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Transient pockets on XIAP-BIR2: toward the characterization of putative binding sites of small-molecule XIAP inhibitors

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Abstract

Protein-protein interactions are abundant in signal transduction pathways and thus of crucial importance in the regulation of apoptosis. However, designing small-molecule inhibitors for these potential drug targets is very challenging as such proteins often lack well-defined binding pockets. An example for such an interaction is the binding of the anti-apoptotic BIR2 domain of XIAP to the pro-apoptotic caspase-3 that results in the survival of damaged cells. Although small-molecule inhibitors of this interaction have been identified, their exact binding sites on XIAP are not known as its crystal structures reveal no suitable pockets. Here, we apply our previously developed protocol for identifying transient binding pockets to XIAP-BIR2. Transient pockets were identified in snapshots taken during four different molecular dynamics simulations that started from the caspase-3:BIR2 complex or from the unbound BIR2 structure and used water or methanol as solvent. Clustering of these pockets revealed that surprisingly many pockets opened in the flexible linker region that is involved in caspase-3 binding. We docked three known inhibitors into these transient pockets and so determined five putative binding sites. In addition, by docking two inactive compounds of the same series, we show that this protocol is also able to distinguish between binders and nonbinders which was not possible when docking to the crystal structures. These findings represent a first step toward the understanding of the binding of small-molecule XIAP-BIR2 inhibitors on a molecular level and further highlight the importance of considering protein flexibility when designing small-molecule protein-protein interaction inhibitors.

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Acknowledgments

We thank Jan Fuhrmann and Dirk Neumann (Center for Bioinformatics, Saarland University) for making available their BALLPass implementation to us.

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  1. Susanne Eyrisch

    Present address: Priaxon AG, Gmunder Str. 37-37a, 81379, München, Germany

Authors and Affiliations

  1. Center for Bioinformatics, Building E2 1, P.O. Box 151150, 66041, Saarbruecken, Germany

    Susanne Eyrisch & Volkhard Helms

  2. Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port St. Lucie, FL, 34987, USA

    Jose L. Medina-Franco

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  1. Susanne Eyrisch
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Correspondence to Volkhard Helms.

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Eyrisch, S., Medina-Franco, J.L. & Helms, V. Transient pockets on XIAP-BIR2: toward the characterization of putative binding sites of small-molecule XIAP inhibitors. J Mol Model 18, 2031–2042 (2012). https://doi.org/10.1007/s00894-011-1217-y

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