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A Cluster-Based Strategy for Assessing the Overlap between Large Chemical Libraries and Its Application to a Recent Acquisition
 

Summary: A Cluster-Based Strategy for Assessing the Overlap between Large Chemical Libraries
and Its Application to a Recent Acquisition
Michael F. M. Engels,*, Alan C. Gibbs,| Edward P. Jaeger,§ Danny Verbinnen,
Victor S. Lobanov,§ and Dimitris K. Agrafiotis§
Johnson and Johnson Pharmaceutical Research and Development, Division of Janssen Pharmaceutica,
Turnhoutsweg 30, 2340 Beerse, Belgium, Johnson and Johnson Pharmaceutical Research & Development,
L.L.C., 665 Stockton Drive, Exton, Pennsylvania 19341, and Johnson and Johnson Pharmaceutical Research
and Development, L.L.C., 8 Clarke Drive, Cranbury, New Jersey 08512
Received May 29, 2006
We report on the structural comparison of the corporate collections of Johnson & Johnson Pharmaceutical
Research & Development (JNJPRD) and 3-Dimensional Pharmaceuticals (3DP), performed in the context
of the recent acquisition of 3DP by JNJPRD. The main objective of the study was to assess the druglikeness
of the 3DP library and the extent to which it enriched the chemical diversity of the JNJPRD corporate
collection. The two databases, at the time of acquisition, collectively contained more than 1.1 million
compounds with a clearly defined structural description. The analysis was based on a clustering approach
and aimed at providing an intuitive quantitative estimate and visual representation of this enrichment. A
novel hierarchical clustering algorithm called divisive k-means was employed in combination with Kelley's
cluster-level selection method to partition the combined data set into clusters, and the diversity contribution
of each library was evaluated as a function of the relative occupancy of these clusters. Typical 3DP chemotypes
enriching the diversity of the JNJPRD collection were catalogued and visualized using a modified maximum

  

Source: Agrafiotis, Dimitris K. - Molecular Design and Informatics Group, Johnson & Johnson Pharmaceutical Research and Development

 

Collections: Chemistry; Computer Technologies and Information Sciences