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Novel Broad Spectrum Inhibitors Targeting the Flavivirus Methyltransferase.

Brecher M, Chen H, Liu B, Banavali NK, Jones SA, Zhang J, Li Z, Kramer LD, Li H - PLoS ONE (2015)

Bottom Line: The flavivirus methyltransferase (MTase) is an essential enzyme that sequentially methylates the N7 and 2'-O positions of the viral RNA cap, using S-adenosyl-L-methionine (SAM) as a methyl donor.In vitro methylation experiments demonstrated significant MTase inhibition by 13 of these compounds, with the most potent compound displaying sub-micromolar inhibitory activity.The most active compounds showed broad spectrum activity against the MTase proteins of multiple flaviviruses.

View Article: PubMed Central - PubMed

Affiliation: Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY, 12208 United States of America.

ABSTRACT
The flavivirus methyltransferase (MTase) is an essential enzyme that sequentially methylates the N7 and 2'-O positions of the viral RNA cap, using S-adenosyl-L-methionine (SAM) as a methyl donor. We report here that small molecule compounds, which putatively bind to the SAM-binding site of flavivirus MTase and inhibit its function, were identified by using virtual screening. In vitro methylation experiments demonstrated significant MTase inhibition by 13 of these compounds, with the most potent compound displaying sub-micromolar inhibitory activity. The most active compounds showed broad spectrum activity against the MTase proteins of multiple flaviviruses. Two of these compounds also exhibited low cytotoxicity and effectively inhibited viral replication in cell-based assays, providing further structural insight into flavivirus MTase inhibition.

No MeSH data available.


NSC 306711 and 610930 binding to the SAM-binding pocket of the WNV MTase.Predicted poses of compounds 306711 and 610920 in the WNV MTase SAM-binding pocket. (A) Compound 306711 orientation with respect to the full protein structure (in surface depiction on left and cartoon depiction on right); (B) Compound 610920 orientation with respect to the full protein structure (in surface depiction on left and cartoon depiction on right). Cu atoms in compound 306711 are shown as purple spheres.
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pone.0130062.g008: NSC 306711 and 610930 binding to the SAM-binding pocket of the WNV MTase.Predicted poses of compounds 306711 and 610920 in the WNV MTase SAM-binding pocket. (A) Compound 306711 orientation with respect to the full protein structure (in surface depiction on left and cartoon depiction on right); (B) Compound 610920 orientation with respect to the full protein structure (in surface depiction on left and cartoon depiction on right). Cu atoms in compound 306711 are shown as purple spheres.

Mentions: We noticed that although the compounds were initially identified through docking into the SAM-binding pocket of the DENV3 MTase, it appears that the compounds are overall less active against the DENV3 MTase than against the others (Table 2). One explanation could be that because the substrate used in the assays was an authentic sequence of the WNV and it might not be optimal for the DENV3. This is particularly reasonable as the N7 function of flavivirus MTase requires distinct viral stem-loop structure for optimal reaction [43]. An alternative explanation is that the compounds may bind the MTases differently. To address this concern, we independently docked these two compounds into the WNV MTase (fig 8). The docking conformations were quite different from those for the Dengue MTase, suggesting that one explanation for the differences in activity could be attributed to different binding poses of the molecules in the two binding sites. Whether the compounds bind similarly or differently to these MTases will require mutational and biochemical experiments and/or co-crystal structure with bound inhibitor. However, these are outside the scope of the present study.


Novel Broad Spectrum Inhibitors Targeting the Flavivirus Methyltransferase.

Brecher M, Chen H, Liu B, Banavali NK, Jones SA, Zhang J, Li Z, Kramer LD, Li H - PLoS ONE (2015)

NSC 306711 and 610930 binding to the SAM-binding pocket of the WNV MTase.Predicted poses of compounds 306711 and 610920 in the WNV MTase SAM-binding pocket. (A) Compound 306711 orientation with respect to the full protein structure (in surface depiction on left and cartoon depiction on right); (B) Compound 610920 orientation with respect to the full protein structure (in surface depiction on left and cartoon depiction on right). Cu atoms in compound 306711 are shown as purple spheres.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4476580&req=5

pone.0130062.g008: NSC 306711 and 610930 binding to the SAM-binding pocket of the WNV MTase.Predicted poses of compounds 306711 and 610920 in the WNV MTase SAM-binding pocket. (A) Compound 306711 orientation with respect to the full protein structure (in surface depiction on left and cartoon depiction on right); (B) Compound 610920 orientation with respect to the full protein structure (in surface depiction on left and cartoon depiction on right). Cu atoms in compound 306711 are shown as purple spheres.
Mentions: We noticed that although the compounds were initially identified through docking into the SAM-binding pocket of the DENV3 MTase, it appears that the compounds are overall less active against the DENV3 MTase than against the others (Table 2). One explanation could be that because the substrate used in the assays was an authentic sequence of the WNV and it might not be optimal for the DENV3. This is particularly reasonable as the N7 function of flavivirus MTase requires distinct viral stem-loop structure for optimal reaction [43]. An alternative explanation is that the compounds may bind the MTases differently. To address this concern, we independently docked these two compounds into the WNV MTase (fig 8). The docking conformations were quite different from those for the Dengue MTase, suggesting that one explanation for the differences in activity could be attributed to different binding poses of the molecules in the two binding sites. Whether the compounds bind similarly or differently to these MTases will require mutational and biochemical experiments and/or co-crystal structure with bound inhibitor. However, these are outside the scope of the present study.

Bottom Line: The flavivirus methyltransferase (MTase) is an essential enzyme that sequentially methylates the N7 and 2'-O positions of the viral RNA cap, using S-adenosyl-L-methionine (SAM) as a methyl donor.In vitro methylation experiments demonstrated significant MTase inhibition by 13 of these compounds, with the most potent compound displaying sub-micromolar inhibitory activity.The most active compounds showed broad spectrum activity against the MTase proteins of multiple flaviviruses.

View Article: PubMed Central - PubMed

Affiliation: Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY, 12208 United States of America.

ABSTRACT
The flavivirus methyltransferase (MTase) is an essential enzyme that sequentially methylates the N7 and 2'-O positions of the viral RNA cap, using S-adenosyl-L-methionine (SAM) as a methyl donor. We report here that small molecule compounds, which putatively bind to the SAM-binding site of flavivirus MTase and inhibit its function, were identified by using virtual screening. In vitro methylation experiments demonstrated significant MTase inhibition by 13 of these compounds, with the most potent compound displaying sub-micromolar inhibitory activity. The most active compounds showed broad spectrum activity against the MTase proteins of multiple flaviviruses. Two of these compounds also exhibited low cytotoxicity and effectively inhibited viral replication in cell-based assays, providing further structural insight into flavivirus MTase inhibition.

No MeSH data available.