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Research Article

Use of Electron Density Critical Points as Chemical Function-Based Reduced Representations of Pharmacological Ligands

John Binamé,^† Nathalie Meurice,*^† Laurence Leherte,^† Janice Glasgow,^‡ Suzanne Fortier,^§ and Daniel P. Vercauteren^†

Laboratoire de Physico-Chimie Informatique, Facults Universitaires Notre-Dame de la Paix, 61 Rue de Bruxelles, B-5000 Namur, Belgium, and School of Computing and Department of Chemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada

J. Chem. Inf. Comput. Sci., 2004, 44 (4), pp 1394–1401

DOI: 10.1021/ci034157x

Publication Date (Web): June 23, 2004

†

Facultés Universitaires Notre-Dame de la Paix.

Corresponding author phone: 32 81 72 45 58; fax: 32 81 72 45 30; e-mail: nathalie.meurice@fundp.ac.be. F.N.R.S. Scientific Research Worker.

‡

School of Computing, Queen's University.

Department of Chemistry, Queen's University.

Abstract

In this paper, we propose a reduced representation of molecules of pharmacological interest based on their chemical functions. The proposed representations of the molecules are obtained by a topological analysis of their electron density maps at medium resolution, leading to graphs of critical points. The distribution of the different types of critical points are compared at various levels of resolution for a training set of 22 molecules in order to define the optimal resolution level leading to the best representation of the various chemical functions. The reduced representations can in the future be used for molecular similarity research and pharmacophore proposals.

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