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http://dx.doi.org/10.5012/bkcs.2013.34.2.545

Importance of Accurate Charges in Binding Affinity Calculations: A Case of Neuraminidase Series  

Park, Kichul (Department of Bioinformatics, Korea University)
Sung, Nack Kyun (Department of Bioinformatics, Korea University)
Cho, Art E. (Department of Bioinformatics, Korea University)
Publication Information
Bulletin of the Korean Chemical Society / v.34, no.2, 2013 , pp. 545-548 More about this Journal
Abstract
It has been shown that calculating atomic charges using quantum mechanical level theory greatly improves the accuracy of docking. A protocol was developed and shown to be effective. That this protocol works is just a manifestation of the fact that electrostatic interactions are important in protein-ligand binding. In order to investigate how the same protocol helps in prediction of binding affinities, we took a series of known cocrystal structures of influenza neuraminidase inhibitors with the receptor and performed docking with Glide SP, Glide XP, and QPLD, the last being a workflow that incorporates QM/MM calculations to replace the fixed atomic charges of force fields with quantum mechanically recalculated ones at a given docking pose, and predicted the binding affinities of each cocrystal. The correlation with experimental binding affinities considerably improved with QPLD compared to Glide SP/XP yielding $r^2$ = 0.83. The results suggest that for binding sites, such as that of neuraminidase, which are laden with hydrophilic residues, protocols such as QPLD which utilizes QM-based atomic charges can better predict the binding affinities.
Keywords
Docking; Binding affinity; QPLD; Glide; Neuraminidase;
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