Inhibition of Histo-blood Group Antigen Binding as a Novel Strategy to Block Norovirus Infections

<div><p>Noroviruses (NoVs) are the most important viral pathogens that cause epidemic acute gastroenteritis. NoVs recognize human histo-blood group antigens (HBGAs) as receptors or attachment factors. The elucidation of crystal structures of the HBGA-binding interfaces of a number of human NoVs representing different HBGA binding patterns opens a new strategy for the development of antiviral compounds against NoVs through rational drug design and computer-aided virtual screening methods. In this study, docking simulations and virtual screening were used to identify hit compounds targeting the A and B antigens binding sites on the surface of the capsid P protein of a GII.4 NoV (VA387). Following validation by re-docking of the A and B ligands, these structural models and AutoDock suite of programs were used to screen a large drug-like compound library (derived from ZINC library) for inhibitors blocking GII.4 binding to HBGAs. After screening >2 million compounds using multistage protocol, 160 hit compounds with best predicted binding affinities and representing a number of distinct chemical classes have been selected for subsequent experimental validation. Twenty of the 160 compounds were found to be able to block the VA387 P dimers binding to the A and/or B HBGAs at an IC₅₀<40.0 µM, with top 5 compounds blocking the HBGA binding at an IC₅₀<10.0 µM in both oligosaccharide- and saliva-based blocking assays. Interestingly, 4 of the top-5 compounds shared the basic structure of cyclopenta [a] dimethyl phenanthren, indicating a promising structural template for further improvement by rational design.</p></div

The basic features of the 20 most inhibitory lead-like compounds.

a<p>determined by docking;</p>b<p>determined by blocking assays; the data were indicated by mean ± standard deviation.</p

Parameters used for docking simulation.

<p>Parameters used for docking simulation.</p

Distribution of the lowest Ki values of the top 255 compounds docked at the HBGA binding sites of the VA387 P dimer.

<p>Distribution of the lowest Ki values of the top 255 compounds docked at the HBGA binding sites of the VA387 P dimer.</p

Predicted docking poses for the A trisaccharides docked to the VA387 P dimer clusters at the proved HBGA binding site.

<p>The majority of the predicted poses (each represented by a magenta ball) docked to the experimentally resolved HBGA binding site that was formed by Ser343, Arg345, His347, Asp374, Gln376, Ser441 and Gly442 (circled by a yellow dashed line). Some of the poses docked to a nearby site that was previously suggested as an alternative binding site for HBGA (Tan et al., 2003). The structure of the P dimer of VA387 (2OBS) is shown using ribbon model, each monomer in green and blue, respectively. The amino acids that constitute the experimentally mapped HBGA binding site were shown using stick model and circled by a yellow dashed line, while amino acids forming the nearby site were also shown in stick model. The squared region containing the HBGA binding site is enlarged in the up-left panel.</p

Structures of the top 20 hit compounds against binding of VA387 to the A and B saliva.

<p>Structures of the top 20 hit compounds against binding of VA387 to the A and B saliva.</p

Parameters used in the primary and secondary screening of the VHTS.

<p>Parameters used in the primary and secondary screening of the VHTS.</p