Unique macrocycles in the Taiwan traditional Chinese medicine database.

Abstract

Chemical space coverage within natural product databases is an important criterion for the selection of databases for virtual screening. Chemical space analysis can also provide valuable hints towards chemical substructures that are responsible for medical activity. We therefore developed a protocol for structurally characterizing the chemical space covered in specific natural product databases by comparing it to a "standard" natural product scaffold distribution. In this contribution, we analyzed the structural characteristics of the traditional Chinese medicine database@Taiwan as an example. While we did not find classes of very characteristic small molecule scaffolds, we found that there are a number of specific macrocyclic scaffolds that are highly enriched in the traditional Chinese medicine database@Taiwan and not documented elsewhere. This surprising finding points towards underused regions in chemical space with a big potential for biological impact.