The Impact of Tautomer Forms on Pharmacophore-Based Virtual Screening

• Published in: Journal of chemical information and modeling 2006-11, Vol.46 (6), p.2342-2354
• Main Authors: Oellien, Frank, Cramer, Jörg, Beyer, Carsten, Ihlenfeldt, Wolf-Dietrich, Selzer, Paul M
• Format: Article
• Language: English
• Subjects: Catalysis; CDC2 Protein Kinase - chemistry; Chemistry, Pharmaceutical - methods; Combinatorial Chemistry Techniques; Computer based modeling; Computers; Cyclin-Dependent Kinase 2 - chemistry; Data base management systems; Drug Evaluation; Humans; Hydrogen - chemistry; Ligands; Matrix Metalloproteinase 8 - chemistry; Models, Chemical; Molecular Conformation; Pharmacology; Proteins - chemistry; Silicon; Technology, Pharmaceutical - methods
• ISSN: 1549-9596; 1549-960X
• DOI: 10.1021/ci060109b

In the field of in silico screening, many applications do not automatically consider possible tautomeric states of molecules. However, the detection of new compound candidates might rely on correct structural description, which is important for the perfect fit toward the biologically relevant interactions. In this paper, we present a new exhaustive tautomer enumeration approach implemented by means of the CACTVS software package. The approach contains a set of 21 predefined SMIRKS-based transforms and a powerful transformation engine that is capable of generating most tautomers described comprehensively in the literature or found in databases in the field of medicinal chemistry. User-defined tautomer rules applied to specific structural databases or scientific issues can be implemented easily and used instead of the predefined rules. In addition, we describe the impact of tautomer-enriched databases on pharmacophore screening approaches for human matrix metalloproteinase 8 as an example of a protein-based pharmacophore screening scenario and for human cyclin-dependent kinases as an example of a ligand-based pharmacophore screening approach. In both test cases, as a preprocessing step, we have used our new tautomer enumerator tool for the tautomer enrichment of the screening data sets and have used it as a postprocessing step to remove tautomeric duplicates from the results. We could demonstrate that the tautomer-enriched screening data sets show significant advantages compared to their non-enhanced counterparts. The discrimination between hits and nonhits was significantly better in the case of tautomer-enriched databases. Moreover, it has been proved that tautomer-enhanced databases will lead to a higher number of potential hits.