Abstract
The role of molecular diversity in the design of combinatorial libraries is discussed with respect to the strategic issues that arise from the sheer numerical scale of combinatorial chemistry and high-throughput screening, and the issues that arise when applying binding site information to the design process. A method for the analysis of binding sites, that can be used to explore the common features and the differences between a set of related binding sites, is presented. The method is applied to the analysis of nucleotide binding sites.
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Floyd, C.D., Lewis, C.N. and Whittaker, M. More leads in the haystack. Chem. Br., 1996, 31–35.
Kubinyi, H. Similarity and dissimilarity: a medicinal chemist’s view. Perspect. Drug Disc. Des. 1998, 9/10/11, 225–252.
Houghten, R.A. Combinatorial Libraries: Finding the needle in the haystack. Current Biology, 1994, 4, 564–567.
Newton C.G. Molecular Diversity in Drug Design. Application to High-speed Synthesis and High-Throughput Screening. In: Molecular Diversity in Drug Design, Ed. Dean P.M. and Lewis R.A., Kluwer, 1999, Ch. 2.
Barnard, J.M., Downs, G.M., Willett, P., Tyrrell, S.M. and Turner, D.B. Rapid diversity analysis in combinatorial libraries using Markush structure techniques. 213th ACS National Meeting, San Francisco, California, April 13, 1997.
Ecker, D.J. and Crooke, S.T. Combinatorial drug discovery: which methods will produce the greatest value? Biotech., 1995, 13, 351–360.
Lajiness, M. Evaluation of the Performance of Dissimilarity Selection Methodology. In QSAR: Rational Approaches to the Design of Bioactive Compounds, Eds Silipo, C. and Vittoria, A., Escom, 1991, pp. 201–204.
Patterson, D.E., Cramer, R.D., Ferguson, A.M., Clark, R.D. and Weinberger, L.E. Neighbourhood Behaviour: A Useful Concept for Validation of Molecular Diversity Descriptors. J. Med. Chem., 1996, 39, 3049–3059.
Gillet, V.J., Willett, P. and Bradshaw, J. Identification of biological activity profiles using substructural analysis and genetic algorithms. J. Chem. Inf. Comput. Sci., 1998, 38, 165–179.
Cramer, R.D., Clark, R.D., Patterson, D.E. and Ferguson, A.M. Bioisosterism as a Molecular Diversity Descriptor: Steric Fields of Single Topomeric Conformers. J. Med. Chem., 1996, 39, 3060–3069.
World Drug Index, Derwent Publications Ltd. 14 Great Queen Street, London, WC2B, UK.
Daylight Chemical Information Systems, Inc., 27401 Los Altos, 370 Mission Viejo, CA 92691 USA.
Farmer, P.S. and Ariëns, E.J. Speculations on the design of non-peptide peptidomimetics. Trends Pharmacol. Sci., 1982, 3, 362–365.
Mason, J.S. and Hermsmeier, M.A. Diversity Assessment. Curr. Opin. Chem. Biol. 1999, 3, 342–349.
Gerber, P.R. and Müller, K. Superimposing Several Sets of Atomic Coordinates. Acta Crystalographr. A, 1987, 43, 426–428.
Ward, J.H. Hierarchical Grouping for Evaluating Clustering Methods. J. Am. Stat. Assoc., 1963, 58, 236–244.
Mojena, R. Hierarchical grouping methods and stopping rules: An evaluation. The Computer Journal, 1977, 20, 359–363.
Sobolev, V., Wade, R. Vriend, G., and Edeman, M. Molecular Docking Using Surface Complementarity. PROTEINS: Structure, Function and Genetics, 1996, 25, 120–129.
Sobolev, V. and Edelman, M. Modeling the Quinone-B Binding Site of Photosystem-I1 Reaction Centre Using Notions of Complementarity and Contact-Surfacebetween Atoms. PROTEINS: Structure, Function and Genetics, 1995, 21, 214–225.
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Smith, J., Dean, P.M., Lewis, R.A. (2002). Issues in Molecular Diversity and the Role of Ligand Binding Sites. In: Dean, P.M., Lewis, R.A. (eds) Molecular Diversity in Drug Design. Springer, Dordrecht. https://doi.org/10.1007/0-306-46873-5_1
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DOI: https://doi.org/10.1007/0-306-46873-5_1
Publisher Name: Springer, Dordrecht
Print ISBN: 978-0-7923-5980-7
Online ISBN: 978-0-306-46873-5
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