Novel Inhibitor Design for Hemagglutinin against H1N1 Influenza Virus by Core Hopping Method

Li, Xiao-Bo; Wang, Shu-Qing; Xu, Wei-Ren; Wang, Run-Ling; Chou, Kuo-Chen

Many marvelous biological functions in proteins and DNA and their profound dynamic mechanisms, such as switch between active and inactive states [47, 48] , cooperative effects [49] , allosteric transition [50, 51] , intercalation of drugs into DNA [52] , and assembly of microtubules [53] , can be revealed by . The binding pocket is defined by those residues that have at least one heavy atom with a distance 5 Ã… from the NAG ligand [37] . The four loops (loop1, loop2, loop3, and loop4) that play an important role in interacting with the ligand are represented by round ribbons of four different colors as well as their key residues Ser92, Glu72, Pro143, and Arg227, respectively. The motions of such four residues were monitored during the molecular dynamic simulation. The docked poses for ZINC01602230, Neo and Neo6 are shown with the stick model colored in purple, yellow and dark green, respectively. doi:10.1371/journal.pone.0028111.g001 studying their internal motions [54] . Likewise, to really understand the action mechanism of a receptor with its ligand, we should consider not only the static structures concerned but also the dynamical information obtained by simulating their internal motions or dynamic process.