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

The crystal structure for the HA1 subtype from the recent pandemic H1N1/09 virus was downloaded from the PDB Bank [32] . Its PDB ID is 3AL4. The antigenicity of the HA1 from the swine-origin A (H1N1)-2009 influenza A virus is quite similar to that of the HA from the 1918 pandemic virus [23] . The bindingsite was identified by the SiteMap tool in Schrodinger Suite 2009 (www.schrodinger.com) as described in [34, 35, 36] . The bind-site encompassed the ligand N-Acetyl-D-Glucosamine (NAG), which is observed in complex with HA1 of the crystal structure (PDB: 3AL4). Shown in Fig. 1 is a close-up view for the binding site of protein HA1 rendered by the molecular surface. The binding pocket is formed by those residues that have at least one heavy atom (i.e., an atom other than hydrogen) with a distance Æ’5 Ã… away from any heavy atom of NAG ligand when it is bound to the receptor at the binding site, as elaborated in [37] . The segments of loop1, loop2, loop3, and loop4, which play an important role in the interactions with the ligand, are shown by four different colors with their respective key residues: Ser92, Glu72, Pro143, and Arg227 ( Fig. 1) . The motions of such four residues were monitored during the molecular dynamics simulations.