A role for chemoinformatics in structure-based de novo ligand design

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A. Peter Johnson, Krisztina Boda, Tamas Lengyel, Shane Weaver, and Aniko Vigh. School of Chemistry, University of Leeds, Leeds, LS2 9JT, United Kingdom
The SPROUT program for de novo ligand design benefits from extensive use made of chemical information extracted from a variety of databases and knowledge bases. Databases of x-ray structures such as CSD and the Brookhaven file provide support for the generation of conformations which should be of relatively low energy because they correspond to ones frequently found in these databases. Supplier catalogues, combined with retrosynthetic fragmentation of MDDR provide starting materials for the SynSPROUT variation in which structures are built up by virtual synthesis using common synthetic reactions stored in a reaction knowledge base. An alternative fragmentation of MDDR provides drug like entities which are flood docked to all possible target sites in a protein cavity. Analysis of the estimated binding affinity scores for all poses allows an informed choice of a subset of target sites for further structure generation.
 

Herman Skolnik Award Symposium
2:00 PM-4:20 PM, Tuesday, August 24, 2004 Pennsylvania Convention Center -- 110A&B, Oral

Division of Chemical Information

The 228th ACS National Meeting, in Philadelphia, PA, August 22-26, 2004