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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 DENV3 MTase.Predicted poses of compounds 306711 and 610920 in the DENV3 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) Binding pocket interactions for compound 306711; (C) Compound 610920 orientation with respect to the full protein structure (in surface depiction on left and cartoon depiction on right); (D) Binding pocket interactions for compound 610920. Labels indicate protein amino acid residues that can possibly form H-bonds (black-dotted lines) with the ligands in these poses. Cu atoms in compound 306711 are shown as purple spheres.
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pone.0130062.g007: NSC 306711 and 610930 binding to the SAM-binding pocket of the DENV3 MTase.Predicted poses of compounds 306711 and 610920 in the DENV3 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) Binding pocket interactions for compound 306711; (C) Compound 610920 orientation with respect to the full protein structure (in surface depiction on left and cartoon depiction on right); (D) Binding pocket interactions for compound 610920. Labels indicate protein amino acid residues that can possibly form H-bonds (black-dotted lines) with the ligands in these poses. Cu atoms in compound 306711 are shown as purple spheres.

Mentions: The docked conformations in the SAH/36A binding site on the DENV MTase of the top two inhibitors identified (NSC306711 and NSC610930) were examined to understand their binding abilities (fig 7A and 7C). Both compounds fit into the binding pocket with multiple electrostatic and non-polar contacts with the enzyme (as indicated by atoms present within 3.5 Å). There are seven electrostatic contacts between NSC306711 and the MTase, specifically with the sidechains of residues Ser56, Lys61, and Ser159, and the backbone of residues Gly58, Cys82, Gly86, and Asp146 (fig 7B). The larger size of this compound allows it to extend out of the pocket and drape over a helical scaffold, making close contacts with 14 amino acid residues from the enzyme (shown as sticks and surfaces in fig 7B). NSC610930 has six electrostatic contacts with the MTase, with sidechains of residues Ser56 and Thr104, and backbones of residues Gly81, Asp146, Glu149, and Arg160 (fig 7D). Due to its smaller size, it is nestled in the binding pocket and makes close contact with only 9 enzyme residues (shown as sticks and surfaces in fig 7D). The larger number of electrostatic and non-polar contacts between NSC306711 and the enzyme can explain its higher inhibitory capacity as compared to NSC610930.


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 DENV3 MTase.Predicted poses of compounds 306711 and 610920 in the DENV3 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) Binding pocket interactions for compound 306711; (C) Compound 610920 orientation with respect to the full protein structure (in surface depiction on left and cartoon depiction on right); (D) Binding pocket interactions for compound 610920. Labels indicate protein amino acid residues that can possibly form H-bonds (black-dotted lines) with the ligands in these poses. Cu atoms in compound 306711 are shown as purple spheres.
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pone.0130062.g007: NSC 306711 and 610930 binding to the SAM-binding pocket of the DENV3 MTase.Predicted poses of compounds 306711 and 610920 in the DENV3 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) Binding pocket interactions for compound 306711; (C) Compound 610920 orientation with respect to the full protein structure (in surface depiction on left and cartoon depiction on right); (D) Binding pocket interactions for compound 610920. Labels indicate protein amino acid residues that can possibly form H-bonds (black-dotted lines) with the ligands in these poses. Cu atoms in compound 306711 are shown as purple spheres.
Mentions: The docked conformations in the SAH/36A binding site on the DENV MTase of the top two inhibitors identified (NSC306711 and NSC610930) were examined to understand their binding abilities (fig 7A and 7C). Both compounds fit into the binding pocket with multiple electrostatic and non-polar contacts with the enzyme (as indicated by atoms present within 3.5 Å). There are seven electrostatic contacts between NSC306711 and the MTase, specifically with the sidechains of residues Ser56, Lys61, and Ser159, and the backbone of residues Gly58, Cys82, Gly86, and Asp146 (fig 7B). The larger size of this compound allows it to extend out of the pocket and drape over a helical scaffold, making close contacts with 14 amino acid residues from the enzyme (shown as sticks and surfaces in fig 7B). NSC610930 has six electrostatic contacts with the MTase, with sidechains of residues Ser56 and Thr104, and backbones of residues Gly81, Asp146, Glu149, and Arg160 (fig 7D). Due to its smaller size, it is nestled in the binding pocket and makes close contact with only 9 enzyme residues (shown as sticks and surfaces in fig 7D). The larger number of electrostatic and non-polar contacts between NSC306711 and the enzyme can explain its higher inhibitory capacity as compared to NSC610930.

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.