Development of a quantitative structure activity relations (QSAR) model to guide the design of fluorescent dyes for detecting amyloid fibrils

References

• Agdeppa ED, Kepe V, Liu J, Flores-Torres S, Satyamurthy N, Petric A, Cole GM, Small GW, Huang SC, Barrio JR (2001). Binding characteristics of radiofluorinated 6-dialkylamino-2-napthylethylidene derivatives as PET imaging probes of b-amyloid plaques in Alzheimer's disease. J. Neurosci. 21: 181–185.
   Web of Science ®Google Scholar
• Agdeppa ED, Kepe V, Liu J, Small GW, Huang SC, Satyamurthy N, Petric A, Barrio JR (2003). 2-Dialkylamino- 6-acylmalononitrile substituted naphthalenes (DDNP analogs): novel diagnostic and therapeutic tools in Alzheimer’s disease. Mol. Imag. Biol. 5: 407–417.
   Google Scholar
• Boyd RD, Seward CM (1991). The substituent parameter database: a powerful tool for QSAR analysis. In: QSAR: Rational Approaches to the Design of Bioactive Compounds. Pharmacochemistry Library Series, Elsevier, Amsterdam, vol. 16. pp. 167–170.
   Google Scholar
• Colston J, Horobin RW, Rashid-Doubell F, Pediani J, Johal KK (2003). Why fluorescent probes for endoplasmic reticulum are selective: an experimental and QSAR-modeling study. Biotech. & Histochem. 78: 323–332.
   PubMed Web of Science ®Google Scholar
• Cooper JH (1974). Selective amyloid staining as a function of amyloid composition and structure. Lab. Invest. 31: 232–238.
   PubMed Web of Science ®Google Scholar
• Dewar MS, Zoebish EG, Healy EF (1985). Development and use of quantum mechanical molecular 76. AM1: a new general purpose quantum mechanical molecular model. J. Am. Chem. Soc. 107: 3902–3909.
   Web of Science ®Google Scholar
• Geladi P, Kowalski B (1986). partial least squares regression: a tutorial. Anal. Chim. Acta185: 1–17.
   Web of Science ®Google Scholar
• Givehchi A, Schneider G (2004). Impact of descriptor vector scaling on the classification of drugs and nondrugs with artificial neural networks. J. Mol. Model. 10: 204–211.
   PubMed Web of Science ®Google Scholar
• Hocquet A, Langgard M (1998). An evaluation of the MM+ force field. Molec. Modeling Ann. 4: 94–112.
   Web of Science ®Google Scholar
• Klunk WE, Engler H, Nordberg A, Wang YM, Blomqvist G, Holt DP, Bergstrom M, Savitcheva I, Huang GF, Estrada S, Ausen B, Debnath ML, Barletta J, Price JC, Sandell J, Lopresti BJ, Wall A, Koivisto P, Antoni G, Mathis CA, Langstrom B (2004). Imaging brain amyloid in Alzheimer’s disease with Pittsburgh Compound–B. Ann. Neurol. 55: 306–319.
   PubMed Web of Science ®Google Scholar
• Klunk WE, Wang YM, Mathis CA (2004). Amyloid deposits in transgenic PS1/APP mice do not bind the amyloid PET tracer, PIB, in the same manner as human brain amyloid. Neurobiol. Aging25: 232–233.
   Web of Science ®Google Scholar
• Kung MP, Hou C, Zhuang ZP, Skovronsky D, Kung HF (2004). Binding of two potential imaging agents targeting amyloid plaques in postmortem brain tissues of patients with Alzheimer's disease. Brain Res. 1025: 98–105.
   PubMed Web of Science ®Google Scholar
• Li H, Ung CY, Yap CW, Xue Y, Li ZR, Cao ZW, Chen YZ (2005). Prediction of genotoxicity of chemical compounds by statistical learning methods. Chem. Res. Toxicol. 18: 1071–1080.
   PubMed Web of Science ®Google Scholar
• Palyulin VA, Radchenko EV, Zefirov NS (2000). Molecular field topology analysis method in QSAR studies of organic compounds. J. Chem. Inf. Comp. Sci. 40: 659–667.
   PubMedGoogle Scholar
• Schmidt ML, Schuck T, Sheridan S, Kung MP, Kung H, Zhuang ZP, Bergeron C, Lamarche JS, Skovronsky D, Giasson BI, Trojanowski JQ (2001). The fluorescent Congo red derivative, (trans, trans)-1-bromo-2,5-bis-(3-hydroxycarbonyl-4-hydroxy)styrylbenzene (BSB), labels diverse beta-pleated sheet structures in postmortem human neurodegenerative disease brains. Am. J. Pathol. 159: 937–943.
   PubMed Web of Science ®Google Scholar
• Tetko IV (2002). Neural network studies. 4. Introduction to associative neural networks. J. Chem. Inf. Comput. Sci. 42: 717–728.
   PubMedGoogle Scholar
• Tetko IV, Gasteiger J, Todeschini R, Mauri A, Livingstone D, Ertl P, Palyulin VA, Radchenko EV, Zefirov NS, Makarenko AS, Tanchuk VY, Prokopenko VV (2005). Virtual computational chemistry laboratory-design and description. J. Comput. Aid. Mol. Des. 19: 453–463.
   PubMed Web of Science ®Google Scholar
• Trygg J, Wold S (2002). Orthogonal projections to latent structures. J. Chemomet. 16: 119–128.
   Web of Science ®Google Scholar
• Verhoeff NP, Wilson AA, Takeshita S, Trop L, Hussey D, Singh K, Kung HF, Kung MP, Houle S (2004). In vivo imaging of Alzheimer disease beta-amyloid with [11C]SB-13 PET. Am. J. Geriat. Psych. 12: 584–595.
   PubMed Web of Science ®Google Scholar
• Volkova KD, Kovalska VB, Balanda AO, Losytskyy MY, Golub AG, Vermeij RJ, Subramaniam V, Tolmachev OI, Yarmoluk SM (2008). Specific fluorescent detection of fibrillar α-synuclein using mono- and trimethine cyanine dyes. Bioorg. Med. Chem. 16: 1452–1459.
   PubMed Web of Science ®Google Scholar
• Volkova KD, Kovalska VB, Inshyn DI, Slominskii YL, Tolmachev OI, Yarmoluk SM (2010). Novel fluorescent trimethine cyanine dye 7519 for amyloid fibril inhibition assay. Biotech. & Histochem. 86: 188–191.
   PubMed Web of Science ®Google Scholar
• Voropay ES, Samtsov MP, Kaplevsky KN, Maskevich AA, Stepuro VI, Povarova OI, Kuznetsova IM, Turoverov KK, Fink AL, Uversky VN (2003). Spectral properties of thioflavine T and its complexes with amyloid fibrils. J. Appl. Spectrosc. 70: 868–874.
   Google Scholar
• VCCLAB, Virtual Computational Chemistry Laboratory. http://www.vcclab.org.
   Google Scholar
• Ye L, Morgenstern JL, Gee AD, Hong GZ, Brown J, Lockhart A (2005). Evidence for the presence of three distinct binding sites for the thioflavin T class of Alzheimer’s disease PET imaging agents on beta-amyloid peptide fibrils. J. Biol. Chem. 280: 7677–7684.
   PubMed Web of Science ®Google Scholar