Molecular Modeling of the Binding of the Allosteric Inhibitor Optactin at a New Binding Site in Neuraminidase A from Streptococcus pneumoniae

Neuraminidase A (NanA) from the pathogenic bacteria Streptococcus pneumoniae catalyzes the cleavage of terminal sialic acid residues from oligosaccharide receptors on the surface of human respiratory epithelium cells and is considered to be the key virulence factor. The search for new regulatory ligand-binding sites in the structure of this enzyme is of fundamental interest and can reveal new targets to design drugs for treating pneumonia, meningitis, and other human infectious diseases. The low molecular weight compound optactin has been recently shown to inhibit the activity of the homologous Neuraminidase B (NanB). Furthermore, optactin binds at a separate site of the protein structure, which is topologically different from the catalytic center. The bioinformatic and structural analysis using the pocketZebra method was used to annotate a new, previously unknown site in the NanA structure. This new site is analogous to the optactin binding site in NanB and characterized by the high content of subfamily-specific positions, what indicates the importance of this site for the enzyme function. Molecular modeling was used to study optactin binding at the allosteric sites of the homologous neuraminidases NanA and NanB. Tyr250, Thr251, Lys334, Gln494, Lys499, Lys597, Thr657, and Glu658 residues were shown to stabilize the optactin molecule in the NanB structure, with water molecules playing an important role in the coordination of the ligand. Molecular modeling has shown that optactin binding by NanA is complicated due to substitutions in the subfamily-specific positions of the allosteric center. The peculiarities of the structural organization of the new NanA binding site facilitate the targeted search for complementary ligands that can selectively regulate the activity of this enzyme.