Indirect similarity based methods for effective scaffold-hopping in chemical compounds

Methods that can screen large databases to retrieve a structurally diverse set of compounds with desirable bioactivity properties are critical in the drug discovery and development process. This paper presents a set of such methods that are designed to find compounds that are structurally different to a certain query compound while retaining its bioactivity properties (scaffold hops). These methods utilize various indirect ways of measuring the similarity between the query and a compound that take into account additional information beyond their structure-based similarities. The set of techniques that are presented capture these indirect similarities using approaches based on analyzing the similarity network formed by the query and the database compounds. Experimental evaluation shows that most of these methods substantially outperform previously developed approaches both in terms of their ability to identify structurally diverse active compounds as well as active compounds in general.