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Prospective Identification of Biologically Active Structures by Topomer Shape Similarity Searching

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journal contribution
posted on 03.09.1999, 00:00 by Richard D. Cramer, Michael A. Poss, Mark A. Hermsmeier, Thomas J. Caulfield, Mark C. Kowala, Maria T. Valentine
The principle of bioisosterismsimilarly shaped molecules are more likely to share biological properties than are other moleculeshas long helped to guide drug discovery. An algorithmic implementation of this principle, based on shape comparisons of a single rule-generated “topomer” conformation per molecule, had been found to be the descriptor most consistently predictive of similar biological properties, in retrospective studies, and also to be well-suited for searching large (>1012) “virtual libraries” of potential reaction products. Therefore a prospective trial of this shape similarity searching method was carried out, with synthesis of 425 compounds and testing of them for inhibition of binding of angiotensin II (A-II). The 63 compounds that were identified by shape searching as most similar to any of four query structures included all of the seven compounds found to be highly active, with none of the other 362 structures being highly active (p < 0.001). Additional consistent relations (p < 0.05) were found, among all 425 compounds, between the degree of shape similarity to the nearest query structure and the frequency of various levels of observed activity. Known “SAR” (rules specifying structural features required for A-II antagonism) were also regenerated within the biological data for the 63 shape similar structures.