Understanding of Drug-Target Interactions: A case Study in Influenza Virus A Subtype H5N1

摘要

This study aims at gaining insight into molecular mechanisms of action of three drug targets of the life cycle of influenza virus A subtype H5N1, namely Hemagglutinin (H5), Neuraminidase (N1) and M2 ion channel (M2), using molecular mechanics and molecular dynamics techniques. In hemagglutinin, interest is focused on the high pathogenicity of the H5 due to the -RRRKK- insertion. MD simulations carried out for H5 in both high and low pathogenic forms (HPH5 and LPH5), aimed at understanding why HPH5 was experimentally observed to be 5-fold better cleaved by furin relative to the non-inserted sequence of LPH5. As the results, the cleavage loop of HPH5 was found to fit well and bind strongly into the catalytic site of human furin, serving as a conformation suitable for the proteolytic reaction. The second target, neuraminidase was studied by two different approaches. Firstly with MD simulations, rotation of the -NHAc and -OCHEt_2 side chains of oseltamivir (OTV), leading directly to rearrangement of the catalytic cavity, was found to be a primary source of the lower susceptibility of OTV to neuraminidase subtype Nl than to N2 and N9. In addition, three inhibitors, OTV, zanamivir (ZNV) and peramivir (PRV), complexed with neuraminidase subtype Nl were studied to understand the drug-target interactions. The structural properties, position and conformation of PRV and its side chains are uniformly preferential, i.e., its conformation fits very well with the Nl active site. At the Nl target, another approach, combinatorial chemistry, was used to design a library of new potent inhibitors, which well fit to the active site and the 150-loop residues of Nl. Investigation was also extended to the M2 proton channel. Five different protonation states of the selectivity filter residue (His) where OH, 1H, 2aH, 2dH and 4H represent the systems with none, mono-protonated, di-protonated at adjacent and opposite positions, and tetra-protonated, respectively, were taken into account both in free forms and their complexes with amantadine and rimantadine inhibitors. In agreement with the experimental observations, water was inhibited by amantadine significantly better than rimantadine in the 1H and 2Ha systems.