title: Binding mode analysis of anti-influenza drugs in H1N1 (2009) and H5N1 influenza A virus and designing of potential H1N1 inhibitors.
abstract: The main goal of this study is to understand the molecular-level interactions of neuraminidase inhibitor. The molecular docking, molecular dynamics and binding energy calculation analyses were carried out and the results revealed that the 150-cavitiy in the active site may play an important role in binding of drugs. Free energy calculations revealed that electrostatic interaction is more favourable for Oseltamivir interaction with H1N1 and van der Waals interaction is more favourable for H5N1, whereas Zanamivir favours the electrostatic interaction in both the strains (H1N1 and H5N1). Energy-optimised pharmacophore mapping was created using Oseltamivir drug. The pharmacophore model contained two hydrogen-bond acceptor and two hydrogen bond donor sites. Using these pharmacophore features, we screened a compound database to find a potential ligand that could inhibit the H1N1 protein. The current research will pave the way to find potent neuraminidase inhibitors against H1N1 (2009) strain.
authors: Department of Bioinformatics, Alagappa University, Karaikudi  630 004, Tamil Nadu, India.
authors: Kh Dhanachandra
authors: KhD
authors: Singh
authors: Department of Bioinformatics, Alagappa University, Karaikudi  630 004, Tamil Nadu, India.
authors: Palani
authors: P
authors: Kirubakaran
authors: Department of Bioinformatics, Alagappa University, Karaikudi  630 004, Tamil Nadu, India.
authors: Selvaraman
authors: S
authors: Nagamani
authors: Department of Bioinformatics, Alagappa University, Karaikudi  630 004, Tamil Nadu, India.
authors: Muthusamy
authors: M
authors: Karthikeyan
mesh_terms: D000595:Amino Acid Sequence; D000998:Antiviral Agents / Q000737:chemistry* / Q000378:metabolism / Q000494:pharmacology*; D055808:Drug Discovery; D006801:Humans; D053118:Influenza A Virus, H1N1 Subtype / Q000737:chemistry* / Q000378:metabolism; D053124:Influenza A Virus, H5N1 Subtype / Q000737:chemistry* / Q000378:metabolism; D007251:Influenza, Human / Q000188:drug therapy / Q000821:virology; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D009439:Neuraminidase / Q000037:antagonists & inhibitors* / Q000737:chemistry / Q000378:metabolism; D011485:Protein Binding; D055672:Static Electricity; D014764:Viral Proteins / Q000037:antagonists & inhibitors* / Q000737:chemistry / Q000378:metabolism
chemical_list: D000998:Antiviral Agents; D014764:Viral Proteins; D009439:Neuraminidase