6YA5

2009 H1N1 PA Endonuclease in complex with LU2

Summary for 6YA5

• Entry DOI: 10.2210/pdb6ya5/pdb
• Descriptor: Polymerase acidic protein,Polymerase acidic protein, MANGANESE (II) ION, MAGNESIUM ION, ... (9 entities in total)
• Functional Keywords: influenza, polymerase, endonuclease, hydrolase, viral protein
• Biological source: Influenza A virus (A/California/07/2009(H1N1)); More
• Total number of polymer chains: 1
• Total formula weight: 22013.13

Authors

Radilova, K.,Brynda, J. (deposition date: 2020-03-11, release date: 2020-09-09, Last modification date: 2024-01-24)

Primary citation

Zima, V.,Radilova, K.,Kozisek, M.,Albinana, C.B.,Karlukova, E.,Brynda, J.,Fanfrlik, J.,Flieger, M.,Hodek, J.,Weber, J.,Majer, P.,Konvalinka, J.,Machara, A.
Unraveling the anti-influenza effect of flavonoids: Experimental validation of luteolin and its congeners as potent influenza endonuclease inhibitors.
Eur.J.Med.Chem., 208:112754-112754, 2020

PubMed Abstract: The biological effects of flavonoids on mammal cells are diverse, ranging from scavenging free radicals and anti-cancer activity to anti-influenza activity. Despite appreciable effort to understand the anti-influenza activity of flavonoids, there is no clear consensus about their precise mode-of-action at a cellular level. Here, we report the development and validation of a screening assay based on AlphaScreen technology and illustrate its application for determination of the inhibitory potency of a large set of polyols against PA N-terminal domain (PA-Nter) of influenza RNA-dependent RNA polymerase featuring endonuclease activity. The most potent inhibitors we identified were luteolin with an IC of 72 ± 2 nM and its 8-C-glucoside orientin with an IC of 43 ± 2 nM. Submicromolar inhibitors were also evaluated by an in vitro endonuclease activity assay using single-stranded DNA, and the results were in full agreement with data from the competitive AlphaScreen assay. Using X-ray crystallography, we analyzed structures of the PA-Nter in complex with luteolin at 2.0 Å resolution and quambalarine B at 2.5 Å resolution, which clearly revealed the binding pose of these polyols coordinated to two manganese ions in the endonuclease active site. Using two distinct assays along with the structural work, we have presumably identified and characterized the molecular mode-of-action of flavonoids in influenza-infected cells.

PubMed: 32883638
DOI: 10.1016/j.ejmech.2020.112754

Experimental method

X-RAY DIFFRACTION (2 Å)