Hierarchical clustering analysis of flexible GBR 12909 dialkyl piperazine and piperidine analogs

Kathleen M. Gilbert, Carol A. Venanzi

Research output: Contribution to journalArticlepeer-review

8 Scopus citations


Pharmacophore modeling of large, drug-like molecules, such as the dopamine reuptake inhibitor GBR 12909, is complicated by their flexibility. A comprehensive hierarchical clustering study of two GBR 12909 analogs was performed to identify representative conformers for input to three-dimensional quantitative structure-activity relationship studies of closely-related analogs. Two data sets of more than 700 conformers each produced by random search conformational analysis of a piperazine and a piperidine GBR 12909 analog were studied. Several clustering studies were carried out based on different feature sets that include the important pharmacophore elements. The distance maps, the plot of the effective number of clusters versus actual number of clusters, and the novel derived clustering statistic, percentage change in the effective number of clusters, were shown to be useful in determining the appropriate clustering level. Six clusters were chosen for each analog, each representing a different region of the torsional angle space that determines the relative orientation of the pharmacophore elements. Conformers of each cluster that are representative of these regions were identified and compared for each analog. This study illustrates the utility of using hierarchical clustering for the classification of conformers of highly flexible molecules in terms of the three-dimensional spatial orientation of key pharmacophore elements.

Original languageEnglish (US)
Pages (from-to)209-225
Number of pages17
JournalJournal of Computer-Aided Molecular Design
Issue number4
StatePublished - Apr 2006

All Science Journal Classification (ASJC) codes

  • Drug Discovery
  • Computer Science Applications
  • Physical and Theoretical Chemistry


  • Clustering
  • Cocaine
  • Conformational analysis
  • Dopamine reuptake inhibitor
  • GBR 12909
  • Hierarchical
  • Molecular mechanics
  • Pharmacophore modeling
  • XCluster


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