title: Novel druggable hot spots in avian influenza neuraminidase H5N1 revealed by computational solvent mapping of a reduced and representative receptor ensemble.
abstract: The influenza virus subtype H5N1 has raised concerns of a possible human pandemic threat because of its high virulence and mutation rate. Although several approved anti-influenza drugs effectively target the neuraminidase, some strains have already acquired resistance to the currently available anti-influenza drugs. In this study, we present the synergistic application of extended explicit solvent molecular dynamics (MD) and computational solvent mapping (CS-Map) to identify putative 'hot spots' within flexible binding regions of N1 neuraminidase. Using representative conformations of the N1 binding region extracted from a clustering analysis of four concatenated 40-ns MD simulations, CS-Map was utilized to assess the ability of small, solvent-sized molecules to bind within close proximity to the sialic acid binding region. Mapping analyses of the dominant MD conformations reveal the presence of additional hot spot regions in the 150- and 430-loop regions. Our hot spot analysis provides further support for the feasibility of developing high-affinity inhibitors capable of binding these regions, which appear to be unique to the N1 strain.
authors.affiliation: Bioinformatics Graduate Program, Boston University, Boston, MA 02215, USA. mlandon@bu.edu
authors.forename: Melissa R
authors.initials: MR
authors.lastname: Landon
authors.forename: Rommie E
authors.initials: RE
authors.lastname: Amaro
authors.forename: Riccardo
authors.initials: R
authors.lastname: Baron
authors.forename: Chi Ho
authors.initials: CH
authors.lastname: Ngan
authors.forename: David
authors.initials: D
authors.lastname: Ozonoff
authors.forename: J Andrew
authors.initials: JA
authors.lastname: McCammon
authors.forename: Sandor
authors.initials: S
authors.lastname: Vajda
mesh_terms: D001665:Binding Sites; D003198:Computer Simulation; D016503:Drug Delivery Systems / Q000379:methods*; D004791:Enzyme Inhibitors / Q000737:chemistry; D053124:Influenza A Virus, H5N1 Subtype / Q000201:enzymology; D008958:Models, Molecular; D009038:Motion; D009439:Neuraminidase / Q000737:chemistry*; D011487:Protein Conformation; D011991:Receptors, Virus / Q000737:chemistry*; D012997:Solvents
chemical_list: D004791:Enzyme Inhibitors; D011991:Receptors, Virus; D012997:Solvents; D009439:Neuraminidase