Binding Free Energy Calculations for Theophylline/Caffeine to RNA Aptamer

An alchemical free energy method along a thermodynamic pathway was applied to calculate the binding free energy of theophylline (or caffeine) with an RNA aptamer. To keep the ligand at the binding site during the decoupling of the ligand from the surrounding environment, a distant restraining potent...

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Bibliographic Details
Published in:Journal of Computer Chemistry, Japan Japan, 2014, Vol.13(3), pp.193-195
Main Authors: TANIDA, Yoshiaki, MITSUI, Takashi, MATSUURA, Azuma
Format: Article
Language:English
Subjects:
alchemical transformation
binding affinity
free energy
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Summary:An alchemical free energy method along a thermodynamic pathway was applied to calculate the binding free energy of theophylline (or caffeine) with an RNA aptamer. To keep the ligand at the binding site during the decoupling of the ligand from the surrounding environment, a distant restraining potential between the ligand's center of mass and the binding site was used. The calculated”absolute” binding affinities are in good agreement with the experimental values. We show that the alchemical free energy calculation is a powerful tool in the realm of rational computational drug design and lead optimization.
ISSN:1347-1767
1347-3824
DOI:10.2477/jccj.2014-0029