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Authors
Fujiwara, Shin-ichi Department of Biological Regulation, Faculty of Medicine, Tottori University Researchers DB KAKEN
Amisaki, Takashi Department of Biological Regulation, Faculty of Medicine, Tottori University Researchers DB KAKEN
Keywords
human serum albumin
molecular dynamics simulation
binding free energy
multiple binding site
warfarin
fatty acid
Abstract
Human serum albumin (HSA) binds with drugs and fatty acids (FAs). This study was initiated to elucidate the relationship between the warfarin binding affinity of HSA and the positions of bound FA molecules. Molecular dynamics simulations of 11 HSA-warfarin-myristate complexes were performed. HSA-warfarin binding free energy was then calculated for each of the complexes by the molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) method. The results indicated that the magnitude of the binding free energy was smaller in HSA-warfarin complexes that had 4 or more myristate molecules than in complexes with no myristate molecules. The unfavorable effect on the HSA-warfarin binding affinity was caused sterically by the binding of a myristate molecule to the FA binding site closest to the warfarin binding site. On the other hand, the magnitude of HSA-warfarin binding free energy was largest when 3 myristate molecules were bound to the high-affinity sites. The strongest HSA-warfarin binding was attributable to favorable entropic contribution related to larger atomic fluctuations of the amino acid residues at the warfarin binding site. In the binding of 2 myristate molecules to the sites with the highest and second-highest affinities, allosteric modulation that enhanced electrostatic interactions between warfarin and some of the amino acid residues around the warfarin binding site was observed. This study clarified the structural and energetic properties of steric/allosteric effects of FAs on the HSA-warfarin binding affinity and illustrated the approach to analyze protein-ligand interactions in situations such that multiple ligands bind to the other sites of the protein.
Publisher
The Pharmaceutical Society of Japan
Content Type
Journal Article
Link
ISSN
00092363
NCID
AA00602100
Journal Title
Chemical & pharmaceutical bulletin
Volume
59
Issue
7
Start Page
860
End Page
867
Published Date
2011-07-01
Publisher-DOI
Text Version
Publisher
Rights
© 2011 The Pharmaceutical Society of Japan
Citation
Shin-ichi Fujiwara, Takashi Amisaki.. Steric and Allosteric Effects of Fatty Acids on the Binding of Warfarin to Human Serum Albumin Revealed by Molecular Dynamics and Free Energy Calculations. Chemical & pharmaceutical bulletin. 2011, 59(7), 860-867
Department
Faculty of Medicine/Graduate School of Medical Sciences/University Hospital
Language
English