Paper Citing NAMD - Abstract
Landon, Melissa R.; Amaro, Rommie E.; Baron, Riccardo; Ngan, Chi Ho; Ozonoff, David; McCammon, J. Andrew; Vajda, Sandor
Novel druggable hot spots in avian influenza neuraminidase H5N1 revealed by computational solvent mapping of a reduced and representative receptor ensemble
CHEMICAL BIOLOGY & DRUG DESIGN, 71:106-116, FEB 2008
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 (MID) 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 MID 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.
