SAR by MS:  Discovery of a New Class of RNA-Binding Small Molecules for the Hepatitis C Virus:  Internal Ribosome Entry Site IIA Subdomain

Seth, Punit P.; Miyaji, Alycia; Jefferson, Elizabeth A.; Sannes‐Lowery, Kristin A.; Osgood, Stephen A.; Propp, Stephanie; Ranken, Ray; Massire, Christian; Sampath, Rangarajan; Ecker, David J.; Swayze, Eric E.; Griffey, Richard H.

doi:10.1021/jm050815o

Cited by 150 publications

(197 citation statements)

References 26 publications

(47 reference statements)

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“…It is noteworthy that the pathway of IFN inhibition of viral replication occurs via an IRES-dependent mechanism (11). Both the IRES structure and the mechanism of HCV translation initiation (e.g., 12, 13) have been the subject of intense research in recent years as a therapeutic target (14)(15)(16)(17). As an example, the synthetic steroid mifepristone specifically inhibits in vitro translation initiation from the HCV IRES (18).…”

mentioning

confidence: 99%

RETRACTED: Selection of cyclic peptide aptamers to HCV IRES RNA using mRNA display

Litovchick

Szostak

2008

Proc. Natl. Acad. Sci. U.S.A.

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The hepatitis C virus (HCV) is a positive strand RNA flavivirus that is a major causative agent of serious liver disease, making new treatment modalities an urgent priority. Because HCV translation initiation occurs by a mechanism that is fundamentally distinct from that of host mRNAs, it is an attractive target for drug discovery. The translation of HCV mRNA is initiated from an internal ribosomal entry site (IRES), independent of cap and poly(A) recognition and bypassing eIF4F complex formation. We used mRNA display selection technology combined with a simple and robust cyclization procedure to screen a peptide library of >1013 different sequences and isolate cyclic peptides that bind with high affinity and specificity to HCV IRES RNA. The best peptide binds the IRES with subnanomolar affinity, and a specificity of at least 100-fold relative to binding to several other RNAs of similar length. The peptide specifically inhibits HCV IRES-initiated translation in vitro with no detectable effect on normal cap-dependent translation initiation. An 8-aa cyclic peptide retains most of the activity of the full-length 27-aa bicyclic peptide. These peptides may be useful tools for the study of HCV translation and may have potential for further development as an anti-HCV drug.

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mentioning

confidence: 99%

RETRACTED: Selection of cyclic peptide aptamers to HCV IRES RNA using mRNA display

Litovchick

Szostak

2008

Proc. Natl. Acad. Sci. U.S.A.

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“…Recent cryo-EM studies confirm the conformational flexibility of domain II through comparison of 40S-bound binary and 80S-bound initiation complexes of the HCV IRES (14). Motivated by the discovery of a riboswitch-like binding site for benzimidazole translation inhibitors (19) in the extended form of subdomain IIa (21), we hypothesized that a cognate ligand may serve as the biological actuator of the RNA switch that ultimately facilitates ribosomal release from the IRES. Inspection of the crystal structure previously determined for an inhibitor complex of subdomain IIa suggested that benzimidazole derivatives might be fortuitous ligands that exploit a recognition site for guanine.…”

Section: Discussionmentioning

confidence: 99%

“…1D) that bind to the internal loop and block translation by capturing distinct conformational states of the RNA (7). Structure analysis revealed that benzimidazole inhibitors such as compound 1 (19,20) interact with an extended architecture of IIa in which the stems flanking the internal loop are coaxially stacked on both sides of the ligand-binding pocket ( Fig. 1E) (21).…”

mentioning

confidence: 99%

Functional conservation despite structural divergence in ligand-responsive RNA switches

Boerneke¹,

Dibrov²,

Gu³

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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An internal ribosome entry site (IRES) initiates protein synthesis in RNA viruses, including the hepatitis C virus (HCV). We have discovered ligand-responsive conformational switches in viral IRES elements. Modular RNA motifs of greatly distinct sequence and local secondary structure have been found to serve as functionally conserved switches involved in viral IRES-driven translation and may be captured by identical cognate ligands. The RNA motifs described here constitute a new paradigm for ligandcaptured switches that differ from metabolite-sensing riboswitches with regard to their small size, as well as the intrinsic stability and structural definition of the constitutive conformational states. These viral RNA modules represent the simplest form of ligand-responsive mechanical switches in nucleic acids.

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“…Isis-11 was prepared as a mixture of enantiomers according to a previously published procedure with minor modifications. 33 The identity and purity of all the compounds were confirmed by mass spectrometry as well as 1 H-and 13 C-NMR spectroscopy. Full experimental details can be provided upon request.…”

Section: Methodsmentioning

confidence: 97%

“…29 In the IRES context, 2-aminobenzimidazole derivatives have also been shown to interact with the SLIIa structural element of the HCV-like IRES, 30,31 and to interfere with viral multiplication at low micromolar concentrations. 32,33 However, to the best of our knowledge, their potential to bind other types of IRES elements as well as cap-dependent translation has not been examined.…”

Section: Introductionmentioning

confidence: 99%

Local RNA flexibility perturbation of the IRES element induced by a novel ligand inhibits viral RNA translation

et al. 2015

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(2015) Local RNA flexibility perturbation of the IRES element induced by a novel ligand inhibits viral RNA translation, RNA Biology, 12:5, 555-568, DOI: 10.1080/15476286.2015 The internal ribosome entry site (IRES) element located at the 5´untranslated genomic region of various RNA viruses mediates cap-independent initiation of translation. Picornavirus IRES activity is highly dependent on both its structural organization and its interaction with host factors. Small molecules able to interfere with RNA function are valuable candidates for antiviral agents. Here we show that a small molecule based on benzimidazole (IRAB) inhibited foot-andmouth disease virus (FMDV) IRES-dependent protein synthesis in cells transfected with infectious RNA leading to a decrease of the virus titer, which was higher than that induced by a structurally related benzimidazole derivative. Interestingly, IRAB preferentially inhibited IRES-dependent translation in cell free systems in a dose-dependent manner. RNA structural analysis by SHAPE demonstrated an increased local flexibility of the IRES structure upon incubation with IRAB, which affected 3 stem-loops (SL) of domain 3. Fluorescence binding assays conducted with individual aminopurinelabeled oligoribonucleotides indicated that the SL3A binds IRAB (EC 50 18 mM). Taken together, the results derived from SHAPE reactivity and fluorescence binding assays suggested that the target site of IRAB within the FMDV IRES might be a folded RNA structure that involves the entire apical region of domain 3. Our data suggest that the conformational changes induced by this compound on a specific region of the IRES structure which is essential for its activity is, at least in part, responsible for the reduced IRES efficiency observed in cell free lysates and, particularly, in RNA-transfected cells.

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SAR by MS: Discovery of a New Class of RNA-Binding Small Molecules for the Hepatitis C Virus: Internal Ribosome Entry Site IIA Subdomain

Cited by 150 publications

References 26 publications

RETRACTED: Selection of cyclic peptide aptamers to HCV IRES RNA using mRNA display

RETRACTED: Selection of cyclic peptide aptamers to HCV IRES RNA using mRNA display

Functional conservation despite structural divergence in ligand-responsive RNA switches

Local RNA flexibility perturbation of the IRES element induced by a novel ligand inhibits viral RNA translation

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