bbc 2015
BBC2015_booklet
BBC2015_booklet
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BeNeLux Bioinformatics Conference – Antwerp, December 7-8 <strong>2015</strong><br />
Abstract ID: P<br />
Category: Poster<br />
10th Benelux Bioinformatics Conference <strong>bbc</strong> <strong>2015</strong><br />
P25. IDENTIFICATION OF NOVEL ALLOSTERIC DRUG TARGETS<br />
USING A “DUMMY” LIGAND APPROACH<br />
Susanne M.A. Hermans, Christopher Pfleger & Holger Gohlke * .<br />
Department of Mathematics and Natural Sciences, Institute for Pharmaceutical and Medicinal Chemistry, Heinrich-<br />
Heine-University, Düsseldorf, Germany. * gohlke@uni-duesseldorf.de<br />
Targeting allosteric sites is a promising strategy in drug discovery due to their regulatory role in almost all cellular<br />
processes. Currently, there is no standard method to identify novel pockets and to detect whether a pocket has a<br />
regulatory effect on the protein. Here, we present a new and efficient approach to probe information transfer through<br />
proteins in the context of dynamically dominated allostery that exploits “dummy” ligands as surrogates for allosteric<br />
modulators.<br />
INTRODUCTION<br />
Allosteric regulation is the coupling between separated<br />
sites in biomacromolecules such that an action at one site<br />
changes the function at a distant site. Allosteric drugs are<br />
popular, they often have less side effects then orthosteric<br />
drugs because the allosteric sites are less conserved. The<br />
identification of novel allosteric pockets is complicated by<br />
the large variation in allosteric regulation, ranging from<br />
rigid body motions to disorder/order transitions, with<br />
dynamically dominated allostery in between (Motlagh et<br />
al., 2014). Here we focus on dynamically dominated<br />
allostery with minimal or no conformational changes.<br />
Novel pockets do not have a known ligand, therefore we<br />
generate “dummy” ligands to function as surrogates for<br />
allosteric ligands. We have developed an efficient<br />
approach to probe information transfer through proteins<br />
using “dummy” ligands and detect if allosteric coupling is<br />
present between the novel pocket and the orthosteric site.<br />
METHODS<br />
In a preliminary study to test the general feasibility, the<br />
approach was applied to conformations extracted from a<br />
MD trajectory of the holo and apo structures of LFA1.<br />
The grid-based PocketAnalyzer program (Craig et al.,<br />
2011) is used to detect putative binding sites. “Dummy”<br />
ligands were generated for each detected pocket along the<br />
ensemble. Finally, the Constraint Network Analysis<br />
(CNA) software, which links biomacromolecular structure,<br />
(thermo-)stability, and function, is used to probe the<br />
allosteric response by monitoring altered stability<br />
characteristics of the protein due to the presence of the<br />
“dummy” ligand (Pfleger et al., 2013; Krüger et al., 2013;<br />
Pfleger, 2014). The results were compared to those of the<br />
holo structure with the bound allosteric ligand to validate<br />
the “dummy” ligand approach.<br />
RESULTS & DISCUSSION<br />
Remarkably, the usage of “dummy” ligands almost<br />
perfectly reproduced the results obtained from the known<br />
allosteric effector. Although it turned out that the intrinsic<br />
rigidity of the “dummy” ligands over-stabilizes the LFA1<br />
structure, these results are already encouraging. Even for<br />
the LFA1 apo structures, where the allosteric pocket is<br />
partially closed, the results are in agreement with known<br />
allosteric effectors. Overall, the results obtained from the<br />
validation of the “dummy” ligand approach are<br />
encouraging. This suggests that our “dummy” ligand<br />
approach for the characterization of unexplored allosteric<br />
pockets is a promising step towards identifying novel drug<br />
targets.<br />
REFERENCES<br />
Craig, I.R. et al. J. Chem. Inf. Model. 51 2666–2679 (2011).<br />
Krüger, D. M. et al. Nucleic Acids Res. 41 340–348 (2013).<br />
Motlagh, H.N. et al. Nature 508 7496 331–339 (2014).<br />
Pfleger, C. et al. J. Chem. Inf. Model. 53 1007–1015 (2013).<br />
Pfleger, C. Doctoral Thesis, Heinrich Heine University, Düsseldorf,<br />
Germany (2014).<br />
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