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STD NMR spectroscopy and molecular modeling investigation of the binding of N-acetylneuraminic acid derivatives to rhesus rotavirus VP8* core.

Abstract
The VP8* subunit of rotavirus spike protein VP4 contains a sialic acid (Sia)-binding domain important for host cell attachment and infection. In this study, the binding epitope of the N-acetylneuraminic acid (Neu5Ac) derivatives has been characterized by saturation transfer difference (STD) nuclear magnetic resonance (NMR) spectroscopy. From this STD NMR data, it is proposed that the VP8* core recognizes an identical binding epitope in both methyl alpha-D-N-acetylneuraminide (Neu5Acalpha2Me) and the disaccharide methyl S-(alpha-D-N-acetylneuraminosyl)-(2-->6)-6-thio-beta-D-galactopyranoside (Neu5Ac-alpha(2,6)-S-Galbeta1Me). In the VP8*-disaccharide complex, the Neu5Ac moiety contributes to the majority of interaction with the protein, whereas the galactose moiety is solvent-exposed. Molecular dynamics calculations of the VP8*-disaccharide complex indicated that the galactose moiety is unable to adopt a conformation that is in close proximity to the protein surface. STD NMR experiments with methyl 9-O-acetyl-alpha-D-N-acetylneuraminide (Neu5,9Ac(2)alpha2Me) in complex with rhesus rotavirus (RRV) VP8* revealed that both the N-acetamide and 9-O-acetate moieties are in close proximity to the Sia-binding domain, with the N-acetamide's methyl group being saturated to a larger extent, indicating a closer association with the protein. RRV VP8* does not appear to significantly recognize the unsaturated Neu5Ac derivative [2-deoxy-2,3-didehydro-D-N-acetylneuraminic acid (Neu5Ac2en)]. Molecular modeling of the protein-Neu5Ac2en complex indicates that key interactions between the protein and the unsaturated Neu5Ac derivative when compared with Neu5Acalpha2Me would not be sustained. Neu5Acalpha2Me, Neu5Ac-alpha(2,6)-S-Galbeta1Me, Neu5,9Ac(2)alpha2Me, and Neu5Ac2en inhibited rotavirus infection of MA104 cells by 61%, 35%, 30%, and 0%, respectively, at 10 mM concentration. NMR spectroscopic, molecular modeling, and infectivity inhibition results are in excellent agreement and provide valuable information for the design of inhibitors of rotavirus infection.
AuthorsThomas Haselhorst, Helen Blanchard, Martin Frank, Mark J Kraschnefski, Milton J Kiefel, Alex J Szyczew, Jeffery C Dyason, Fiona Fleming, Gavan Holloway, Barbara S Coulson, Mark von Itzstein
JournalGlycobiology (Glycobiology) Vol. 17 Issue 1 Pg. 68-81 (Jan 2007) ISSN: 0959-6658 [Print] England
PMID16973731 (Publication Type: Evaluation Studies, Journal Article, Research Support, Non-U.S. Gov't)
Chemical References
  • Disaccharides
  • RNA-Binding Proteins
  • Sialic Acids
  • Viral Nonstructural Proteins
  • methyl 9-O-acetyl-N-acetylneuraminide
  • methyl N-acetylneuraminide
  • methyl S-(N-acetylneuraminosyl)-(2-6)-6-thiogalactopyranoside
  • NS35 protein, rotavirus
  • 2-deoxy-2,3-dehydro-N-acetylneuraminic acid
  • 9-O-acetyl-N-acetylneuraminic acid
  • N-Acetylneuraminic Acid
Topics
  • Animals
  • Cells, Cultured
  • Cercopithecus aethiops
  • Computer Simulation
  • Disaccharides (chemistry, metabolism, pharmacology)
  • Dose-Response Relationship, Drug
  • Magnetic Resonance Spectroscopy (methods)
  • Models, Biological
  • Models, Molecular
  • Molecular Conformation
  • N-Acetylneuraminic Acid (analogs & derivatives, chemistry, metabolism, pharmacology)
  • Protein Binding
  • RNA-Binding Proteins (chemistry, metabolism)
  • Rotavirus (drug effects)
  • Sialic Acids (chemistry, metabolism, pharmacology)
  • Structure-Activity Relationship
  • Viral Nonstructural Proteins (chemistry, metabolism)

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