Dihydropyrancarboxamides Related to Zanamivir:  A New Series of Inhibitors of Influenza Virus Sialidases. 2. Crystallographic and Molecular Modeling Study of Complexes of 4-Amino-4H-pyran-6-carboxamides and Sialidase from Influenza Virus Types A and B

Abstract

The first paper in this series (see previous article) described structure-activity studies of carboxamide analogues of zanamivir binding to influenza virus sialidase types A and B and showed that inhibitory activity of these compounds was much greater against influenza A enzyme. To understand the large differences in affinities, a number of protein-ligand complexes have been investigated using crystallography and molecular dynamics. The crystallographic studies show that the binding of ligands containing tertiary amide groups is accompanied by the formation of an intramolecular planar salt bridge between two amino acid residues in the active site of the enzyme. It is proposed that the unexpected strong binding of these inhibitors is a result of the burial of hydrophobic surface area and salt-bridge formation in an environment of low dielectric. In sialidase from type A virus, binding of the carboxamide moeity and salt-bridge formation have only a minor effect on the positions of the surrounding residues, whereas in type B enzyme, significant distortion of the protein is observed. The results suggest that the decreased affinity in enzyme from influenza B is directly correlated with the small changes that occur in the amino acid residue interactions accompanying ligand binding. Molecular dynamics calculations have shown that the tendency for salt-bridge formation is greater in influenza A sialidase than influenza B sialidase and that this tendency is a useful descriptor for the prediction of inhibitor potency.

Comparison of the Activities of Zanamivir, Oseltamivir, and RWJ-270201 against Clinical Isolates of Influenza Virus and Neuraminidase Inhibitor-Resistant Variants

“…We confirmed that this substitution led to a low level of virus resistance to zanamivir (8-fold) and a moderate level of resistance to RWJ-270201 (27-fold), despite the apparent need for reorientation for the interaction of RWJ-270201. The reorientation of the side chain of Glu276 could be energetically less favorable in influenza B virus NAs than in influenza A virus NAs, because the region surrounding Glu276 is hydrophobic in influenza B viruses and hydrophilic in influenza A viruses (23). Differences in binding of inhibitors to influenza A and B virus NAs have been reported previously (1,23).…”

Comparison of the Anti-Influenza Virus Activity of RWJ-270201 with Those of Oseltamivir and Zanamivir

“…In the case of influenza B neuraminidase, it has been reported that the rearrangement of Glu 276 is energetically less favorable (1,14). Although both oseltamivir carboxylate and RWJ-270201 have hydrophobic groups.…”

In Vitro Selection and Characterization of Influenza A (A/N9) Virus Variants Resistant to a Novel Neuraminidase Inhibitor, A-315675

“…The affinity of a compound such as oseltamivir carboxylate, which depends on this movement for optimal binding (19), is expected to be significantly affected by this mutation in N9. Structure-activity relationship data for zanamivir suggest that E276 is not required to move for high potency in N1, N2, N9, and B enzymes, so the fold resistance of zanamivir is minimal for K292 mutants (12,21,23,32,33).…”