cDNA from organophosphate-susceptible and organophosphate-resistant cattle ticks Insect Biochemistry and Molecular Biology 32 2002 815 820
13. J. Benting, and R. Nauen Biochemical evidence that an S431F mutation in acetylcholinesterase-1 of Aphis gossypii mediates resistance to pirimicarb and omethoate Pest Management Science 60 2004 1051 1055
14. S. Toda, S. Komazaki, T. Tomita, and Y. Kono Two amino acid substitutions in acetylcholinesterase associated with pirimicarb and organophosphorous insecticide resistance in the cotton aphid, Aphis gossypii Glover (Homoptera: Aphididae) Insect Molecular Biology 13 2004 549 553
15. T. Nabeshima, T. Kozaki, T. Tomita, and Y. Kono An amino acid substitution on the second acetylcholinesterase in the pirimicarb-resistant strains of the peach potato aphid, Myzus persicae Biochemical and Biophysical Research Communications 307 2003 15 22
16. J.R. Gao, S. Kambhampati, and K.Y. Zhu Molecular cloning and characterization of a greenbug (Schizaphis graminum) cDNA encoding acetylcholinesterase possibly evolved from a duplicate gene lineage Insect Biochemistry and Molecular Biology 32 2002 765 775
17. J.H. Baek, J.I. Kim, D.W. Lee, B.K. Chung, T. Miyata, and S.H. Lee Identification and characterization of ace1-type acetylcholinesterase likely associated with organophosphate resistance in Plutella xylostella Pesticide Biochemistry and Physiology 81 2005 164 175
18. D.W. Lee, S.S. Kim, S.W. Shin, W.T. Kim, and K.S. Boo Molecular characterization of two acetylcholinesterase genes from the oriental tobacco budworm, Helicoverpa assulta (Guenee) Biochimica et Biophysica Acta 1760 2006 125 133
19. M. Alon, F. Alon, R. Nauen, and S. Morin Organophosphates' resistance in the B-biotype of Bemisia tabaci (Hemiptera: Aleyrodidae) is associated with a point mutation in an ace1-type acetylcholinesterase and overexpression of carboxylesterase Insect Biochemistry and Molecular Biology 38 2008 940 949
20. Y. Bourne, J. Grassi, P.E. Bougis, and P. Marchot Conformational flexibility of the acetylcholinesterase tetramer suggested by X-ray crystallography Journal of Biological Chemistry 274 1999 30370 30376
21. J. Wiesner, Z. Kriz, K. Kuca, D. Jun, and J. Koca Acetylcholinesterases- the structural similarities and differences Journal of Enzyme Inhibition and Medicinal Chemistry 22 2007 417 424
22. I. Silman, and J.L. Sussman Acetylcholinesterase: how is structure related to function Chemico-Biological Interactions 175 2008 3 10
23. W.G. Lewis, L.G. Green, F. Grynszpan, Z. Radić, P.R. Carlier, P. Taylor, M.G. Finn, and K.B. Sharpless Click chemistry in situ: acetylcholinesterase as a reaction vessel for the selective assembly of a femtomolar inhibitor from an array of building blocks Angewandte Chemie International Edition 41 2002 1053 1057
24. X.L. Zhu, W.C. Yang, N.X. Yu, S.G. Yang, and G.F. Yang Computational simulations of structural role of the active-site W374C mutation of acetyl-coenzyme-A carboxylase: multi-drug resistance mechanism Journal of Molecular Modeling 17 2011 495 503
25. X.L. Zhu, G.F. Hao, C.G. Zhan, and G.F. Yang Computational simulations of the interactions between acetyl-coenzyme-A carboxylase and clodinafop: resistance mechanism due to active and nonactive site mutations Journal of Chemical Information and Modeling 49 2009 1936 1943
26. G.F. Hao, X.L. Zhu, F.Q. Ji, L. Zhang, G.F. Yang, and C.G. Zhan Understanding mechanism of drug resistance due to a codon deletion in protoporphrinogen oxidase through computational modeling Journal of Physical Chemistry B 113 2009 4865 4875
27. Y. Bourne, H.C. Kolb, Z. Radic, K.B. Sharpless, P. Taylor, and P. Marchot Freeze-frame inhibitor captures acetylcholinesterase in a unique conformation Proceedings of the National Academy of Sciences of the United States of America 101 2004 1449 1454
28. E.H. Rydberg, B. Brumshtein, H.M. Greenblatt, D.M. Wong, D. Shaya, L.D. Williams, P.R. Carlier, Y.P. Pang, I. Silman, and J.L. Sussman Complexes of alkylene-linked tacrine dimers with Torpedo californica acetylcholinesterase: binding of Bis5-tacrine produces a dramatic rearrangement in the active-site gorge Journal of Medicinal Chemistry 49 2006 5491 5500
29. G.M. Morris, D.S. Goodsell, R.S. Halliday, R. Huey, W.E. Hart, R.K. Belew, and A.J. Olson Automated docking using a lamarckian genetic algorithm and an empirical binding free energy function Journal of Computational Chemistry 19 1998 1639 1662
30. M.J. Frisch, G.W. Trucks, H.B. Schlegel, G.E. Scuseria, M.A. Robb, J.R. Cheeseman, J.A. Montgomery Jr., T. Verven, K.N. Kudin, J.C. Burant, J.M. Millam, S.S. Iyengar, J. Tomasi, V. Barone, B. Mennucci, M. Cossi, G. Scalmani, N. Rega, G.A. Petersson, H. Nakatsuji, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, M. Klene, X. Li, J.E. Knox, H.P. Hratchian, J.B. Cross, C. Adamo, J. Jaramillo, R. Gomperts, R.E. Stratmann, O. Yazyev, A.J. Austin, R. Cammi, C. Pomelli, J.W. Ochterski, P.Y. Ayala, K. Morokumo, G.A. Voth, P. Salvador, J.J. Dannenberg, V.G. Zakrzewski, S. Dapprich, A.D. Daniels, M.C. Strain, O. Farkas, D.K. Malick, A.D. Rabuck, K. Raghavachari, J.B. Foresman, J.V. Ortiz, Q. Cui, A.G. Baboul, S. Clifford, J. Cioslowski, B.B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R.L. Martin, D.J. Fox, T. Keith, M.A. Al-Laham, C.Y. Peng, A. Nanayakkara, M. Challacombe, P.M. Gill, M.W. Wong, C. Gonzalez, and J.A. Pople Gaussian 03, Revision A.1 2003 Gaussian, Inc. Pittsburgh
31. W.D. Cornell, P. Cieplak, C.I. Bayly, and P.A. Kollmann Application of RESP charges to calculate conformational energies, hydrogen bond energies, and free energies of solvation Journal of the American Chemical Society 115 1993 9620 9631
32. J. Antosiewicz, S.T. Wlodek, and J.A. McCammon Acetylcholinesterase: role of the enzyme's charge distribution in steering charged ligands toward the active site Biopolymers 39 1996 85 94
33. W.L. Jorgensen, J. Chandrasekhar, and J.D. Madura Comparison of simple potential functions for simulating liquid water Journal of Chemical Physics 79 1983 926 935
34. V. Hornak, R. Abel, A. Okur, B. Strockbine, A. Roitberg, and C. Simmerling Comparison of multiple Amber force fields and development of improved protein backbone parameters Proteins 65 2006 712 725
35. D.A. Case, T. Darden, T.E. Cheatham III, C. Simmerling, J. Wang, R.E. Duke, and R. Luo AMBER8 Users' Manual 2004 University of California
36. J.P. Ryckaert, G. Ciccotti, and H.J.C. Berendsen Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes Journal of Computational Physics 23 1977 327 341
37. D. Sitkoff, K.A. Sharp, and B. Honig Accurate calculation of hydration free energies using macroscopic solvent models Journal of Physical Chemistry 98 1994 1978 1988
38. M.L. Connolly Analytical molecular surface calculation Journal of Applied Crystallography 16 1983 548 558
39. F.Q. Ji, C.W. Niu, C.N. Chen, Q. Chen, G.F. Yang, Z. Xi, and C.G. Zhan Computational design and discovery of conformationally flexible inhibitors of acetohydroxyacid synthase to overcome drug resistance associated with the W586L mutation ChemMedChem 3 2008 1203 1206
40. Y.M. Pan, D.Q. Gao, and C.G. Zhan Modeling the catalysis of anti-cocaine catalytic antibody: competing reaction pathways and free energy barriers Journal of the American Chemical Society 130 2008 5140 5149