Virtual screening pipeline and ligand modelling for H5N1 neuraminidase

• Published in: Biochemical and biophysical research communications 2009-06, Vol.383 (4), p.445-449
• Main Authors: D’Ursi, Pasqualina, Chiappori, Federica, Merelli, Ivan, Cozzi, Paolo, Rovida, Ermanna, Milanesi, Luciano
• Format: Article
• Language: English
• Subjects: 150-cavity; Antiviral Agents - chemistry; Antiviral Agents - isolation & purification; Antiviral Agents - pharmacology; Catalytic Domain; Crystallography, X-Ray; Data filtering; Docking; Drug Design; Enzyme Inhibitors - chemistry; Enzyme Inhibitors - isolation & purification; Enzyme Inhibitors - pharmacology; H5N1 neuraminidase; Influenza A Virus, H5N1 Subtype - enzymology; Ligands; Models, Chemical; Neuraminidase - antagonists & inhibitors; Neuraminidase - chemistry; Neuraminidase inhibitors; Virtual screening pipeline
• ISSN: 0006-291X; 1090-2104
• DOI: 10.1016/j.bbrc.2009.04.030

The H5N1 virus neuraminidase structure was solved in two different conformations depending on the inhibitor concentration. In the absence of oseltamivir or at a low concentration, the neuraminidase structure assumes an open form that closes at a high oseltamivir concentration due to the shift of the so-called 150-loop near the active site. Although the close conformation is similar to all the other structurally known neuraminidase types, it doesn’t appear to be the most likely physiological condition for N1. To investigate the specific ligand binding properties of the open form, we screened by docking simulation, a large dataset of ligands and compared the results with closed form. The virtual screening procedure was implemented in a docking pipeline that also performs a step-by-step, target specific, filtering approach for data reduction. The selected ligands display binding ability involving multiple sites of interaction including the active site and an adjacent cavity made available by the 150-loop shift. Two ligands are especially interesting and are proposed as substituents to design oseltamivir derivatives specifically suited for the open conformation.