Mapping of dopamine D3 receptor binding site by pharmacological characterization of mutants expressed in CHO cells with the Semliki Forest virus system.

Nine mutants and the wild-type human dopamine D3 receptor were expressed at high levels in BHK and CHO cells using the Semliki Forest virus system and were analysed for receptor binding with several structurally different dopamine D3 ligands. The mutation His349Leu showed a significant decrease in pKi values for raclopride, dopamine and GR218231, but an increase in affinity for GR99841. Thr369Val had an increase in pKi for both GR99841 and 7-OH-DPAT. The receptor modelling based on sequence alignment with bacteriorhodopsin indicated that Thr369 and His349 are located on the inside of the ligand binding pocket and the effect of the mutagenesis was therefore expected. The change in binding affinity for Thr369Val could be due to the location in the transmembrane domain VII close to the aspartate residue in domain III, the postulated counter ion for dopamine.

RECAP--retrosynthetic combinatorial analysis procedure: a powerful new technique for identifying privileged molecular fragments with useful applications in combinatorial chemistry.

The use of combinatorial chemistry for the generation of new lead molecules is now a well established strategy in the drug discovery process. Central to the use of combinatorial chemistry is the design and availability of high quality building blocks which are likely to afford hits from the libraries that they generate. Herein we describe "RECAP" (Retrosynthetic Combinatorial Analysis Procedure), a new computational technique designed to address this building block issue. RECAP electronically fragments molecules based on chemical knowledge. When applied to databases of biologically active molecules this allows the identification of building block fragments rich in biologically recognized elements and privileged motifs and structures. This allows the design of building blocks and the synthesis of libraries rich in biological motifs. Application of RECAP to the Derwent World Drug Index (WDI) and the molecular fragments/ building blocks that this generates are discussed. We also describe a WDI fragment knowledge base which we have built which stores the drug motifs and mention its potential application in structure based drug design programs.

Drug-motif-based diverse monomer selection: method and application in combinatorial chemistry.

This article describes a strategy to explore monomer diversity while incorporating drug motif knowledge into the design and selection of monomers for combinatorial chemistry. The process involves collecting from available electronic databases all those molecules that potentially could be monomers. In this manner we have assembled five DAYLIGHT databases, each containing one of the common functional groups: carboxylic acids, aldehydes, nitriles, primary amines, and secondary amines. The molecules in the databases are then subjected to fingerprint and cluster analysis using the Jarvis-Patrick algorithm and profiles of the compounds are calculated relating to molecular weight, H-bond counts, and rotatable bond flexibility. The cluster information and profiles of the molecules are stored back into the databases for similarity and diversity searches, and for profile prescreening of monomers. To apply drug motif knowledge to a selection an application to an aldehyde set is discussed, in which representatives of each cluster in the aldehyde database are compared with drug molecules in the Standard Derwent File (SDF) in one of three ways to select drug motif-based monomers for purchase or synthesis.

A model of the adrenergic beta-2 receptor and binding sites for agonist and antagonist.

From the known experimental data on adrenergic ligands and beta-2 receptor a model for the ligand binding sites was proposed and built. Agonist and antagonist have overlapping but different binding sites. The model correlates well with the structural information known from a series of adrenergic ligands.