Structural Analysis and Virtual Screening for Membrane Fusion Inhibitors targeting Group 2 Influenza A Hemagglutinin Initial Analysis of Crystal Structure

The co-crystal of HA X-31 and a promising small molecule inhibitor, tert-butyl hydroquinone (TBHQ) 1 , was solved back in 2008 (PDBID: 3EYM) 8. Visual inspection of the 3EYM's TBHQ binding pocket via Chimera 7 reaffirmed TBHQ's drug-like potential and the interactions noted in Russel et al. The structural differences between Group 1 and Group 2 HA were confirmed using the matchmaker function provided in Chimera. Two hemagglutinin subtypes from the two structurally distinct phylogenetic groups, 2009 H1 (PDBID: 3LZG) and H3 (PDBID: 3EYM), were selected for structural comparison. Using chains B and F of 3EYM as the reference structure with chains H and J of 3LZG, the two HA were overlaid with a RMSD value of 0.618 between 111 atom pairs. The orientation of key residue LYS 58 of HA2 in the RMSD fit structure coincides with past observations 8. The intermonomer salt bridge between LYS 58 (HA2) and GLU 59 (HA2) occupies TBHQ binding mode in 3LZG. The 2008 paper also mentions the importance of two key Hydrogen Bonds interacting with both the hydroxyl groups on TBHQ, although upon closer inspection the distance of the supposed hydrogen bond is 3.5 Angstroms long. This distance is too long under most circumstances to be considered a hydrogen bond. In addition, B-factors of two key interacting residues ranged from 80-90, suggesting that the given PDB structure represents one of many possible rotomers. TBHQ's were RMSD fit to each other using Chimera's match command with a value of <0.1 Angstroms which indicates that the conformations of the three TBHQ are similar. With the crystal structures from the Russel et al. paper analyzed, Autodock Vina 6 and Autodock 4 (AD4) 4 were to be used consecutively to screen a large library of potential drug candidates. Control Dockings conducted first to validate the use of Vina and AD4 in a virtual