Perspective

Recent Progress in Understanding Activity Cliffs and Their Utility in Medicinal Chemistry

Miniperspective

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
J. Med. Chem., 2014, 57 (1), pp 18–28
DOI: 10.1021/jm401120g
Publication Date (Web): August 27, 2013
Copyright © 2013 American Chemical Society
*Phone: 49-228-2699-306. E-mail: bajorath@bit.uni-bonn.de.
Biography

Dagmar Stumpfe studied Biology at the University of Bonn, Germany. In 2006, she joined the Department of Life Science Informatics at the University of Bonn headed by Prof. Jürgen Bajorath for her Ph.D. thesis, where she worked on methods for computer-aided chemical biology with a focus on the exploration of compound selectivity. Since 2009, Dagmar has been working as a postdoctoral fellow in the department, and her current research interests include computational chemical biology and large-scale structure–activity relationship analysis.

Biography

Ye Hu studied Clinical Medicine at the Southeast University, China, from 1999 to 2004. In 2006, she joined the Life Science Informatics Master program at the University of Bonn and obtained her Master degree in 2008. In October 2008, she began her Ph.D. studies in the group of Prof. Jürgen Bajorath focusing on systematic computational analysis of molecular scaffolds of bioactive compounds and associated characteristics. Since July 2011, she has been working as a postdoctoral fellow in the department. Her current research interests include large-scale mining of ligand–target interaction data and structure–activity relationship analysis.

Biography

Dilyana Dimova studied Computer Science at the Saarland University, Germany. In 2010, she joined the Department of Life Science Informatics headed by Prof. Jürgen Bajorath for her Ph.D. studies. She has initially investigated the development of graphical methods for systematic analysis of multitarget structure–activity relationships. Currently, Dilyana is in the third year of her Ph.D. studies and mainly focuses on large-scale exploration of activity cliffs and structure–activity relationships.

Biography

Jürgen Bajorath is Professor and Chair of Life Science Informatics at the University of Bonn. He is also an Affiliate Professor in the Department of Biological Structure at the University of Washington, Seattle. His research interests include drug discovery, computer-aided medicinal chemistry and chemical biology, and chemoinformatics. For further details, please see: http://www.lifescienceinformatics.uni-bonn.de.

Abstract

Abstract Image

The activity cliff concept is of high relevance for medicinal chemistry. Recent studies are discussed that have further refined our understanding of activity cliffs and suggested different ways of exploiting activity cliff information. These include alternative approaches to define and classify activity cliffs in two and three dimensions, data mining investigations to systematically detect all possible activity cliffs, the introduction of computational methods to predict activity cliffs, and studies designed to explore activity cliff progression in medicinal chemistry. The discussion of these studies is complemented with new findings revealing the frequency of activity cliff formation when different molecular representations are used and the distribution of activity cliffs across different targets. Taken together, the results have a number of implications for the practice of medicinal chemistry.

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Article Views: 4,490 Times
Received 24 July 2013
Published online 27 August 2013
Published in print 9 January 2014
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