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  • Poster presentation
  • Open Access

Compound optimization through data set-dependent chemical transformations

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Journal of Cheminformatics20146 (Suppl 1) :P5

  • Published:


  • Active Compound
  • Specific Target
  • Property Space
  • Chemical Transformation
  • Molecular Property

Matched molecular pairs (MMPs) have previously been used to extract chemical transformations and study their effect on molecular properties such as activity [1, 2]. Chemical transformations have been used to direct compound optimization efforts towards defined activity profiles [3]. Here we introduce a methodology to assess effects of chemical transformations based on MMPs of compounds active against specific targets. The effects of selected chemical transformations on drug design-relevant molecular properties were analyzed. For different data sets, transformations that were frequently found and induced favorable property changes were identified. These transformations were then iteratively applied to modify active compounds and move them into favorable regions of ADME-relevant property space. Activity of newly designed compounds was tracked using nearest-neighbor searches in ChEMBL. The results of our study indicate that activity-conservative data-set dependent transformation can aid in the design of new active compounds with favorable ADME characteristics [4].

Authors’ Affiliations

Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Dahlmannstrasse 2, D-53113 Bonn, Germany


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© de León and Bajorath; licensee Chemistry Central Ltd. 2014

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver ( applies to the data made available in this article, unless otherwise stated.