Exploring Structural Relationships between Bioactive and Commercial Chemical Space and Developing Target Hypotheses for Compound Acquisition

Analog series were systematically extracted from more than 650 000 bioactive compounds originating from medicinal chemistry and screening sources and more than 3.6 million commercial compounds that were not biologically annotated. Then, analog series-based (ASB) scaffolds were generated. For each scaffold from a bioactive series, a target profile was derived and ASB scaffolds shared by bioactive and commercial compounds were determined. On the basis of our analysis, large segments of commercial chemical space were not yet explored biologically. Shared ASB scaffolds established structural relationships between bioactive and commercial chemical space, and the target profiles of these scaffolds were transferred to commercially available analogs of active compounds. This made it possible to derive target hypotheses for more than 37 000 compounds without biological annotations covering more than 1000 different targets. For many molecules, alternative target assignments were available. Target hypotheses for these compounds should be of interest, for example, for hit expansion, acquisition of compounds to design or further extend focused libraries for drug discovery, or testing of expanded analog series on different targets. They can also be used to search for analogs and complement compound series during target-directed optimization. Therefore, all of the commercial molecules with new target hypotheses as well as key scaffolds identified in our analysis and their target profiles are made freely available.

Assessing Scaffold Diversity of Kinase Inhibitors Using Alternative Scaffold Concepts and Estimating the Scaffold Hopping Potential for Different Kinases

Publicly available kinase inhibitors provide a large source of information for structure-activity relationship analysis and kinase drug design. In this study, publicly available inhibitors of the human kinome were collected and analog series formed by kinase inhibitors systematically identified. Then, alternative scaffold concepts were applied to assess diversity and promiscuity of kinase inhibitors. Over the past two years, the number of publicly available kinase inhibitors with high-confidence activity data more than doubled, but coverage of the human kinome only slightly increased. Approximately 70% of current kinase inhibitors belonged to analog series. However, the detectable degree of promiscuity among these kinase inhibitors remained low. Approximately 76% of all inhibitors were only annotated with a single kinase, compared to ~70% two years ago. For many kinases, the assessment of scaffold diversity among their inhibitors and the distribution of differently defined scaffolds over analog series made it possible to assess scaffold hopping potential. Our analysis revealed that the consideration of conventional compound-based scaffolds most likely leads to an overestimation of scaffold hopping frequency, at least for compounds forming analog series.