Combination of Pharmacophore Matching, 2D Similarity Search, and in Vitro Biological Assays in the Selection of Potential 5-HT6 Antagonists from Large Commercial Repositories

Krisztina Dobi, Beáta Flachner, Mária Pukáncsik, Eniko Máthé, Melinda Bognár, Mária Szaszkõ, Csaba Magyar, István Hajdú, Zsolt Lorincz, István Simon, Ferenc Fülöp, Sándor Cseh, György Dormán

Research output: Contribution to journalArticle

5 Citations (Scopus)


Rapid in silico selection of target-focused libraries from commercial repositories is an attractive and cost-effective approach. If structures of active compounds are available, rapid 2D similarity search can be performed on multimillion compound databases, but the generated library requires further focusing. We report here a combination of the 2D approach with pharmacophore matching which was used for selecting 5-HT6 antagonists. In the first screening round, 12 compounds showed >85% antagonist efficacy of the 91 screened. For the second-round (hit validation) screening phase, pharmacophore models were built, applied, and compared with the routine 2D similarity search. Three pharmacophore models were created based on the structure of the reference compounds and the first-round hit compounds. The pharmacophore search resulted in a high hit rate (40%) and led to novel chemotypes, while 2D similarity search had slightly better hit rate (51%), but lacking the novelty. To demonstrate the power of the virtual screening cascade, ligand efficiency indices were also calculated and their steady improvement was confirmed.

Original languageEnglish
Pages (from-to)864-880
Number of pages17
JournalChemical Biology and Drug Design
Issue number4
Publication statusPublished - Oct 1 2015


  • G-Protein coupled receptor
  • biological screening
  • combinatorial chemistry
  • drug discovery
  • virtual screening

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Medicine
  • Pharmacology
  • Drug Discovery
  • Organic Chemistry

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