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Fully Automated Flexible Docking of Ligands into Flexible Synthetic Receptors Using Forward and Inverse Docking Strategies

Andreas Kämper,^† Joannis Apostolakis,*^‡ Matthias Rarey,^§ Christel M. Marian, and Thomas Lengauer^†

Max-Planck-Institut fr Informatik, Stuhlsatzenhausweg 85, D-66123 Saarbrcken, Germany, Institut fr Informatik, Ludwig-Maximilians-Universitt, Amalienstrasse 17, D-80333 Mnchen, Germany, Zentrum fr Bioinformatik Hamburg, Universitt Hamburg, Bundesstrasse 43, D-20146 Hamburg, Germany, and Institut fr Theoretische Chemie und Computerchemie, Heinrich-Heine-Universitt, Geb. 26.32, Universittsstrasse 1, D-40225 Dsseldorf, Germany

J. Chem. Inf. Model., 2006, 46 (2), pp 903–911

DOI: 10.1021/ci050467z

Publication Date (Web): January 31, 2006

†

Max-Planck-Institut für Informatik.

Corresponding author phone: +49-89-2180-4057; fax: +49-89-2180-4054; e-mail: joannis.apostolakis@ifi.lmu.de.

‡

Ludwig-Maximilians-Universität.

Universität Hamburg.

Heinrich-Heine-Universität.

Abstract

The prediction of the structure of host−guest complexes is one of the most challenging problems in supramolecular chemistry. Usual procedures for docking of ligands into receptors do not take full conformational freedom of the host molecule into account. We describe and apply a new docking approach which performs a conformational sampling of the host and then sequentially docks the ligand into all receptor conformers using the incremental construction technique of the FlexX software platform. The applicability of this approach is validated on a set of host−guest complexes with known crystal structure. Moreover, we demonstrate that due to the interchangeability of the roles of host and guest, the docking process can be inverted. In this inverse docking mode, the receptor molecule is docked around its ligand. For all investigated test cases, the predicted structures are in good agreement with the experiment for both normal (forward) and inverse docking. Since the ligand is often smaller than the receptor and, thus, its conformational space is more restricted, the inverse docking approach leads in most cases to considerable speed-up. By having the choice between two alternative docking directions, the application range of the method is significantly extended. Finally, an important result of this study is the suitability of the simple energy function used here for structure prediction of complexes in organic media.

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