Computer-aided Drug Design Targeting At Nonstructural Protein Of Influenza A Virus

Influenza A virus is the major pathogen not only carrying seasonal influenza but also causing flu pandemic in history. The emerging influenza pandemic caused by H1N1 influenza virus in 2009 is still circulating world wide, otherwise, human cases caused by other subtypes of influenza A viruse, like H5N1 and H9N2, are increasing.Therefore, the type A influenza poses a great threat to public health Athough the vaccination remains the efficient means in control the disease, however, to those emerging and antigenic mutation viruses, treatment with antiviral agents will play the key role in decreasing pain and death in the infected patiens. The development of new anti-influenza drugs has already became a common understanding. NS1 protein is an important virulence factor for the replication of Influenza A virus, protects the virus against the antiviral state induced by interferonα/β.Therefore NS1 represents a suitable target for antiviral compound screening. The purpose of this research is to investigate the potential drug targets on NS1, explore the binding sites and modes of four novel found NS1 inhibitors, and screen new lead compounds targeting at NS1.3D models of whole length monomer and dimer NS1 protein of HK,PR,Tx,WSN,GD strains were constructed by homology modeling, the models were refined by molecular dynamics, and finaly Procheck and Profile 3D were used to assess the the reliability of the models.To find the suitable sites for screening inhibitors of NS1, possible binding pockets were probed using pocket probing methods in DS2.1.The results showed that four pockets are suitable for antiviral drug screening, which are site1,site3, site5 and site6.Four NS1 inhibitors, which are NSC109834,NSC128164,NSC125044,and NSC95676 , were found recently, however, their exact binding site and binding modes on NS1 are not clear yet. We used the docking methods to bind those inhibitors on the possible active sites of NS1, to find their binding site and functionary mechanisms.The results showed that all the inhibitors were all binding on site1 but with different binding modes, NSC128164,NSC125044,NSC109834 can also binding on site3. This means that they can block the binding between NS1 and RNA or NS1 and CPSF30. Electrostatic repulsive force and spaceoccupying effects are major forces for NSC109834, NSC128164, NSC125044 in blocking the RNA binding property of NS1.The compound NSC95676 has the spaceoccupying effects and Arg38 repulsion.We took dsRNA binding pocket as target and screened from ZINC8.0 database about 1,140,000 compounds to find the possible NS1 inhibitors. After two steps screening, eight compounds were picked out, which are ZINC00197916, ZINC01723322, ZINC02827168, ZINC04103765, ZINC05065460, ZINC06721146, ZINC13151400, and ZINC08012842. All the lead compounds have two hydrophobic ends linked by a backbone.Except ZINC02827168 like the compound NSC95676, the binding modes of other compounds are similar to NS1 inhibitors NSC109834, NSC128164, and NSC125044, and the binding are contributed by electrostatic repulsive force and spaceoccupying effects.