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Conformational inhibition of the hepatitis C virus internal ribosome entry site RNA.

Parsons J, Castaldi MP, Dutta S, Dibrov SM, Wyles DL, Hermann T - Nat. Chem. Biol. (2009)

Bottom Line: The internal ribosome entry site (IRES), a highly conserved structured element of the hepatitis C virus (HCV) genomic RNA, is an attractive target for antiviral drugs.Here we show that benzimidazole inhibitors of the HCV replicon act by conformational induction of a widened interhelical angle in the IRES subdomain IIa, which facilitates the undocking of subdomain IIb from the ribosome and ultimately leads to inhibition of IRES-driven translation in HCV-infected cells.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA.

ABSTRACT
The internal ribosome entry site (IRES), a highly conserved structured element of the hepatitis C virus (HCV) genomic RNA, is an attractive target for antiviral drugs. Here we show that benzimidazole inhibitors of the HCV replicon act by conformational induction of a widened interhelical angle in the IRES subdomain IIa, which facilitates the undocking of subdomain IIb from the ribosome and ultimately leads to inhibition of IRES-driven translation in HCV-infected cells.

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The HCV IRES RNA target. (a) Secondary structure of the HCV 5′ NTR (nucleotides 1–341 of HCV genotype 1b) that contains the IRES element. In addition to residues of the NTR, the IRES includes 26 nt of the reading frame in the hairpin loop of domain IV. (b) Secondary structure of the IRES subdomain IIa. Arrows indicate protection from RNase A digestion at an internal loop of IIa in the presence of benzimidazole 1.8(c) Three-dimensional structure of the IIa-1 RNA (Supplementary Fig. 1a) corresponding to the subdomain IIa.9 Mg2+ ions are shown as spheres. (d) Benzimidazole inhibitors of the HCV replicon. Compound 1 has a binding affinity for the IRES subdomain IIa of KD=0.72μM, as determined by mass spectrometry, and inhibits HCV replicon at EC50=5.4μM.8 Compound 2 is a precursor to 1.
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Figure 1: The HCV IRES RNA target. (a) Secondary structure of the HCV 5′ NTR (nucleotides 1–341 of HCV genotype 1b) that contains the IRES element. In addition to residues of the NTR, the IRES includes 26 nt of the reading frame in the hairpin loop of domain IV. (b) Secondary structure of the IRES subdomain IIa. Arrows indicate protection from RNase A digestion at an internal loop of IIa in the presence of benzimidazole 1.8(c) Three-dimensional structure of the IIa-1 RNA (Supplementary Fig. 1a) corresponding to the subdomain IIa.9 Mg2+ ions are shown as spheres. (d) Benzimidazole inhibitors of the HCV replicon. Compound 1 has a binding affinity for the IRES subdomain IIa of KD=0.72μM, as determined by mass spectrometry, and inhibits HCV replicon at EC50=5.4μM.8 Compound 2 is a precursor to 1.

Mentions: Hepatitis C virus (HCV) infection affects ~170 million people worldwide and is a major cause of chronic hepatitis as well as hepatocellular carcinoma.1 Current therapies suffer from low efficiency and serious side effects. Therefore, there is an urgent need for novel antiviral agents for the treatment of HCV infection. Among the potential targets for HCV inhibitors is the highly conserved 5′ untranslated region (UTR) of the viral RNA genome which harbors an internal ribosome entry site (IRES). The HCV IRES binds with high affinity2 to host cell 40S ribosomal subunits and initiates translation in a cap-independent fashion.3,4 The IRES element adopts an ordered structure5 which is dominated by independently-folding RNA domains.6,7 The subdomain IIa is the target for benzimidazole inhibitors (1, 2) that reduce viral RNA levels in the HCV replicon at micromolar concentrations (Fig. 1).8 Here, we have used fluorescence labeling guided by structure information to study the mechanics of target interaction of the benzimidazole inhibitors.


Conformational inhibition of the hepatitis C virus internal ribosome entry site RNA.

Parsons J, Castaldi MP, Dutta S, Dibrov SM, Wyles DL, Hermann T - Nat. Chem. Biol. (2009)

The HCV IRES RNA target. (a) Secondary structure of the HCV 5′ NTR (nucleotides 1–341 of HCV genotype 1b) that contains the IRES element. In addition to residues of the NTR, the IRES includes 26 nt of the reading frame in the hairpin loop of domain IV. (b) Secondary structure of the IRES subdomain IIa. Arrows indicate protection from RNase A digestion at an internal loop of IIa in the presence of benzimidazole 1.8(c) Three-dimensional structure of the IIa-1 RNA (Supplementary Fig. 1a) corresponding to the subdomain IIa.9 Mg2+ ions are shown as spheres. (d) Benzimidazole inhibitors of the HCV replicon. Compound 1 has a binding affinity for the IRES subdomain IIa of KD=0.72μM, as determined by mass spectrometry, and inhibits HCV replicon at EC50=5.4μM.8 Compound 2 is a precursor to 1.
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Figure 1: The HCV IRES RNA target. (a) Secondary structure of the HCV 5′ NTR (nucleotides 1–341 of HCV genotype 1b) that contains the IRES element. In addition to residues of the NTR, the IRES includes 26 nt of the reading frame in the hairpin loop of domain IV. (b) Secondary structure of the IRES subdomain IIa. Arrows indicate protection from RNase A digestion at an internal loop of IIa in the presence of benzimidazole 1.8(c) Three-dimensional structure of the IIa-1 RNA (Supplementary Fig. 1a) corresponding to the subdomain IIa.9 Mg2+ ions are shown as spheres. (d) Benzimidazole inhibitors of the HCV replicon. Compound 1 has a binding affinity for the IRES subdomain IIa of KD=0.72μM, as determined by mass spectrometry, and inhibits HCV replicon at EC50=5.4μM.8 Compound 2 is a precursor to 1.
Mentions: Hepatitis C virus (HCV) infection affects ~170 million people worldwide and is a major cause of chronic hepatitis as well as hepatocellular carcinoma.1 Current therapies suffer from low efficiency and serious side effects. Therefore, there is an urgent need for novel antiviral agents for the treatment of HCV infection. Among the potential targets for HCV inhibitors is the highly conserved 5′ untranslated region (UTR) of the viral RNA genome which harbors an internal ribosome entry site (IRES). The HCV IRES binds with high affinity2 to host cell 40S ribosomal subunits and initiates translation in a cap-independent fashion.3,4 The IRES element adopts an ordered structure5 which is dominated by independently-folding RNA domains.6,7 The subdomain IIa is the target for benzimidazole inhibitors (1, 2) that reduce viral RNA levels in the HCV replicon at micromolar concentrations (Fig. 1).8 Here, we have used fluorescence labeling guided by structure information to study the mechanics of target interaction of the benzimidazole inhibitors.

Bottom Line: The internal ribosome entry site (IRES), a highly conserved structured element of the hepatitis C virus (HCV) genomic RNA, is an attractive target for antiviral drugs.Here we show that benzimidazole inhibitors of the HCV replicon act by conformational induction of a widened interhelical angle in the IRES subdomain IIa, which facilitates the undocking of subdomain IIb from the ribosome and ultimately leads to inhibition of IRES-driven translation in HCV-infected cells.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA.

ABSTRACT
The internal ribosome entry site (IRES), a highly conserved structured element of the hepatitis C virus (HCV) genomic RNA, is an attractive target for antiviral drugs. Here we show that benzimidazole inhibitors of the HCV replicon act by conformational induction of a widened interhelical angle in the IRES subdomain IIa, which facilitates the undocking of subdomain IIb from the ribosome and ultimately leads to inhibition of IRES-driven translation in HCV-infected cells.

Show MeSH
Related in: MedlinePlus