No abstract

Rutaecarpine alkaloids have the capacity to inhibit specific 2,3,7,8-[1,6-3H]tetrachlorodibenzo-p-dioxin (TCDD) binding in rat liver cytosol, as analysed by electrofocusing in polyacrylamide gel. The IC50 value for binding of 7,8-dehydrorutaecarpine was estimated to approximately 7 nM indicating a high-affinity interaction, whereas rutaecarpine appeared less active (IC50 approximately 110 nM). These findings are of interest in view of the fact that analogues to these compounds may be formed following UV-irradiation of tryptophan and that such photo-products have been suggested to constitute (the) endogenous ligand(s) for the TCDD receptor. As further support of this notion, the rutaecarpine alkaloids investigated could be fitted into a rectangle of 6.8 x 13.7 A, a characteristic common for most high affinity ligands of the TCDD receptor hitherto studied. In view of their structural similarity to dehydrorutaecarpine and the agreement of their mol. wt with that of the photoproduct with the highest affinity for the TCDD receptor, we suggest deaza-analogues of dehydrorutaecarpine to represent possible candidates for the endogenous TCDD receptor ligand.

In the present study we investigate whether augmentation of pharmacophores with excluded (ligand-inaccessible) volumes can condense the lengthy unspecific hit lists often obtained in 3D-database searching. Our pharmacophores contained hydrophobic features defined by the hormone, hydrogen bond donor and acceptor features of the liganded rat THR-alpha X-ray structure, and excluded volumes located at the positions and scaled according to the sizes of atoms delineating the binding cavity. We now show, for the first time, that it is perfectly feasible with the Catalyst software to search, in 1-2 h, medium-sized databases such as Maybridge (with 5 x 10(5) compounds registered as multiple conformers) with pharmacophores containing numerous (approximately 10(2)) excluded volumes. The excluded volumes did not slow the search significantly; for pharmacophores containing more features they also reduced the size of the hit list the most. For example, with a 7-feature pharmacophore, the Maybridge hit list shrank from 4 to 1. The single remaining compound was subsequently shown to bind to THR-alpha with an IC50 of 69 microM. Thus, we conclude that structure-based pharmacophores augmented with numerous excluded volumes can effectively prune and focus hit lists. The performance of multiple excluded volume-supplemented structure-based pharmacophores in 3D-database mining as implemented with the Catalyst software compares very favorably with other published procedures, with respect to speed, specificity, and ease of use.