Molecular docking and receptor-specific 3D-QSAR studies of acetylcholinesterase inhibitors

Molecular Diversity

Volumn 16, Issue 4, 2012, Pages 803-823

  Deb, Pran Kishore ^a   Sharma, Anuradha ^a   Piplani, Poonam ^a   Akkinepally, Raghuram Rao ^b  

^a PANJAB UNIVERSITY   (India)

^b KAKATIYA UNIVERSITY   (India)

Author keywords

3D QSAR; Acetylcholinesterase inhibitors; ADME prediction; Consensus scoring; Molecular docking

Indexed keywords

8 QUINOLINOL; AMINO ACID; BENZENE; CARBONYL DERIVATIVE; CHOLINESTERASE INHIBITOR; DONEPEZIL; HALOGEN; RIVASTIGMINE; TACRINE 8 HYDROXYQUINOLINE; TACRINE DERIVATIVE; UNCLASSIFIED DRUG; ACETYLCHOLINESTERASE; LIGAND;

ALZHEIMER DISEASE; ARTICLE; BINDING AFFINITY; BINDING SITE; BIOLOGICAL ACTIVITY; CIS ISOMER; CONFORMATION; CONSENSUS; CRYSTAL STRUCTURE; HYDROGEN BOND; HYDROPHILICITY; LIGAND BINDING; MOLECULAR DOCKING; MONTE CARLO METHOD; PRIORITY JOURNAL; PROTEIN STRUCTURE; QUANTITATIVE STRUCTURE ACTIVITY RELATION; REGRESSION ANALYSIS; SCORING SYSTEM; SENILE PLAQUE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER PROGRAM; ENZYME ACTIVE SITE; HUMAN; METHODOLOGY; REPRODUCIBILITY;

ACETYLCHOLINESTERASE; ALZHEIMER DISEASE; BINDING SITES; CATALYTIC DOMAIN; CHOLINESTERASE INHIBITORS; HUMANS; LIGANDS; MODELS, MOLECULAR; MOLECULAR DOCKING SIMULATION; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; REPRODUCIBILITY OF RESULTS; SOFTWARE;

EID: 84878047440     PISSN: 13811991     EISSN: 1573501X     Source Type: Journal    
DOI: 10.1007/s11030-012-9394-x     Document Type: Article

References (59)

1. Lahiri DK, Farlow MR, Greig NH, Sambamurti K (2002) Current drug targets for Alzheimer's disease treatment. Drug Dev Res 56: 267-281. doi: 10.1002/ddr.10081 (Pubitemid 35168304)
2. Inestrosa NC, Dinamarca MC, Alvarez A (2008) Amyloid-cholinesterase interactions. Implications for Alzheimer's disease. FEBS J 275: 625-632. doi: 10.1111/j.1742-4658.2007.06238.x (Pubitemid 351160969)
3. Querfurth HW, LaFerla FM (2010) Alzheimer's disease. N Engl J Med 362: 329-344. doi: 10.1056/NEJMra0909142
4. Pepeu G, Giovannini MG (2009) Cholinesterase inhibitors and beyond. Curr Alzheimer Res 6: 86-96. doi: 10.2174/156720509787602861
5. Smith DA (2009) Treatment of Alzheimer's disease in the long-term care setting. Am J Health Syst Pharm 66: 899-907. doi: 10.2146/ajhp070622
6. Selkoe DJ (1999) Translating cell biology into therapeutic advances in Alzheimer's disease. Nature 399: A23-A31. doi: 10.1038/399a023
7. Carletti E, Colletier JP, Dupeux F, Trovaslet M, Masson P, Nachon F (2010) Structural evidence that human acetylcholinesterase inhibited by tabun ages through O-dealkylation. J Med Chem 53: 4002-4008. doi: 10.1021/jm901853b
8. Kryger G, Harel M, Giles K, Toker L, Velan B, Lazar A, Kronman C, Barak D, Ariel N, Shafferman A, Silman I, Sussman JL (2000) Structures of recombinant native and E202Q mutant human acetylcholinesterase complexed with the snake-venom toxin fasciculin-II. Acta Crystallogr D 56: 1385-1394. doi: 10.1107/S0907444900010659
9. Kryger G, Silman I, Sussman JL (1999) Structure of acetylcholinesterase complexed with E2020 (Aricept): implications for the design of new anti-Alzheimer drugs. Structure 7: 297-307. doi: 10.1016/S0969-2126(99)80040-9 (Pubitemid 29159689)
10. Raves ML, Harel M, Pang YP, Silman I, Kozikowski AP, Sussman JL (1997) Structure of acetylcholinesterase complexed with the nootropic alkaloid, (-)-huperzine A. Nat Struct Biol 4: 57-63. doi: 10.1038/nsb0197-57 (Pubitemid 27020926)
11. Greenblatt HM, Kryger G, Lewis T, Silman I, Sussman JL (1999) Structure of acetylcholinesterase complexed with (-)-galanthamine at 2.3 Å resolution. FEBS Lett 463: 321-326. doi: 10.1016/S0014-5793(99)01637-3 (Pubitemid 30001943)
12. Harel M, Schalk I, Ehret-sabatier L, Bouet F, Goeldner M, Hirth C, Axelsen PH, Silman I, Sussman JL (1993) Quaternary ligand binding to aromatic residues in the active-site gorge of acetylcholinesterase. Proc Natl Acad Sci USA 90: 9031-9035. doi: 10.1073/pnas.90.19.9031 (Pubitemid 23306445)
13. Doucet-Personeni C, Bentley PD, Fletcher RJ, Kinkaid A, Kryger G, Pirard B, Taylor A, Taylor R, Taylor J, Viner R, Silman I, Sussman JL, Greenblatt HM, Lewis T (2001) A structure-based design approach to the development of novel, reversible AChE inhibitors. J Med Chem 44: 3203-3215. doi: 10.1021/jm010826r (Pubitemid 32917100)
14. Millard CB, Koellner G, Ordentlich A, Shafferman A, Silman I, Sussman JL (1999) Reaction products of acetylcholinesterase and VX reveal a mobile histidine in the catalytic triad. J Am Chem Soc 121: 9883-9884. doi: 10.1021/ja992704i (Pubitemid 29517432)
15. Greenblatt HM, Guillou C, Guenard D, Argaman A, Botti S, Badet B, Thal C, Silman I, Sussman JL (2004) The complex of a bivalent derivative of galanthamine with torpedo acetylcholinesterase displays drastic deformation of the active-site gorge: implications for structure-based drug design. J Am Chem Soc 126: 15405-15411. doi: 10.1021/ja0466154 (Pubitemid 39577474)
16. Rydberg EH, Brumshtein B, Greenblatt HM, Wong DM, Shaya D, Williams LD, Carlier PR, Pang YP, Silman I, Sussman JL (2006) Complexes of alkylene-linked tacrine dimers with Torpedo californica acetylcholinesterase: binding of bis(5)-tacrine produces a dramatic rearrangement in the active-site gorge. J Med Chem 49: 5491-5500. doi: 10.1021/jm060164b (Pubitemid 44373181)
17. Harel M, Quinn DM, Nair HK, Silman I, Sussman JL (1996) The X-ray structure of a transition state analog complex reveals the molecular origins of the catalytic power and substrate specificity of acetylcholinesterase. J Am Chem Soc 118: 2340-2346. doi: 10.1021/ja952232h (Pubitemid 26124248)
18. Ravelli RB, Raves ML, Ren Z, Bourgeois D, Roth M, Kroon J, Silman I, Sussman JL (1998) Static Laue diffraction studies on acetylcholinesterase. Acta Crystallogr D 1: 1359-1366. doi: 10.1107/S0907444998005277 (Pubitemid 28560413)
19. Sussman JL, Harel M, Frolow F, Oefner C, Goldman A, Toker L, Silman I (1991) Atomic structure of acetylcholinesterase from Torpedo californica: a prototypic acetylcholine-binding protein. Science 253: 872-879. doi: 10.1126/science.1678899 (Pubitemid 21917225)
20. Silman I, Sussman JL (2008) Acetylcholinesterase: How is structure related to function. Chem Biol Interact 175: 3-10. doi: 10.1016/j.cbi.2008.05. 035
21. Reyes AE, Chacon MA, Dinamarca MC, Cerpa W, Morgan C, Inestrosa NC (2004) Acetylcholinesterase-Aβ complexes are more toxic than Aβ fibrils in rat hippocampus: effect on rat beta-Amyloid aggregation, laminin expression, reactive astrocytosis, and neuronal cell loss. Am J Pathol 164: 2163-2174. doi: 10.1016/S0002-9440(10)63774-1 (Pubitemid 38669363)
22. Castro A, MartInez A (2006) Targeting beta-Amyloid pathogenesis through acetylcholinesterase inhibitors. Curr Pharm Des 12: 4377-4387. doi: 10.2174/138161206778792985 (Pubitemid 44718295)
23. Bartolini M, Bertucci C, Cavrini V, Andrisano V (2003) β-Amyloid aggregation induced by human acetylcholinesterase: inhibition studies. Biochem Pharmacol 65: 407-416. doi: 10.1016/S0006-2952(02)01514-9 (Pubitemid 36084557)
24. Guo J, Hurley MM, Wright JB, Lushington GH (2004) A docking score function for estimating ligand-protein interactions: application to acetylcholinesterase inhibition. J Med Chem 47: 5492-5500. doi: 10.1021/jm049695v (Pubitemid 39382797)
25. Nagaraju A, Laurent L, Janet G, Vassilios P (2006) 3D QSAR studies of AChE inhibitors based on molecular docking scores and CoMFA. Bioorg Med Chem Lett 16: 6277-6280. doi: 10.1016/j.bmcl.2006.09.030 (Pubitemid 44709910)
26. Chaudhary SS, Roy KK, Shakya N, Saxena G, Sammi SR, Nazir A, Nath C, Saxena AK (2010) Novel carbamates as orally active acetylcholinesterase inhibitors found to improve scopolamine-induced cognition impairment: pharmacophore-based virtual screening, synthesis, and pharmacology. J Med Chem 53: 6490-6505. doi: 10.1021/jm100573q
27. Santos JSO, Lesnard A, Agondanou JH, Dupont N, Godard AM, Stiebing S, Rochais C, Fabis F, Dallemagne P, Bureau R, Rault S (2010) Virtual screening discovery of new acetylcholinesterase inhibitors issued from CERMN chemical library. J Chem Inf Model 50: 422-428. doi: 10.1021/ci900491t
28. Gupta S, Mohan CG (2011) 3D-pharmacophore model based virtual screening to identify dual-binding site and selective acetylcholinesterase inhibitors. Med Chem Res 20: 1422-1430. doi: 10.1007/s00044-010-9373-7
29. Lakshmi Narayana B, Pran Kishore D, Balakumar C, Venkata Rao K, Rajwinder K, Raghuram Rao A, Narashima Murthy J, Ravikumar M (2012) Molecular modeling evaluation of non-steroidal aromatase inhibitors. Chem Biol Drug Des 79: 674-682. doi: 10.1111/j.1747-0285.2011.01277.x
30. Fernandez-Bachiller MI, Perez C, Gonzalez-Munoz GC, Conde S, Lopez MG, Villarroya M, GarcIa AG, Rodriguez-Franco MI (2010) Novel tacrine-8- hydroxyquinoline hybrids as multifunctional agents for the treatment of alzheimer's disease, with neuroprotective, cholinergic, antioxidant, and copper-complexing properties. J Med Chem 53: 4927-4937. doi: 10.1021/jm100329q
31. Marco-Contelles J, Leon R, de los Rios C, Samadi A, Bartolini M, Andrisano V, Huertas O, Barril X, Luque FJ, RodrIguez-Franco MI, Lopez B, Lopez MG, GarcIa AG, Carreiras MC, Villarroya M (2009) Tacripyrines, the first tacrine-dihydropyridine hybrids, as multitarget-directed ligands for the treatment of Alzheimer's disease. J Med Chem 52: 2724-2732. doi: 10.1021/jm801292b
32. Camps P, Formosa X, Galdeano C, Gomez T, Munoz-Torrero D, Scarpellini M, Viayna E, Badia A, Victoria-Clos M, Camins A, Pallas M, Bartolini M, Mancini F, Andrisano V, Estelrich J, Lizondo M, Bidon-Chanal A, Luque FJ (2008) Novel donepezil-based inhibitors of acetyl- and butyrylcholinesterase and acetylcholinesterase-induced β-Amyloid aggregation. J Med Chem 51: 3588-3598. doi: 10.1021/jm8001313 (Pubitemid 351875014)
33. Rosini M, Simoni E, Bartolini M, Cavalli A, Ceccarini L, Pascu N, McClymont DW, Tarozzi A, Bolognesi ML, Minarini A, Tumiatti V, Andrisano V, Mellor IR, Melchiorre C (2008) Inhibition of acetylcholinesterase, β-Amyloid aggregation and NMDA receptors in alzheimer's disease: a promising direction for the multi-target-directed ligands gold rush. J Med Chem 51: 4381-4384. doi: 10.1021/jm800577j
34. Rizzo S, Riviere C, Piazzi L, Bisi A, Gobbi S, Bartolini M, Andrisano V, Morroni F, Tarozzi A, Monti JP, Rampa A (2008) Benzofuran-based hybrid compounds for the inhibition of cholinesterase activity, β-Amyloid aggregation, and Aβ neurotoxicity. J Med Chem 51: 2883-2886. doi: 10.1021/jm8002747 (Pubitemid 351706016)
35. Bolognesi ML, Bartolini M, Cavalli A, Andrisano V, Rosini M, Minarini A, Melchiorre C (2004) Design, synthesis and biological evaluation of conformationally restricted rivastigmine analogues. J Med Chem 47: 5945-5952. doi: 10.1021/jm049782n (Pubitemid 39507336)
36. RodrIguez-Franco MI, Fernandez-Bachiller MI, Perez C, Hernandez-Ledesma B, Bartolome B (2006) Novel tacrine-melatonin hybrids as dual-Acting drugs for alzheimer disease, with improved acetylcholinesterase inhibitory and antioxidant properties. J Med Chem 49: 459-462. doi: 10.1021/jm050746d (Pubitemid 43157478)
37. Luo W, Yu QS, Kulkarni SS, Parrish DA, Holloway HW, Tweedie D, Shafferman A, Lahiri DK, Brossi A, Greig NH (2006) Inhibition of human acetyl- and butyrylcholinesterase by novel carbamates of (-)- and (+)- tetrahydrofurobenzofuran and methanobenzodioxepine. J Med Chem 49: 2174-2185. doi: 10.1021/jm050578p
38. Tumiatti V, Milelli A, Minarini A, Rosini M, Bolognesi ML, Micco M, Andrisano V, Bartolini M, Mancini F, Recanatini M, Cavalli A, Melchiorre C (2008) Structure-Activity relationships of acetylcholinesterase noncovalent inhibitors based on a polyamine backbone. 4. Further investigation on the inner spacer. J Med Chem 51: 7308-7312. doi: 10.1021/jm8009684
39. GLIDE Maestro, version 9.1 (2010) Schrodinger, LLC, New York
40. Friesner RA, Banks JL, Murphy RB, Halgren TA, Klicic JJ, Mainz DT, Repasky MP, Knoll EH, Shelley M, Perry JK, Shaw DE, Francis P, Shenkin PS (2004) Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem 47: 1739-1749. doi: 10.1021/jm0306430 (Pubitemid 38380917)
41. GOLD, version 4.0 (2000) Cambridge Crystallographic Data Centre, Cambridge
42. Jones G, Willett P, Glen RC, Leach AR, Talor R (1997) Development and validation of a genetic algorithm for flexible docking. J Mol Biol 267: 727-748. doi: 10.1006/jmbi.1996.0897 (Pubitemid 27170693)
43. Eldridge MD, Murray CW, Auton TR, Paolini GV, Mee RP (1997) Empirical scoring functions: I. the development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes. J Comput Aided Mol Des 11: 425-445. doi: 10.1023/A:1007996124545 (Pubitemid 127505895)
44. Mooij WTM, Verdonk ML (2005) General and targeted statistical potentials for protein-ligand interactions. Proteins 61: 272-287. doi: 10.1002/prot.20588 (Pubitemid 41429135)
45. LIGANDFIT, Discovery Studio Modeling Environment Release, version 2.1 (2008) Accelrys Software Inc, San Diego
46. Muegge I (2006) PMF scoring revisited. J Med Chem 49: 5895-5902. doi: 10.1021/jm050038s (Pubitemid 44484936)
47. Gehlhaar DK, Verkhivker GM, Rejto PA, Sherman CJ, Fogel DB, Freer ST (1995) Molecular recognition of the inhibitor AG-1343 by HIV-1 Protease: conformationally flexible docking by evolutionary programming. Chem Biol 2: 317-324. doi: 10.1016/1074-5521(95)90050-0
48. Ajay NJ (2006) Scoring functions for protein-ligand docking. Curr Protein Pept Sci 7: 407-420. doi: 10.2174/138920306778559395 (Pubitemid 44524490)
49. Krammer A, Kirchhoff PD, Jiang X, Venkatachalam CM, Waldman M (2005) LigScore: a novel scoring function for predicting binding affinities. J Mol Graph Model 23: 395-407. doi: 10.1016/j.jmgm.2004.11.007 (Pubitemid 40386869)
50. Meng EC, Shoichet BK, Kuntz ID (1992) Automated docking with grid-based energy evaluation. J Comput Chem 13: 505-524. doi: 10.1002/jcc.540130412
51. MacroModel, version 9.8 (2010) Schrödinger, LLC, New York
52. QikProp, version 3.3 (2010) Schrödinger, LLC, New York
53. Roy K (2007) On some aspects of validation of predictive quantitative structure-Activity relationship models. Expert Opin Drug Discov 2: 1567-1577. doi: 10.1186/1752-153X-2-S1-P9 (Pubitemid 350285346)
54. 3 receptor subtype. Bioorg Med Chem Lett 21: 818-823. doi: 10.1016/j.bmcl.2010.11.094
55. Everitt BS, Landau S, Leese M (2001) Cluster analysis. Arnold, London
56. Roy PP, Roy K (2008) On some aspects of variable selection for partial least squares regression models. QSAR Comb Sci 27: 302-313. doi: 10.1002/qsar.200710043
57. Roy K, Paul S (2009) Exploring 2D and 3D QSARs of 2,4-Diphenyl-1,3- oxazolines for Ovicidal Activity Against Tetranychus urticae. QSAR Comb Sci 28: 406-425. doi: 10.1002/qsar.200810130
58. Darlington RB (1990) Regression and linear models. McGraw-Hill, New York
59. Mitra I, Saa A, Roy K (2009) Quantitative structure-Activity relationship modeling of antioxidant activities of hydroxybenzalacetones using quantum chemical, physicochemical and spatial descriptors. Chem Biol Drug Des 73: 526-536. doi: 10.1111/j.1747-0285.2009.00801.x