Quantitative structure–activity relationship analysis of β-amyloid aggregation inhibitors
10.1007/s10822-010-9405-x
Crossref journal-article
Springer Science and Business Media LLC
Journal of Computer-Aided Molecular Design (297)
Bibliography

Stempler, S., Levy-Sakin, M., Frydman-Marom, A., Amir, Y., Scherzer-Attali, R., Buzhansky, L., Gazit, E., & Senderowitz, H. (2010). Quantitative structure–activity relationship analysis of β-amyloid aggregation inhibitors. Journal of Computer-Aided Molecular Design, 25(2), 135–144.

Authors 8
  1. Shiri Stempler (first)
  2. Michal Levy-Sakin (additional)
  3. Anat Frydman-Marom (additional)
  4. Yaniv Amir (additional)
  5. Roni Scherzer-Attali (additional)
  6. Ludmila Buzhansky (additional)
  7. Ehud Gazit (additional)
  8. Hanoch Senderowitz (additional)
References 47 Referenced 6
  1. Cohen AS, Calkins E (1959) Electron microscopic observation on a fibrous component in amyloid of diverse origins. Nature 183:1202 (10.1038/1831202a0) / Nature by AS Cohen (1959)
  2. Sunde M, Blake CCF (1998) From the globular to the fibrous state: protein structure and structural conversion in amyloid formation. Q Rev Biophys 31:1–39 (10.1017/S0033583598003400) / Q Rev Biophys by M Sunde (1998)
  3. Gazit E (2002) Mechanistic studies of the process of amyloid fibrils formation by the use of peptide fragments and analogues: implications of the design of fibrilization inhibitors. Curr Med Chem 9:1725–1735 (10.2174/0929867023369187) / Curr Med Chem by E Gazit (2002)
  4. Gandy S (2005) The role of cerebral amyloid β accumulation in common forms of Alzheimer disease. J Clin Invest 115:1121–1129 / J Clin Invest by S Gandy (2005)
  5. Mann D (1989) Cerebral amyloidosis aging and Alzheimer`s disease; a contribution from studies on Down`s syndrome. Neurobiol Aging 10:397–399 (10.1016/0197-4580(89)90073-0) / Neurobiol Aging by D Mann (1989)
  6. Price D, Tanzi R, Borchelt D, Sisodia S (1998) Alzheimer’s disease: genetic studies and transgenic models. Annu Rev Genet 32:461–493 (10.1146/annurev.genet.32.1.461) / Annu Rev Genet by D Price (1998)
  7. Van Leuven F (2000) Single and multiple transgenic mice as models for Alzheimer’s disease. Prog Neurobiol 61:305–312 (10.1016/S0301-0082(99)00055-6) / Prog Neurobiol by F Leuven Van (2000)
  8. Pike CJ, Burdick D, Walencewicz AJ, Glabe CG, Cotman CW (1993) Neurodegeneration induced by beta-amyloid peptides in vitro: the role of peptide assembly state. J Neurosci 13:1676–1687 (10.1523/JNEUROSCI.13-04-01676.1993) / J Neurosci by CJ Pike (1993)
  9. Grace EA, Rabiner CA, Busciglio J (2002) Characterization of neuronal dystrophy induced by fibrilar amyloid beta: implications for Alzheimer’s disease. J Neurosci 114:265–273 (10.1016/S0306-4522(02)00241-5) / J Neurosci by EA Grace (2002)
  10. Walsh DM, Townsend M, Podlisny MB, Shankar GM, Fadeeva JV, El Agnaf O, Hartley DM, Selkoe DJ (2005) Certain inhibitors of synthetic amyloid-β peptide (Aβ) fibrillogenesis block oligomerization of natural Aβ and thereby rescue long-term potentiation. J Neurosci 25:2455–2462 (10.1523/JNEUROSCI.4391-04.2005) / J Neurosci by DM Walsh (2005)
  11. Ono K, Condron MM, Teplow DB (2009) Structure-neurotoxicity relationships of amyloid {beta}-protein oligomers. Proc Natl Acad Sci USA 106:14745–14750 (10.1073/pnas.0905127106) / Proc Natl Acad Sci USA by K Ono (2009)
  12. Lesne S, Koh MT, Kotilinek L, Kayed R, Glabe CG, Yang A, Gallagher M, Ashe KH (2006) A specific amyloid beta protein assembly in the brain impairs memory. Nature 16:352–357 (10.1038/nature04533) / Nature by S Lesne (2006)
  13. Van Marum RJ (2008) Current and future therapy in Alzheimer’s disease. Fundam Clin Pharmacol 22:265–274 (10.1111/j.1472-8206.2008.00578.x) / Fundam Clin Pharmacol by RJ Marum Van (2008)
  14. Soto C (1999) Plaque busters: strategies to inhibit amyloid formation in Alzheimer’s disease. Mol Med Today 5:343–350 (10.1016/S1357-4310(99)01508-7) / Mol Med Today by C Soto (1999)
  15. Rafii MS, Aisen PS (2009) Recent developments in Alzheimer’s disease therapeutics. BMC Med 7:7 (10.1186/1741-7015-7-7) / BMC Med by MS Rafii (2009)
  16. Gilead S, Gazit E (2004) Inhibition of amyloid fibril formation by peptide analogues modified with alpha-aminoisobutyric acid. Angew Chem Int Ed Engl 43:4041–4044 (10.1002/anie.200353565) / Angew Chem Int Ed Engl by S Gilead (2004)
  17. Findeis MA (2000) Approaches to discovery and characterization of inhibitors of amyloid β-peptide polymerization. Biochim Biophys Acta 1502:76–84 (10.1016/S0925-4439(00)00034-X) / Biochim Biophys Acta by MA Findeis (2000)
  18. Frydman-Marom A, 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 48:1981–1986 (10.1002/anie.200802123) / Angew Chem Int Ed by A Frydman-Marom (2009)
  19. Ono K, Hasegawa K, Naiki H, Yamada M (2004) Curcumin has potent anti-amyloidogenic effects for Alzheimer’s beta-amyloid fibrils in vitro. J Neurosci Res 75:742–750 (10.1002/jnr.20025) / J Neurosci Res by K Ono (2004)
  20. Riviere C, Richard T, Vitrac X, Merillon JM, Vlls J, Monti JP (2008) New polyphenols active on β-amyloid aggregation. Bioorg Med Chem Lett 18:828–831 (10.1016/j.bmcl.2007.11.028) / Bioorg Med Chem Lett by C Riviere (2008)
  21. Soto C, Sigurdsson EM, Morelli L, Kumar RA, Castano EM, Frangione B (1998) Beta-sheet breaker peptides inhibit fibrillogenesis in a rat brain model of amyloidosis: implications for Alzheimer’s therapy. Nat Med 4:822–826 (10.1038/nm0798-822) / Nat Med by C Soto (1998)
  22. Gazit E (2002) A possible role for π-stacking in self-assembly of amyloid fibrils. FASEB J 16:77–83 (10.1096/fj.01-0442hyp) / FASEB J by E Gazit (2002)
  23. Tjernberg LO, Näslund J, Lindquist F, Iohansson J, Karlström AR, Thyberg J, Terenius L, Nordstedt C (1996) Arrest of beta-amyloid fibril formation by a pentapeptide ligand. J Biol Chem 271:8545–8548 (10.1074/jbc.271.15.8545) / J Biol Chem by LO Tjernberg (1996)
  24. Howlett DR, Perry AE, Godfrey F, Swatton JE, Jennings KH, Spitzfaden C, Wadsworth H, Wood SJ, Markwell RE (1999) Inhibition of fibril formation in β-amyloid peptide by a novel series of benzofurans. Biochem J 340:283–289 (10.1042/0264-6021:3400283) / Biochem J by DR Howlett (1999)
  25. Cohen T, Frydman-Marom A, Rechter M, Gazit E (2006) Inhibition of amyloid fibril formation and cytotoxicity by hydroxyindole derivatives. Biochemistry 45:4727–4735 (10.1021/bi051525c) / Biochemistry by T Cohen (2006)
  26. Gazit E (2002) Mechanistic studies of the process of amyloid fibrils formation by the use of peptide fragments and analogues: implications of the design of fibrilization inhibitors. Curr Med Chem 9:1725–1735 (10.2174/0929867023369187) / Curr Med Chem by E Gazit (2002)
  27. Porat Y, Abramowitz A, Gazit E (2006) Inhibiton of amyloid fibril formation by polyphenols: structural similarity and aromatic interactions as a common inhibiton mechanism. Chem Biol Drug Des 67:7–37 (10.1111/j.1747-0285.2005.00318.x) / Chem Biol Drug Des by Y Porat (2006)
  28. Levy M, Porat Y, Bacharach E, Shalev DE, Gazit E (2008) Phenolsulfonphthalein, but not phenolphthalein, inhibits amyloid fibril formation: implications for the modulation of amyloid self-assembly. Biochemistry 47:5896–5904 (10.1021/bi800043d) / Biochemistry by M Levy (2008)
  29. Simons JL, Caprathea BW, Callahana M, Grahama JM, Kimurab T, Laia Y, LeVine H, Lipinskia IW, Sakkaba AT, Tasakib Y, Walkera LC, Yasunagab T, Yea Y, Zhuanga N, Augelli-Szafran CE (2009) The synthesis and structure–activity relationship of substituted N-phenyl anthranilic acid analogs as amyloid aggregation inhibitors. Bioorg Med Chem Lett 19:654–657 (10.1016/j.bmcl.2008.12.049) / Bioorg Med Chem Lett by JL Simons (2009)
  30. Reinke AA, Gestwicki JE (2007) Structure–activity relationships of amyloid beta-aggregation inhibitors based on curcumin: influence of linker length and flexibility. Chem Biol Drug Des 70:206–215 (10.1111/j.1747-0285.2007.00557.x) / Chem Biol Drug Des by AA Reinke (2007)
  31. Discovery Studio, Accelrys, Inc. http://www.accelrys.com/dstudio/
  32. http://www.cs.waikato.ac.nz/ml/weka
  33. Feller W (1950) An introduction to probability theory and its applications, vol 1. Wiley, New York / An introduction to probability theory and its applications by W Feller (1950)
  34. Xia X, Maliski EG, Gallant P, Rogers D (2004) Classification of kinase inhibitors using a Bayesian Model. J Med Chem 47:4463–4470 (10.1021/jm0303195) / J Med Chem by X Xia (2004)
  35. Quinlan RJ (1993) C4.5: programs for machine learning. Morgan Kaufmann Publishers, San Mateo / C4.5: programs for machine learning by RJ Quinlan (1993)
  36. Fawcett T (2006) An introduction to ROC analysis. Pattern Recognit Lett 27:861–874 (10.1016/j.patrec.2005.10.010) / Pattern Recognit Lett by T Fawcett (2006)
  37. Rucker C, Rucker G, Meringer MY (2007) Randomization and its variants in QSPR/QSAR. J Chem Inf Model 47:2345–2357 (10.1021/ci700157b) / J Chem Inf Model by C Rucker (2007)
  38. Irwin JJ, Shoichet BK (2005) ZINC—A free database of commercially available compounds for virtual screening ( http://zinc.docking.org ). J Chem Inf Model 45:177–182 (10.1021/ci049714+)
  39. Allen FH (2002) The cambridge structural database: a quarter of a million crystal structures and rising. Acta Cryst B 58:380–388 (10.1107/S0108768102003890) / Acta Cryst B by FH Allen (2002)
  40. Akaishi T, Morimotoa T, Shibaoa M, Watanabea S, Sakai-Katob K, Utsunomiya-Tateb N, Abe K (2008) Structural requirements for the flavonoid fisetin in inhibiting fibril formation of amyloid β protein. Neurosci Lett 444:280–285 (10.1016/j.neulet.2008.08.052) / Neurosci Lett by T Akaishi (2008)
  41. Lashuel HA, Hartley DM, Balakhaneh D, Aggarwal A, Teichberg S, Callaway DJ (2002) New class of inhibitors of amyloid-beta fibril formation. Implications for the mechanism of pathogenesis in Alzheimer’s disease. J Biol Chem 277:42881–44290 (10.1074/jbc.M206593200) / J Biol Chem by HA Lashuel (2002)
  42. Dobson CM (1999) Protein misfolding, evolution and disease. Trends Biochem Sci 24:329–332 (10.1016/S0968-0004(99)01445-0) / Trends Biochem Sci by CM Dobson (1999)
  43. Riviere C, Richard T, Quentin L, Krisa S, Merillon JM, Mont JP (2007) Inhibitory activity of stilbenes on Alzheimer’s b-amyloid fibrils in vitro. Bioorg Med Chem 15:1160–1167 (10.1016/j.bmc.2006.09.069) / Bioorg Med Chem by C Riviere (2007)
  44. Hall LH, Mohney B, Kier LB (1991) The electrotopological state: structure information at the atomic level for molecular graphs. J Chem Inf Comput Sci 31:76–82 (10.1021/ci00001a012) / J Chem Inf Comput Sci by LH Hall (1991)
  45. Hall LH, Kier LB (2000) The E-state as the basis for molecular structure space definition and structure similarity. J Chem Inf Comput Sci 40:784–791 (10.1021/ci990140w) / J Chem Inf Comput Sci by LH Hall (2000)
  46. Convertino M, Pellarin R, Catto M, Carotti A, Caflish A (2009) 9, 10-anthraquinone hinders β-aggregation: how does a small molecule interfere with Aβ -peptide amyloid fibrillation? Protein Sci 18:792–800 (10.1002/pro.87) / Protein Sci by M Convertino (2009)
  47. Morshedi D, Rezaei-Ghaleh N, Ebrahim-Habibi A, Ahmadian S, Nemat-Gorgani M (2007) Inhibition of amyloid fibrillation of lysozyme by indole derivatives—possible mechanism of action. FEBS J 274:6415–6425 (10.1111/j.1742-4658.2007.06158.x) / FEBS J by D Morshedi (2007)
Dates
Type When
Created 14 years, 8 months ago (Dec. 16, 2010, 6:06 a.m.)
Deposited 1 year, 4 months ago (April 1, 2024, 10:36 p.m.)
Indexed 1 year, 4 months ago (April 1, 2024, 11:13 p.m.)
Issued 14 years, 8 months ago (Dec. 17, 2010)
Published 14 years, 8 months ago (Dec. 17, 2010)
Published Online 14 years, 8 months ago (Dec. 17, 2010)
Published Print 14 years, 7 months ago (Feb. 1, 2011)
Funders 0

None

@article{Stempler_2010, title={Quantitative structure–activity relationship analysis of β-amyloid aggregation inhibitors}, volume={25}, ISSN={1573-4951}, url={http://dx.doi.org/10.1007/s10822-010-9405-x}, DOI={10.1007/s10822-010-9405-x}, number={2}, journal={Journal of Computer-Aided Molecular Design}, publisher={Springer Science and Business Media LLC}, author={Stempler, Shiri and Levy-Sakin, Michal and Frydman-Marom, Anat and Amir, Yaniv and Scherzer-Attali, Roni and Buzhansky, Ludmila and Gazit, Ehud and Senderowitz, Hanoch}, year={2010}, month=dec, pages={135–144} }