Scaffold topologies. 1. Exhaustive enumeration up to eight rings.

Mapping the chemical space of small organic molecules is approached from a theoretical graph theory viewpoint, in an effort to begin the systematic exploration of molecular topologies. We present an algorithm for exhaustive generation of scaffold topologies with up to eight rings and an efficient comparison method for graphs within this class. This method uses the return index, a topological invariant derived from the adjacency matrix of the graph. Furthermore, we describe an algorithm that verifies the adequacy of the comparison method. Applications of this method for chemical space exploration in the context of drug discovery are discussed. The key result is a unique characterization of scaffold topologies, which may lead to more efficient ways to query large chemical databases.