Computational study on the inhibition mechanism of cyclodextran against GTF-SI from Streptococcus mutans focusing on the glucan-binding domain

Abstract

Glucosyltransferases (GTFs) from Streptococcus mutans (S. mutans) are enzymes that synthesize glucan, a polymer that forms a biofilm causing dental caries. Cyclodextran (CI), which contains a ring structure formed from D-glucose by α-1,6 glycoside linkage, has been reported to strongly inhibit GTFs. In contrast, cyclodextrin, formed by α-1,4 glycoside linkage, has almost no inhibitory activity. In this study, we examined the inhibition mechanism of CI through computational chemistry, focusing on the glucan-binding domain of GTF-SI, which is one of GTFs produced by S. mutans. Analysis using molecular dynamics simulation and fragment molecular orbital method demonstrated a clear difference in the molecular interaction mechanism between α-1,6- and α-1,4-linked oligosaccharides. The calculated affinity of α-1,6-linked oligosaccharides was higher than that of α-1,4-linked oligosaccharides. Additionally, geometry optimization based on density functional theory revealed that three amino acids—Q1282, K1284, and S1302—play an essential role in the binding with α-1,6-linked oligosaccharides. These results successfully explain the inhibition mechanism of CI.

Keywords

• Cyclodextran
• Cyclodextrin
• Glucosyltransferases
• Streptococcus mutans
• Molecular dynamics simulation
• Density functional theory