Scaffold hopping using two-dimensional fingerprints: true potential, black magic, or a hopeless endeavor? Guidelines for virtual screening.

The scaffold hopping potential of popular 2D fingerprints has been thoroughly investigated. We have found that these types of fingerprints have at least limited scaffold hopping ability including early enrichment of small numbers of active scaffolds at high database ranks. However, it has not been possible to derive Tanimoto coefficient value ranges for individual fingerprints that are generally preferred for scaffold hopping. For selected fingerprints, similarity threshold values have been identified that yield small database selection sets having a high probability to contain a few active scaffolds. Furthermore, essentially all tested fingerprints have shown the ability to enrich scaffold hops in approximately 1% of a screening database. For the test cases reported herein, selecting 0.5-1% of the screening database yields approximately 25% of the available scaffolds. On the basis of our findings, practical guidelines for virtual screening using different types of 2D fingerprints have been formulated.