Abstract
Using searching techniques based on algorithms derived from graph theory, we have established a similarity between a 3-dimensional cluster of side chains implicated in drug binding in influenza sialidase and side chains involved in isocitrate binding in Escherichia coli isocitrate dehydrogenase. The possible implications of the use of such comparative methods in drug design are discussed.
Full Text
The Full Text of this article is available as a PDF (2.0 MB).
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Bernstein F. C., Koetzle T. F., Williams G. J., Meyer E. F., Jr, Brice M. D., Rodgers J. R., Kennard O., Shimanouchi T., Tasumi M. The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol. 1977 May 25;112(3):535–542. doi: 10.1016/s0022-2836(77)80200-3. [DOI] [PubMed] [Google Scholar]
- Chong A. K., Pegg M. S., Taylor N. R., von Itzstein M. Evidence for a sialosyl cation transition-state complex in the reaction of sialidase from influenza virus. Eur J Biochem. 1992 Jul 1;207(1):335–343. doi: 10.1111/j.1432-1033.1992.tb17055.x. [DOI] [PubMed] [Google Scholar]
- Goodford P. J. A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. J Med Chem. 1985 Jul;28(7):849–857. doi: 10.1021/jm00145a002. [DOI] [PubMed] [Google Scholar]
- Grindley H. M., Artymiuk P. J., Rice D. W., Willett P. Identification of tertiary structure resemblance in proteins using a maximal common subgraph isomorphism algorithm. J Mol Biol. 1993 Feb 5;229(3):707–721. doi: 10.1006/jmbi.1993.1074. [DOI] [PubMed] [Google Scholar]
- Mitchell E. M., Artymiuk P. J., Rice D. W., Willett P. Use of techniques derived from graph theory to compare secondary structure motifs in proteins. J Mol Biol. 1990 Mar 5;212(1):151–166. doi: 10.1016/0022-2836(90)90312-A. [DOI] [PubMed] [Google Scholar]
- Taylor G. Drug design. A rational attack on influenza. Nature. 1993 Jun 3;363(6428):401–402. doi: 10.1038/363401a0. [DOI] [PubMed] [Google Scholar]
- Varghese J. N., McKimm-Breschkin J. L., Caldwell J. B., Kortt A. A., Colman P. M. The structure of the complex between influenza virus neuraminidase and sialic acid, the viral receptor. Proteins. 1992 Nov;14(3):327–332. doi: 10.1002/prot.340140302. [DOI] [PubMed] [Google Scholar]
- von Itzstein M., Wu W. Y., Kok G. B., Pegg M. S., Dyason J. C., Jin B., Van Phan T., Smythe M. L., White H. F., Oliver S. W. Rational design of potent sialidase-based inhibitors of influenza virus replication. Nature. 1993 Jun 3;363(6428):418–423. doi: 10.1038/363418a0. [DOI] [PubMed] [Google Scholar]