Targeted studies on the interaction of nicotine and morin molecules with amyloid β-protein

Journal of Molecular Modeling

Volumn 20, Issue 3, 2014, Pages

  Boopathi, Subramaniam ^a   Kolandaivel, Ponmalai ^a  

^a BHARATHIAR UNIVERSITY   (India)

Author keywords

Alzheimer's disease; A protein; Molecular dynamics; Morin; Nicotine; ONIOM

Indexed keywords

AMYLOID BETA PROTEIN; AMYLOID BETA PROTEIN[16-22]; MORIN; NICOTINE; UNCLASSIFIED DRUG; AMYLOID BETA PROTEIN (1 42); AMYLOID BETA-PROTEIN (1-42); FLAVONOID; PEPTIDE FRAGMENT;

ALPHA HELIX; ALZHEIMER DISEASE; ARTICLE; BETA SHEET; DRUG EFFICACY; DRUG MECHANISM; HYDROGEN BOND; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN AGGREGATION; PROTEIN CONFORMATION; PROTEIN INTERACTION; STRUCTURE ANALYSIS; BINDING SITE; CHEMICAL PHENOMENA; CHEMICAL STRUCTURE; CHEMISTRY; HUMAN; KINETICS; METABOLISM; MOLECULAR DOCKING; PROTEIN BINDING; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE;

ALZHEIMER DISEASE; AMYLOID BETA-PEPTIDES; BINDING SITES; FLAVONOIDS; HUMANS; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; KINETICS; MOLECULAR DOCKING SIMULATION; MOLECULAR DYNAMICS SIMULATION; MOLECULAR STRUCTURE; NICOTINE; PEPTIDE FRAGMENTS; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY;

EID: 84894285649     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-014-2109-8     Document Type: Article

References (64)

1. Hardy JA, Higgins GA (1992) Alzheimer's disease: the amyloid cascade hypothesis. Science 256:184-185. doi:10.1126/science.1566067
2. Cohen FE, Kelly JW (2003) Therapeutic approaches to protein-misfolding disease. Nature 426:905-909. doi:10.1038/nature02265
3. Dumoulin M, Johnson JRK, Belloti V, Dobson CM (2007) In: Sipe JD (ed) Protein misfolding and conformational diseases. VCH, Weinheim, pp 285-308
4. Chiti F, Dobson CM (2006) Protein misfolding functional amyloid and human disease. Annu Rev Biochem 75:333-336. doi:10.1111/j.1742-4658.2006.05181.x
5. Haass C, Selkoe DJ (2007) Soluble protein oligomers in neurodegenerative: lesions from the Alzheimer's amyloid β-peptide. Nat Rev Mol Cell Biol 8:101-112. doi:10.1038/nrm2101 (Pubitemid 46432529)
6. Cipriani G, Dolciotti C, Picchi L, Bonuccelli U (2011) Alzheimer and his disease: a brief history. Neurol Sci 32:275-279. doi:10.1007/s10072-010-0454-7
7. Bekris LM, Ku CE, Bird TD, Tsuang DW (2010) Genetics of Alzheimer disease. J Geriatr Psychiatry Neurol 23:213-227. doi:10.1177/0891988710383571
8. Selkoe DJ (2001) Alzheimer's disease: genes, protein and therapy. Physiol Rev 81:741-766. doi:10.1007/s00109-003-0464-5
9. Rak M, Bigio MRD, Mai S, Westaway D, Gough K (2007) Dense-core and diffuse Aβ-plaque in TgCRND8 mice studied with synchrotron FTIR microscopy. Biopolymers 87:207-217. doi:10.1002/bip.20820 (Pubitemid 350075351)
10. Roher AE, Lowenson JD, Clarke S, Woods AS, Cotter RJ, Gowing E, Ball MJ (1993) Beta amyloid (1-42) is a major component of cerebro vascular amyloid deposits: implications for the pathology of Alzheimer disease. Proc Natl Acad Sci USA 90:10836-10840
11. Jarrett JT, Berger EP, Lansbury PT Jr (1993) The carboxy terminus of the beta amyloid protein is critical for the seeding of amyloid formation implications for the pathogenesis of Alzheimer dissease. Biochemistry 32:4693. doi:10.1021/bi00069a001
12. Gravina SA, Ho L, Eckman CB, Long KE, Otvos L Jr, Younkin L, Suzuki N, Younkin SG (1995) Amyloid beta protein (Aβ) in Alzheimer's disease brain. Bio chemical and immune cytochemical analysis with antibodies specific for forms ending at Aβ40 or Aβ42(43). J Biol Chem 270:7013-7016. doi:10.1074/jbc.270.13.7013
13. Pimplikar SW (2008) Reassessing the amyloid cascade hypothesis of Alzheimer disease. Int J Biochem Cell Biol 41:1261-1268. doi:10.1016/j.biocel. 2008.12.015
14. Cheon M, Chang I, Mohanty S, Luheshi LM, Dobson CM, Vendruscolo M, Favrin G (2007) Structural reorganization and potential toxicity of oligomeric species formed during the assembly of amyloid fibrils. PLoS Comput Biol 3:1727. doi:10.1371/journal.pcbi.0030173
15. Viet MH, Ngo ST, Lam NS, Li MS (2011) Inhibition of aggregation of amyloid peptide by beta sheet breaker peptides and their binding affinity. J Phys Chem B 115:7433. doi:10.1021/jb1116728
16. Balbach JJ, Ishii Y, Antzutkin ON, Leapman RD, Rizzo NW, Dyda F, Reed J, Tycko R (2000) Amyloid fibril for mation by Aβ16-22, a seven residue fragment of the Alzheimer's β-amyloid peptide and structure characterization by solid state NMR. Biochemistry 39:13748-13759. doi:10.1021/bi0011330
17. Mehta AK, Lu K, Childers WS, Liang Y, Dublin SN, Dong J, Snyder JP, Pingal SV, Thiyagarajan P (2008) Facial symmetry in protein self assembly. J Am Chem Soc 130:9829-9835. doi:10.1021/ja801511n
18. 10-35): sequence effects. Proc Natl Acad Sci USA 99:14126. doi:10.1073/pnas.212206899
19. Marom AF, Rechter M, Shefler I, Bram Y, Shalev DE, Gazit E (2009) Cognitive-performance recovery of Alzheimer's disease model mice by modulation of early soluble amyloidal assemblies. Angew Chem Int Ed Engl 48:1981-1986. doi:10.1002/ange.200802123
20. Mamikonyan G, Neucla M, Mkrtichyam M, Ghochikyan A, Petrushina I, Moresyan N, Mina E, Kiyatuin A, Glabe CG, Cribbs DH, Agadjanyan MG (2007) Anti Aβ 1-11 antibody binds to different β-amyloid species, inhibits fibril formation and disaggregates performed fibrils but not the most toxic oligomers. J Biol Chem 282:22376-22386. doi:10.1074/jbc.M700088200 (Pubitemid 47267321)
21. Ladiwala ARA, Dordick JS, Tessier PM (2011) Aromatic small molecules remodel toxic soluble oligomers of amyloid beta through three independent pathways. J Biol Chem 286:3209-3218. doi:10.1074/jbc.M110.173856
22. Ono K, Hasegawa K, Yamada M, Naiki H (2002) Nicotine breaks down perfomed Alzheimer's β-amyloid fibrils in vitro. Biol Psychiatry 52:880-886. doi:10.1016/S0006-3223(02)01417-8 (Pubitemid 35223431)
23. Ono K, Hasegawa K, Naiki H, Yamada M (2004) Antiamyloidogenic activity of tannic acid and its activity to destabilize Alzheimer's β-amyloid fibril in vitro. Biochim Biophys Acta 1690:193-202. doi:10.1016/j.bbadis.2004.06.008 (Pubitemid 39423614)
24. Ono K, Hasegawa K, Naiki H, Yamada M (2004) Curcunin has potent anti-amyloidogenic effects for Alzheimer's β-amyloid fibrils in vitro. J Neurosci Res 75:742-750. doi:10.1002/jnr.20025 (Pubitemid 38296087)
25. Chen D, Martin ZS, Soto C, Schein CH (2009) Computation selection of inhibitors of Aβ aggregation and neuronal toxicity. Bioorg Med Chem 17:5189-5197. doi:10.1016/j.bmc.2009.05.047
26. Howard R, Mcshane R, Lindesay J, Itchie C, Beldwin A, Barber R, Burns A, Dening T, Findlay D, Holmes C, Hughes A, Jacoby R, Jones R, Mcketith I, Macharouthu A, O'Brien J, Passmore P, Sheehan B, Juszczak E, Hills R, Ballard C, Brown R, Banerjee S, Onions C, Griffins M, Adams J, Gray R, Johnson T, Bentham P, Phillips P (2012) Donepezil and memantine for moderate-to-severe Alzheimer's disease. N Engl J Med 366:893-903. doi:10.1056/nejmoa1106668
27. Selkoe DJ (2004) Alzheimer's disease: mechanistic understanding predicts novel therapies. Ann Intern Med 140:627-638. doi:10.7326/0003-4819-140-8- 200404200-00010
28. Chong SH, Yim J, Ham S (2013) Structural heterogeneity in familial Alzheimer's disease mutants of amyloid-beta peptides. Mol BioSyst 9:997-1003. doi:10.1039/C2MB25457C
29. Crescenzi O, Tomaselli S, Guerrini R, Salvadori S, O'ursi AM, Temussi PA, Picone D (2002) Solution structure of the Alzheimer amyloid β-peptide(1-42) in an apolar micro environment:similarty with a virus fusion domain. Eur J Biochem 269:5642-5648. doi:10.1046/j.1432-1033.2002.03271.x (Pubitemid 35365553)
30. Kaminski GA, Friesner RA, Tirado-Rives J, Jorgensen WL (2001) Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. J Phys Chem B 105:6474-6487. doi:10.1021/jp003913d (Pubitemid 35339015)
31. 16-22 protofilaments. J Am Chem Soc 103:11066-11072. doi:10.1021/ja8017303
32. Gordon DJ, Sciarretta KL, Meredith SC (2001) Inhibition of β-amyloid(40) fibrilogenesis and disassembly of β-amyloid(40) fibrils by short β-amyloid congeners containing N-methyl amino acids at alternate residues. Biochemistry 40:8237-8245. doi:10.1021/bi002416v (Pubitemid 32661883)
33. Gordon DJ, Tappe R, Meredith SC (2002) Design and characterization of a membrane permeable N-methyl amino acid-containing peptide that inhibits Aβ1-40 fibrillogenesis. J Pept Res 60:37-55. doi:10.1034/j.1399-3011.2002. 11002.x (Pubitemid 34680830)
34. Sciarretta KL, Boire A, Gordon DJ, Meredith SC (2006) Spatial separation of β-sheet domain of β-amyloid: disruption of each β-sheet by N-methyl amino acids. Biochemistry 45:9485-9495. doi:10.1021/bi0605585 (Pubitemid 44223252)
35. Adessi C, Frossard MJ, Boissard C, Fraga S, Bieler S, Ruckle T, Vilbois F, Robinson SM, Mutter M, Bancs WA, Soto C (2003) Pharmacological profiles of peptide drug candidates for the treatment of Alzheimer's disease. J Biol Chem278:13905-13911. doi:10.1074/jbc.M211976200 (Pubitemid 36799931)
36. Salomon AR, Marcinowski mol, Friedland RP, Zagorski MG (1996) Nicotine inhibits amyloid formation by the β-peptide. Biochemistry 35:13568-13578. doi:10.1021/bi9617264
37. Lemkul JA, Bevan DR (2012) Assesing the stability of Alzheimer's amyloid protofibrils using molecular dynamics. Biochemistry 51: 5990-6009. doi:10.1021/jp9110794
38. Paparcone R, Pires MA, Buehler MJ (2010) Mutation alter the geometry and mechanical properties of Alzheimer Aβ(1-40) fibrils. Biochemistry 49:8967-8977. doi:10.1021/bi100953t
39. Lemkul JA, Bevan DR (2012) Morin inhibits the early stages of amyloid β-peptide aggregation by altering tertiary and quaternary interaction to produce "off-path way" structures. Biochemistry 51: 5990-6009. doi:10.1021/bi300113x
40. Cataldo JK, Prochaska JJ, Glantz SA (2010) Cigaratte smoking is a risk factor for Alzheimer disease. An analysis controlling for tobacco industry affiliation. J Alzheimers Dis 19:465-480. doi:10.3233/JAD-2010-1240
41. Rusted JM, Trawley S (2006) Comparable effects of nicotine in smokers and nonsmokers on a prospective memory task. Neuropsychopharmacology 31:1545-1549. doi:10.1038/sj.npp.1300965
42. Warshel A, Levitt M (1976) Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. J Mol Biol 103:227-249. doi:10.1061/0022-2836(76)90311-9
43. Maseras F, Morokuma K (1995) IMOMM: a new integrated Ab-initio + molecular mechanics geometry optimization schemes of equilibrium structures and transition states. J Comput Chem 16:1170-1179. doi:10.1002/jcc.540160911
44. Bakowies D, Thiel W (1996) Hybrid models for combined quantum mechanical and molecular mechanical approaches. J Phys Chem 100:10580-10594. doi:10.1021/jp9536514 (Pubitemid 126788646)
45. - exchange reaction and gas phase protonation of polyether. J Comput Chem 7:718-730. doi:10.1002/jcc.540070604
46. 1 excitation in bacteriorhodopsin with the ONIOM(MO:MM) hybrid method. Theor Chem Accounts 109:125-132. doi:10.1007/s00214-002-0418-y
47. Rosta E, Klahn M, Warshel A (2006) Towards accurate abinitio QM/MM calculation of free energy profile of enzymatic reaction. J Phys Chem B 110:2934-2941. doi:10.1021/jp057109j
48. Kohn W, Becke AD, Parr RG (1996) Density functional theory of electronic structure. J Phys Chem 100:12974-12980. doi:10.1021/jp960669l (Pubitemid 126821039)
49. Beck AD (1996) Density-functional thermochemistry. IV. A new dynamical correlation functional and implications for exact-exchange mixing. J Chem Phys 109:1040-1047. doi:10.1063/1.470829
50. Rapp AK, Casewit CJ, Colwell KS, Goddard WA (1992) UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations. J Am Chem Soc 114:10024-10035. doi:10.1021/ja00051a040
51. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Scalmani G, Barone V, Mennucci B, Petersson GA, Nakatsuji H, Caricato M, Li X, Hratchian HP, Izmaylov AF, Bloino J, Zheng G, Sonnenberg JL, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Vreven T, Montgomery JA, J Jr, Peralta E, Ogliaro F, Bearpark M, Heyd JJ, Brothers E, Kudin KN, Staroverov VN, Keith T, Kobayashi R, Normand J, Raghavachari K, Rendell AJ, Burant C, Iyengar SS, Tomasi J, Cossi M, Rega N, Millam JM, Klene M, Knox JE, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Martin RL, Morokuma K, Zakrzewski VG, Voth GA, Salvador P, Dannenberg JJ, Dapprich S, Daniels AD, Farkas O, Foresman JB, Ortiz JV, Cioslowski JJ, Fox D (2010) Gaussian, Wallingford, CT
52. Tomasi J, Mennucci B, Cammi R (2005) Quantum mechanical continuum solvation models. Chem Rev 105:2999-3094. doi:10.1021/cr9904009
53. Pronk S, Pall S, Schulz R, Larsson P, Bjelkmar P, Apostolov R, Shirts MR, Smith JC, Kasson PM, van der Spoel D, Hess B, Lindahl E (2013) GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics 29:1-10. doi:10.1093/bioinformatics/btt055
54. Berendsen HJC, Postma JPM, van Gunsteren WF, DiNola A, Haak JR (1984) Molecular dynamics with coupling to an external bath. J Chem Phys 81:3684-3690. doi:10.1063/1.448118
55. Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK, Oslon AJ (1984) Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J Comput Chem 19:1639-1662. doi:10.1002/(sici) 1096-987x(19981115)19:14〈1639::aid-jcc10〉3.0.co;2-b
56. Darden T, York D, Padersen L (1993) Particle mesh Ewald: an N*logN method for Ewald sums in large systems. J Chem Phys 98:10089-10092. doi:10.106311.464397
57. Boopathi S, Kolandaivel P (2013) Molecular dynamics simulations and density functional theory studies of NALMA and NAGMA dipeptides. J Biomol Struct Dyn 31:158-173. doi:10.1080/07391102.2012.698380
58. Zeng H, Zhang Y, Peng LJ, Shao H, Menon NK, Yang J, Salomon AR, Friedland RP, Zagorski MG (2001) Nicotine and amyloid formation. Biol Psychiatry 49:248-257. doi:10.1016/s0006-3223(00)01111-2 (Pubitemid 32178434)
59. Echeverria V, Zeitlin R, Burgess S et al (2011) Cotinine reduces amyloid-β aggregation and improves memory in Alzheimer's disease mice. J Alzheimers Dis 24:817-835. doi:10.3233.JAD-2011-102136
60. Ono K, Hamaguchi T, Naiki H, Yamada M (2006) Anti amyloidogenic effects of antioxidants: implications for the prevention and therapeutics of Alzheimer's disease. Biochim Biophys Acta 1762:575-586. doi:10.1016/j.bbadis.2006.03.002 (Pubitemid 43903118)
61. Convertino M, Pellarin R, Catto M, Carotti A, Caflisch A (2009) 9, 10-anthraquinone hinders β-aggregation: how does small molecule interact interfere with Aβ-peptide amyloid formation. Protein Sci 18:792-800. doi:10.1002/pro.87
62. Gaigeot MP, Sprik M (2004) Ab initio molecular dynamics study of uracil in aqueous solution. J Phys Chem B 108:7458-7467. doi:10.1021/jp049940m
63. Ono K, Yoshiike Y, Takashima A, Hasegawa K, Naik H, Yamada M (2003) Potent anti-amyloidogenic and fibril-destabilizing effects of polyphenols in vitro. Implications for the prevention and therapeutics of Alzheimer's disease. J Neurochem 87:172-181. doi:10.10461j.1471-4159.2003.01976.x
64. Ramachandran GN, Sasikharan V (1968) Adv Protein Chem 23:283-437