title: Outside-binding site mutations modify the active site's shapes in neuraminidase from influenza A H1N1.
abstract: The recent occurrence of 2009 influenza A (H1N1) pandemic as well as others has raised concern of a far more dangerous outcome should this virus becomes resistant to current drug therapies. The number of clinical cases that are resistant to oseltamivir (Tamiflu®) is larger than the limited number of neuraminidase (NA) mutations (H275Y, N295S, and I223R) that have been identified at the active site and that are associated to oseltamivir resistance. In this study, we have performed a comparative analysis between a set of NAs that have the most representative mutations located outside the active site. The recently crystallized NA-oseltamivir complex (PDB ID: 3NSS) was used as a wild-type structure. After selecting the target NA sequences, their three-dimensional (3D) structure was built using 3NSS as a template by homology modeling. The 3D NA models were refined by molecular dynamics (MD) simulations. The refined models were used to perform a docking study, using oseltamivir as a ligand. Furthermore, the docking results were refined by free-energy analysis using the MM-PBSA method. The analysis of the MD simulation results showed that the NA models reached convergence during the first 10 ns. Visual inspection and structural measures showed that the mutated NA active sites show structural variations. The docking and MM-PBSA results from the complexes showed different binding modes and free energy values. These results suggest that distant mutations located outside the active site of NA affect its structure and could be considered to be a new source of resistance to oseltamivir, which agrees with reports in the clinical literature.
authors.affiliation: Laboratorio de Modelado Molecular y Bioinformática, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón, México City 11340, México.
authors.forename: Luis
authors.initials: L
authors.lastname: Tolentino-Lopez
authors.forename: Aldo
authors.initials: A
authors.lastname: Segura-Cabrera
authors.forename: Paola
authors.initials: P
authors.lastname: Reyes-Loyola
authors.forename: Mirko
authors.initials: M
authors.lastname: Zimic
authors.forename: Miguel
authors.initials: M
authors.lastname: Quiliano
authors.forename: Veronica
authors.initials: V
authors.lastname: Briz
authors.forename: Angeles
authors.initials: A
authors.lastname: Muñoz-Fernández
authors.forename: Mario
authors.initials: M
authors.lastname: Rodríguez-Pérez
authors.forename: Ian
authors.initials: I
authors.lastname: Ilizaliturri-Flores
authors.forename: Jose
authors.initials: J
authors.lastname: Correa-Basurto
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites / Q000235:genetics; D006801:Humans; D053118:Influenza A Virus, H1N1 Subtype / Q000201:enzymology*; D007251:Influenza, Human / Q000821:virology*; D056004:Molecular Dynamics Simulation; D009154:Mutation; D009439:Neuraminidase / Q000037:antagonists & inhibitors / Q000737:chemistry* / Q000235:genetics*; D053139:Oseltamivir / Q000737:chemistry; D016415:Sequence Alignment
chemical_list: D053139:Oseltamivir; D009439:Neuraminidase