Structural and computational study on inhibitory compounds for endonuclease activity of influenza virus polymerase. Issue 17 (1st September 2015)

• Record Type: Journal Article
• Authors: Fudo, Satoshi; Yamamoto, Norio; Nukaga, Michiyoshi; Odagiri, Takato; Tashiro, Masato; Neya, Saburo; Hoshino, Tyuji
• Is Part Of: Bioorganic & medicinal chemistry. Volume 23:Issue 17(2015)
• Page Start: 5466
• Page End: 5475
• Publication Date: 2015-09-01
• Subjects: PAN polymerase acidic protein N-terminal domain -- MD molecular dynamics -- MM/GBSA molecular mechanics/generalized Born surface area -- H5N1 hemagglutinin type 5 and neuraminidase type -- M2 protein matrix protein 2 -- HIV human immunodeficiency virus -- SBDD structure-based drug design -- IC50 50% inhibitory concentration -- LE ligand efficiency -- EC50 50% effective concentration -- EGCG epigallocatechin gallate -- FRET fluorescence resonance energy transfer -- PR8 A/Perto Rico/8/34 -- H1N1 hemagglutinin type 1 and neuraminidase type 1 -- HRV 3C human rhinovirus 3C protease -- PANΔloop loop-truncated polymerase acidic protein N-terminal domain -- LB Luria–Bertani -- OD600 optical density at 600 nm -- IPTG isopropyl-β-d-thiogalactopyranoside -- RNase H ribonuclease H -- EDTA ethylenediaminetetraacetic acid -- 6-FAM 6-carboxyfluorescein -- BHQ-1 black hole quencher 1 -- ssDNA single-stranded DNA -- RT-PCR real-time polymerase chain reaction -- MDCK Madin–Darby canine kidney -- SFM serum-free medium -- MOI multiplicity of infection -- CC50 50% cytotoxic concentration -- IEFPCM integral equation formalism polarizable continuum model -- RESP restrained electrostatic potential -- QM/MM quantum mechanics/molecular mechanics -- ONIOM our own N-layered integrated molecular orbital and molecular mechanics -- UFF universal force field -- GAFF general AMBER force field -- TIP3P transferable intermolecular potential 3 point -- RMSD root mean square deviation -- SASA solvent-accessible surface area -- LCPO linear combination of pairwise overlaps -- DPBA 2, 4-dioxo-4-phenylbutanoic acid; Influenza virus -- Polymerase acidic protein -- Endonuclease activity -- Inhibitor -- Crystal structure analysis -- Molecular dynamics simulation; Bioorganic chemistry -- Periodicals; Pharmaceutical chemistry -- Periodicals; Biochemistry -- Periodicals; Chemistry, Clinical -- Periodicals; Chemistry, Organic -- Periodicals; Chimie bio-organique -- Périodiques; Chimie pharmaceutique -- Périodiques; 615.19
• DOI: 10.1016/j.bmc.2015.07.046
• Languages: English
• ISSNs: 0968-0896

Abstract

Graphical abstract: Abstract: Seasonal epidemics and occasional pandemics caused by influenza viruses are global threats to humans. Since the efficacy of currently approved drugs is limited by the emerging resistance of the viruses, the development of new antiviral drugs is still demanded. Endonuclease activity, which lies in the influenza polymerase acidic protein N-terminal domain (PAN ), is a potent target for novel antiviral agents. Here, we report the identification of some novel inhibitors for PAN endonuclease activity. The binding mode of one of the inhibitory compounds to PAN was investigated in detail by means of X-ray crystal structure analysis and molecular dynamics (MD) simulation. It was observed in the crystal structure that three molecules of the same kind of inhibitor were bound to one PAN . One of the three molecules is located at the active site and makes a chelation to metal ions. Another molecule is positioned at the space adjacent to the metal-chelated site. The other molecule is located at a site slightly apart from the metal-chelated site, causing a conformational change of Arg124. The last binding site was not observed in previous crystallographic studies. Hence, the stability of inhibitor binding was examined by performing 100-ns MD simulation. During the MD simulation, the three inhibitor molecules fluctuated at the respective binding sites at different amplitudes, while all of the molecules maintained interactions with the protein. Molecular mechanics/generalized Born surface area (MM/GBSA) analysis suggested that the molecule in the last binding site has a higher affinity than the others. Structural information obtained in this study will provide a hint for designing and developing novel potent agents against influenza viruses.