Chemical fragment spaces for de novo design

Chemical fragment spaces are combinations of molecular fragments and connection rules. They offer the possibility to encode an enormously large number of chemical structures in a very compact format. Fragment spaces are useful both in similarity-based (2D) and structure-based (3D) de novo design applications. We present disconnection and filtering rules leading to several thousand unique, medium size fragments when applied to databases of druglike molecules. We evaluate alternative strategies to select subsets of these fragments, with the aim of maximizing the coverage of known druglike chemical space with a strongly reduced set of fragments. For these evaluations, we use the Ftrees fragment space method. We assess a diversity-oriented selection method based on maximum common substructures and a method biased toward high frequency of occurrence of fragments and find that they are complementary to each other.