Shape-Aware Synthon Search (SASS) for virtual screening of synthon-based chemical spaces

Virtual screening of large-scale chemical libraries has become increasingly useful for identifying high-quality candidates for drug discovery. While it is possible to exhaustively screen chemical spaces that number on the order of billions, indirect combinatorial approaches are needed to efficiently navigate larger, synthon-based virtual spaces. We describe Shape-Aware Synthon Search (SASS), a synthon-based virtual screening method that carries out shape similarity searches in the synthon space instead of the enumerated product space. SASS can replicate results from exhaustive searches in ultra-large, combinatorial spaces with high recall on a variety of query molecules while only scoring a small subspace of possible enumerated products, thereby significantly accelerating large-scale, shape-based virtual screening.