ErG: 2D pharmacophore descriptions for scaffold hopping

An extended reduced graph approach (ErG) is presented that uses pharmacophore-type node descriptions to encode the relevant molecular properties. The basic idea of the method can be described as a hybrid approach of reduced graphs (Gillet et al. J. Chem. Inf. Comput. Sci. 2003, 43, 338-345) and binding property pairs (Kearsley et al. J. Chem. Inf. Comput. Sci. 1996, 36, 118-127). However, specific extension modifications to correctly describe the pharmacophoric properties, size, and shape of the molecules under study result in a very stable and good performance as compared to DAYLIGHT fingerprints (DFP). This is exemplified for 11 activity classes of the MDL Drug Data Report database, for which ErG performs as well or better than DFP in 10 cases. On the basis of the example data sets, the ability of ErG to switch from one chemotype to another (often referred to as "scaffold hopping") is highlighted. Additionally, possible pitfalls of reduced graph approaches as well as suitable solutions are discussed with the help of example structures. Overall, it is shown that ErG is a widely applicable method capable of identifying structurally diverse actives for a given active search query. This diversity is achieved by a high degree of molecular abstraction, which in turn results in a low dimensional descriptor vector that allows very low computation times for similarity searches.