Strategies for the determination of pharmacophoric 3D database queries

Strategies are described for constructing pharmacophoric 3D database queries, based on a series of active and inactive analogs. The results are highly selective database queries, which are consistent with the generally accepted pharmacophore for a number of systems. The foundation of these strategies is the method of Mayer, Naylor, Motoc and Marshall [J. Comput.-Aided Mol. Design, 1 (1987) 3] for inferring a unique binding geometry for angiotensin-converting enzyme (ACE) inhibitors. The strategies described here generalize their approach to cases where the chemical features responsible for binding are not a priori apparent, and to cases where the binding geometry deduced by that method is not unique. The key new insight, the selectivity principle, is to rank the multiple solutions produced by the method of Mayer et al. by their selectivity, a value that is related to the proportion of a database that is returned as a database hit list. Retrospective analyses are described for D2-antagonists, ACE inhibitors, fibrinogen antagonists, and beta 2-antagonists.