Journal Title
Title of Journal: J Mol Model
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Abbravation: Journal of Molecular Modeling
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Publisher
Springer-Verlag
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Authors: Michael Brunsteiner Pavel A Petukhov
Publish Date: 2012/03/20
Volume: 18, Issue: 8, Pages: 3927-3939
Abstract
A systematic investigation of the available crystal structures of HDAC8 and of the influence of different receptor structures and docking protocols is presented The study shows that the open conformation of HDAC8 may be preferred by ligands with flexible surface binding groups as such a conformation allows the ligands to minimize their exposure to solvent upon binding This observation allowed us to rationalize the excellent potency of pyrazolebased inhibitors compared to that of isoxazolebased inhibitorsMultiple receptor scoring Accuracies obtained for test set compounds with different combinations of two receptor structures Each row and column is labeled according to the PDB code of the crystal structure the receptor was based upon In each single column and row three entries represent the different water occupancies A preference for HDAC8 structures with an open binding site is observedThis study was in part funded by the National Cancer Institute/National Institute of Health grant R01 CA131970 and Alzheimer’s Drug Discovery Foundation grant 20101103 We also thank Ajay Jane for providing a free academic version of Surflexdock Molecular modeling was in part conducted using free academic licenses for the UCSF Chimera package from the Resource for Biocomputing Visualization and Informatics at the University of California San Francisco supported by NIH grant P41 RR01081 and OpenEye Scientific Software Santa Fe NM USA
Keywords:
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