Volume 3 Supplement 1
Rapid binding site analysis by means of structural interaction fingerprint patterns – an implication to GPCR-targeted CADD
© Kosciolek et al; licensee BioMed Central Ltd. 2011
Published: 19 April 2011
One of the most troublesome stages of Computer Aided Drug Design (CADD) process is analyzing huge amount of data provided by docking studies. Simple scoring functions alone can provide only shallow information about ligand-receptor interactions, since they do not distinguish neither residues nor single atoms. Very often a visual inspection is the only way to determine a binding mode. Here, we introduce an implementation of interaction profiles  based on Structural Interaction Fingerprints (SIFt) , which allow precise and rapid binding site description.
SIFts employed in our modelling agenda form a nine-digit binary pattern for each amino-acid in the receptor, covering all major types of interactions.
Computed over an ensemble of ligands and/or receptor conformations, averaged real number SIFt elegantly depicts overall preferences towards particular interactions. This enables construction of a compact scheme of crucial forces involved in ligand-receptor complex formation, which then facilitate design of a binding mode hypothesis and description of preferred ligand positions within the active site. An application is presented basing on a model of an allosteric domain of mGluR4 receptor  – a challenging computational task, due to untrivial evolutionary relationships for homology model construction purposes, and shortage of experimental data for hypotheses validation.
This study is supported by project UDA-POIG.01.03.010-12-100/08-00 co-financed by European Union from the European Fund of Regional Development (EFRD).
- Chuaqui C, Deng Z, Singh J: Interaction profiles of protein kinase-inhibitor complexes and their application to virtual screening. J Med Chem. 2005, 48: 121-133. 10.1021/jm049312t.View ArticleGoogle Scholar
- Deng Z, Chuaqui C, Singh J: Structural interaction fingerprint (SIFt): a novel method for analyzing three-dimensional protein-ligand binding interactions. J Med Chem. 2004, 47: 337-344. 10.1021/jm030331x.View ArticleGoogle Scholar
- Ngomba RT, Ferraguti F, Badura A, Citraro R, Santolini I, Battaglia G, Bruno V, De Sarro G, Simonyi A, van Luijtelaar G, Nicoletti F: Positive allosteric modulation of metabotropic glutamate 4 (mGlu4) receptors enhances spontaneous and evoked absence seizures. Neuropharmacology. 2008, 54: 344-354. 10.1016/j.neuropharm.2007.10.004.View ArticleGoogle Scholar
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 (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.