Protocols for bridging the peptide to nonpeptide gap in topological similarity searches

Similarity searches based on chemical descriptors have proven extremely useful in aiding large-scale drug screening. Typically an investigator starts with a probe, a drug-like molecule with an interesting biological activity, and searches a database to find similar compounds. In some projects, however, the only known actives are peptides, and the investigator needs to identify drug-like actives. 3D similarity methods are able to help in this endeavor but suffer from the necessity of having to specify the active conformation of the probe, something that is not always possible at the beginning of a project. Also, 3D methods are slow and are complicated by the need to generate low-energy conformations. In contrast, topological methods are relatively rapid and do not depend on conformation. However, unmodified topological similarity methods, given a peptide probe, will preferentially select other peptides from a database. In this paper we show some simple protocols that, if used with a standard topological similarity search method, are sufficient to select nonpeptide actives given a peptide probe. We demonstrate these protocols by using 10 peptide-like probes to select appropriate nonpeptide actives from the MDDR database.