Smiles Arbitrary Target Specification - Applications of SMARTS

Applications of SMARTS

The precise and transparent substructural specification that SMARTS allows has been exploited in a number of applications.

Substructural filters defined in SMARTS have been used to identify undesirable compounds when performing strategic pooling of compounds for high-throughput screening. The REOS (rapid elimination of swill) procedure uses SMARTS to filter out reactive, toxic and otherwise undesirable moieties from databases of chemical structures.

RECAP (Retrosynthetic Combinatorial Analysis Procedure) uses SMARTS to define bond types. RECAP is a molecule editor which generates fragments of structures by breaking bonds of defined types and the original link points in these are specified using isotopic labels. Searching databases of biologically active compounds for occurrences of fragments allows privileged structural motifs to be identified. The Molecular Slicer is similar to RECAP and has been used to identify fragments that are commonly found in marketed oral drugs.

The Leatherface program is a general purpose molecule editor which allows automated modification of a number of substructural features of molecules in databases, including protonation state, hydrogen count, formal charge, isotopic weight and bond order. The molecular editing rules used by Leatherface are defined in SMARTS. Leatherface can be used to standardise tautomeric and ionization states and to set and enumerate these in preparation of databases for virtual screening. Leatherface has been used in Matched Molecular Pair Analysis, which enables the effects of structural changes (e.g. substitution of hydrogen with chlorine) to be quantified, over a range of structural types.

ALADDIN is a pharmacophore matching program that uses SMARTS to define recognition points (e.g. neutral hydrogen bond acceptor) of pharmacophores. A key problem in pharmacophore matching is that functional groups that are likely to be ionised at physiological pH are typically registered in their neutral forms in structural databases. The ROCS shape matching program allows atom types to be defined using SMARTS.