Application of multivariate data analysis methods to Comparative Molecular Field Analysis (CoMFA) data: Proton affinities and pKa prediction for nucleic acids components
Tóm tắt
Multivariate data analysis methods (Principal Component Analysis (PCA) and Partial Least Squares (PLS)) are applied to the analysis of the CoMFA (Comparative Molecular Field Analysis) data for several nucleic acids components. The data set includes nitrogenated bases, nucleosides, linear nucleotides, 3′, 5′-cyclic nucleotides and oligonucleotides. PCA is applied to study the structure of the CoMFA data and to detect possible outliers in the data set. PLS is applied to correlate the CoMFA data with either calculated AM1 proton affinities or with experimental pKa values. The possibility of making a prediction of pKa values directly from 3D structures of the monomers for polynucleotides is also shown. The influence of the superposition criteria and of conformational changes along the glycosidic bond on the pKa prediction are studied as well.
Tài liệu tham khảo
Cramer III, R.D., Patterson, D.E. and Bunce, J.D., J. Am. Chem. Soc., 110 (1988) 5959.
Kim, K.H., ACS Symposium Series, 606 (1995) 302.
Kim, K.H. and Martin, Y.C., J. Med. Chem., 34 (1991) 2056.
Martin, Y.C., Wu, J., Curley, J.F. and Kim, K.H., Abstracts of Papers of the ACS, 211 (1996) 149.
Kim, K.H. and Martin, Y.C., J. Org. Chem., 56 (1991) 2723.
Saenger, W. (Ed.) Principles of Nucleic Acid Structure, Springer-Verlag, New York, NY, 1988.
Brown, R.D. and Martin, Y.C., J. Chem. Inf. Comput. Sci., 36 (1996) 572.
Massart, D.L., Vandeginste, B.G.M., Deming, Y., Michotte, L. and Kaufman, L., Chemometrics. A Textbook, Elsevier, Amsterdam, 1988.
Norinder, U. and Jonsson, J., Quant. Struct.-Act. Relat., 13 (1994) 295.
Burger, K. (Ed.) Biocoordination Chemistry, Ellis Horwood Ltd, Chichester, U.K., 1990.
Casassas, E., Gargallo, R., Gimenez, I., Izquierdo-Ridorsa, A. and Tauler, R., Anal. Chim. Acta, 283 (1993) 538.
Tauler, R., Izquierdo-Ridorsa, A., Gargallo, R. and Casassas, E., Chemometr. Intel. Lab. Syst., 27 (1995) 163.
Casassas, E., Gargallo, R., Izquierdo-Ridorsa, A. and Tauler, R., Reactive Polymers, 27 (1995) 1.
Casassas, E., Marques, I. and Tauler, R., Macromolecules, 27 (1994) 1729.
SYBYL 6.3, Tripos Associates, St. Louis, MO.
Visvanadham, V., Reddy, R.M., Bacquet, R.J. and Erion, M.D., J. Comput. Chem., 14 (1993) 1019.
Dewar, M.J.S., Zoebisch, E.G., Healy, E.F. and Stewart, J.J.P., J. Am. Chem. Soc., 107 (1985) 3902.
Frisch, M.J., Trucks, G.W., Schlegel, H.B., Gill, P.M.W., Johnson, B.G., Robb, M.A., Cheeseman, J.R., Keith, T., Petersson, G.A., Montgomery, J.A., Raghavachari, K., Al-Laham, M.A., Zakrzewski, V.G., Ortiz, J.V., Foresman, J.B., Cioslowski, J., Stefanov, B.B., Nanayakkara, A., Challacombe, M., Peng, C.Y., Ayala, P.Y., Chen, W., Wong, M.W., Andres, J. L., Replogle, E.S., Comperts, R., Martin, R.L., Fow, D.J., Binkley, J.S., Defrees, D.J., Baker, J., Stewart, J.P., Head-Gordon, M., Gonzalez, C. and Pople, J.A., Gaussian 94, Gaussian Inc., Pittsburgh, PA, 1995.
Pointet, K., Milliet, A., Hoyau, S. and Renou-Gonnord, F.R., J. Comput. Chem., 18 (1997) 629.
Stull, D.R. and Prophet, H. (Eds) JANAF Thermochemical Tables, Vol. 37, National Reference Data Service, National Bureau of Standards NSRDS-NBS, U.S. Government Printing Office, Washington, DC, 1971.
Geladi, P., J. Chemometr., 2 (1988) 231.
Wold, S., Albano, C., Dunn, W.J., Edlung, U., Esbenson, K., Geladi, P., Hellberg, S., Lindberg, W. and Sjöström, M., In Kowalski, B.R. (Ed.) Chemometrics: Mathematics and Statistics in Chemistry, Reidel, Dordrecht, The Netherlands, 1984, pp. 17–94.
Diaconis, P. and Efron, B., Sci. Am., 116 (1984) 96.
Wold, S., Technometrics, 4 (1978) 397.
Greco, F., Liguori, A., Sindona, G. and Uccella, N., J. Am. Chem. Soc., 112 (1990) 9092.
Hunter, E.P. and Lias, S.G., J. Phys. Chem. Ref. Data, in press.
Hunter, E.P., Lias, S.G., Brown, R.L. and Stein, S.E., In Mallard, W.G. and Linstrom, P.J. (Eds.) NIST Standard Reference Database Number 69, February 1997, National Institute of Standards and Technology, Gaithersburg, MD (http://webbook.nist.gov).
Del Bene, J.E., J. Phys. Chem., 87 (1983) 367.
Forina, M., Drava, G., Boggia, R., Lanteri, S. and Conti, P., Anal. Chim. Acta, 295 (1994) 109.
Kroemer, R.T., Ettmayer, P. and Hecht, P., J. Med. Chem., 38 (1995) 4917.
Kroemer, R.T., Hecht, P., Guessregen, S. and Liedl, K.R., In Kubinyi, H., Folkers, G. and Martin, Y.C. (Eds.) 3D QSAR in Drug Design, Vol. 3: Recent Advances, Kluwer, Dordrecht, The Netherlands, 1998, pp. 41–56.
Wold, S., Johansson, E. and Cocchi, M., In Kubinyi, H. (Ed.) 3D QSAR in Drug Design. Theory,Methods and Applications, ESCOM, Leiden, The Netherlands, 1993.
Casassas, E., Gargallo, R., Gimenez, I., Izquierdo-Ridorsa, A. and Tauler, R., J. Inorg. Biochem., 56 (1994) 187.
Izatt, R.M., Christensen, J.J. and Rytting, J.H., Chem. Rev., 71 (1971) 439.