Visualisation and subsets of the chemical universe database GDB-13 for virtual screening

摘要

The chemical universe database GDB-13, which enumerates 977 million organic molecules up to 13 atoms of C, N, O, S and Cl following simple chemical stability and synthetic feasibility rules, represents a vast reservoir for new fragments. GDB-13 was classified using the MQN-system discussed in the preceding paper for the analysis of PubChem fragments. Two hundred and fiftyfive subsets of GDB-13 were generated by the combinatorial use of eight restrictive criteria, including fragmentlike (‘‘rule of three’’) and scaffold-like (no acyclic carbon atoms) filters. Virtual screening for analogs of 15 commercial drugs of 13 non-hydrogen atoms or less shows that retrieving MQN-neighbors of a query molecule from GDB- 13 or its subsets provides on average a 38-fold enrichment in structural analogs (Daylight-type substructure fingerprint Tanimoto TSF> 0.7), and a 75-fold enrichment in shapesimilar analogs (ROCS TanimotoCombo score > 1.4). An MQN-searchable version of GDB-13 is provided at www.gdb.unibe.ch.