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In Silico Drug Design Using an Evolutionary Algorithm and Compound Database
- Source :
- YAKUGAKU ZASSHI. 136:107-112
- Publication Year :
- 2016
- Publisher :
- Pharmaceutical Society of Japan, 2016.
-
Abstract
- Computational drug design plays an important role in the discovery of new drugs. Recently, we proposed an algorithm for designing new drug-like molecules utilizing the structure of a known active molecule. To design molecules, three types of fragments (ring, linker, and side-chain fragments) were defined as building blocks, and a fragment library was prepared from molecules listed in G protein-coupled receptor (GPCR)-SARfari database. An evolutionary algorithm which executes evolutionary operations, such as crossover, mutation, and selection, was implemented to evolve the molecules. As a case study, some GPCRs were selected for computational experiments in which we tried to design ligands from simple seed fragments using the Tanimoto coefficient as a fitness function. The results showed that the algorithm could be used successfully to design new molecules with structural similarity, scaffold variety, and chemical validity. In addition, a docking study revealed that these designed molecules also exhibited shape complementarity with the binding site of the target protein. Therefore, this is expected to become a powerful tool for designing new drug-like molecules in drug discovery projects.
Details
- ISSN :
- 13475231 and 00316903
- Volume :
- 136
- Database :
- OpenAIRE
- Journal :
- YAKUGAKU ZASSHI
- Accession number :
- edsair.doi...........8a5e57274a88b6dbaa02fae0ff012757