Lead hopping. Validation of topomer similarity as a superior predictor of similar biological activities

Two extensive studies quantifying the ability of topomer shape similarity to forecast a variety of biological similarities are described. In a prospective trial of "lead hopping", using topomer similarity for virtual screening and queries from the patent literature, biological assays of 308 selected compounds (representing 0.03% of those available, per assay type) yielded 11 successful "lead hops" in the 13 assays attempted. The hit rate averaged over all assays was 39% ("activity" defined as inhibition greater than or equal to 20% at 10 muM), significantly greater than an unexpectedly high negative control hit rate of 15%. The average "Tanimoto 2D fingerprint similarity" between query and "lead hop" structures (0.36) was little more than the Tanimoto similarity between random drug-like structures. Topomer shape and Tammoto 2D fingerprint similarities were also compared retrospectively, in their tendencies to concentrate together potential and actual drugs reported to belong to the same "activity class", for twenty classes. Among the most similar 3% of structures (corresponding to "greater than or equal to 0.85 Tanimoto" for these structures), an average of 62% of the topomer similar selection possessed a near neighbor belonging to the same activity class, roughly a one-third superiority over the "Tanimoto greater than or equal to 0.85" selection containing 48% actives in avoiding false positives. Conversely, the least similar 75% of structures contained 0.3% actives for topomer similarity vs 1.0% actives for Tanimoto 2D fingerprint similarity, a 3-fold superiority for topomers in avoiding false negatives.