The Translation Inhibitor Rocaglamide Targets a Bimolecular Cavity between eIF4A and Polypurine RNA

Iwasaki, Shigeo; Iwasaki, W.; Takahashi, Mari; Sakamoto, Ayako; Watanabe, Chiduru; Shichino, Yuichi; Floor, Stephen N.; Fujiwara, Koichi; Mito, Mari; Dodo, Kosuke; Sodeoka, Mikiko; Imataka, Hiroaki; Honma, Teruki; Fukuzawa, Kaori; Ito, Takuhiro; Ingolia, Nicholas T.

doi:10.1016/j.molcel.2018.11.026

Cited by 144 publications

(308 citation statements)

References 66 publications

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“…Based on a DALI search, RadD is partially similar in three‐dimensional structure to the HsdR subunit of the type I restriction enzyme from Vibrio vulnificus YJ016 (PDB: 3H1T), human eIF4A1 analog RocA, the prototypical DEAD‐box protein from Aglaia genus plants (PDB: 5ZC9), and XPB II from Sulfurisphaera tokodaii (PDB: 5TNU, unpublished work), with Z ‐scores of 18.3, 17.6, and 17.2, respectively . By comparing RadD with these three structures, we find that only RDs are common, and the other domains in the N‐terminal or C‐terminal are different (Supplemental figure S3, Supporting information).…”

Section: Resultsmentioning

confidence: 99%

Crystal structure of a novel ATPase RadD from Escherichia coli

et al. 2019

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The helicase superfamily 2 (SF2) proteins are involved in essentially every step in DNA and RNA metabolism. The radD (yejH) gene, which belongs to SF2, plays an important role in DNA repair. The RadD protein includes all seven conserved SF2 motifs and has shown ATPase activity. Here, we first reported the structure of RadD from Escherichia coli containing two RecA‐like domains, a zinc finger motif, and a C‐terminal domain. Based on the structure of RadD and other SF2 proteins, we then built a model of the RedD‐ATP complex.

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Section: Resultsmentioning

confidence: 99%

Crystal structure of a novel ATPase RadD from Escherichia coli

et al. 2019

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“…However, we also found differential activities for these two compounds, depending on the viral 5′-UTR used for the translation inhibition assays. As shown for RocA, clamping of RNA substrates onto eIF4A by CR-31-B (−) requires polypurine sequences (Iwasaki et al, 2019), whereas Silvestrol can also clamp polypurine-free viral RNA substrates, provided that a stable hairpin structure is present. The recently published crystal structure of human eIF4A in complex with a polypurine RNA substrate and RocA (Iwasaki et al, 2019) explains the observed polypurine dependency of RocA because only purines can efficient stack on the phenyl rings of RocA.…”

Section: Introductionmentioning

confidence: 86%

“…As shown for RocA, clamping of RNA substrates onto eIF4A by CR-31-B (−) requires polypurine sequences (Iwasaki et al, 2019), whereas Silvestrol can also clamp polypurine-free viral RNA substrates, provided that a stable hairpin structure is present. The recently published crystal structure of human eIF4A in complex with a polypurine RNA substrate and RocA (Iwasaki et al, 2019) explains the observed polypurine dependency of RocA because only purines can efficient stack on the phenyl rings of RocA. Although, further structure-based information is missing, we suggest that the dioxane moiety of Silvestrol can mediate polypurinefree RNA clamping onto eIF4A.…”

Section: Introductionmentioning

confidence: 86%

“…6A). However, in the VP30 5′-UTR, this pentapurine stretch is followed by a decapurine stretch that seems to be unstructured and thus predicted to enable RNA clamping (Iwasaki et al, 2019). Such a second purine stretch is absent in the VP35 5′-UTR.…”

Section: Analyses Of the 5′-utr-mediated Inhibitory Activities Of Silmentioning

confidence: 99%

“…Modelling of Silvestrol onto the surface structure of the human eIF4Apolypurine RNA complex Our reporter assay results indicated differences in the mode of action between Silvestrol and rocaglates lacking the dioxane moiety. Since no structural data from co-crystallization of Silvestrol, RNA and eIF4A are available, we modeled the structure of Silvestrol into the published eIF4A-polyAG structure surface (Iwasaki et al, 2019). By comparing the localization of RocA and Silvestrol, we found that the dioxane moiety of Silvestrol can completely cross the surface of the bound RNA substrate, thus enabling Silvestrol to make additional contacts e.g.…”

Section: Analyses Of the 5′-utr-mediated Inhibitory Activities Of Silmentioning

confidence: 99%

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Comparison of broad-spectrum antiviral activities of the synthetic rocaglate CR-31-B (−) and the eIF4A-inhibitor Silvestrol

et al. 2020

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Rocaglates, a class of natural compounds isolated from plants of the genus Aglaia, are potent inhibitors of translation initiation. They are proposed to form stacking interactions with polypurine sequences in the 5′untranslated region (UTR) of selected mRNAs, thereby clamping the RNA substrate onto eIF4A and causing inhibition of the translation initiation complex. Since virus replication relies on the host translation machinery, it is not surprising that the rocaglate Silvestrol has broad-spectrum antiviral activity. Unfortunately, synthesis of Silvestrol is sophisticated and time-consuming, thus hampering the prospects for further antiviral drug development. Here, we present the less complex structured synthetic rocaglate CR-31-B (−) as a novel compound with potent broad-spectrum antiviral activity in primary cells and in an ex vivo bronchial epithelial cell system. CR-31-B (−) inhibited the replication of corona-, Zika-, Lassa-, Crimean Congo hemorrhagic fever viruses and, to a lesser extent, hepatitis E virus (HEV) at non-cytotoxic low nanomolar concentrations. Since HEV has a polypurine-free 5′-UTR that folds into a stable hairpin structure, we hypothesized that RNA clamping by Silvestrol and its derivatives may also occur in a polypurine-independent but structure-dependent manner. Interestingly, the HEV 5′-UTR conferred sensitivity towards Silvestrol but not to CR-31-B (−). However, if an exposed polypurine stretch was introduced into the HEV 5′-UTR, CR-31-B (−) became an active inhibitor comparable to Silvestrol. Moreover, thermodynamic destabilization of the HEV 5′-UTR led to reduced translational inhibition by Silvestrol, suggesting differences between rocaglates in their mode of action, most probably by engaging Silvestrol's additional dioxane moiety.

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Challenges for the Discovery of Non‐Covalent WRN Helicase Inhibitors

Heuser,

Abdul Rahman,

Bechter

et al. 2024

ChemMedChem

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The Werner Syndrome RecQ helicase (WRN) is a synthetic lethal target of interest for the treatment of cancers with microsatellite instability (MSI). Different hit finding approaches were initially tested. The identification of WRN inhibitors proved challenging due to a high propensity for artefacts via protein interference, i.e., hits inhibiting WRN enzymatic activities through multiple, unspecific mechanisms. Previously published WRN Helicase inhibitors (ML216, NSC19630 or NSC617145) were characterized in an extensive set of biochemical and biophysical assays and could be ruled out as specific WRN helicase probes. More innovative screening strategies need to be developed for successful drug discovery of non‐covalent WRN helicase inhibitors.

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The Translation Inhibitor Rocaglamide Targets a Bimolecular Cavity between eIF4A and Polypurine RNA

Abstract: Highlights d Crystallographic structure of the human eIF4A1,AMPPNP,RocA,polypurine RNA complex d Direct base recognition by RocA induces polypurine RNA selectivity on eIF4A1 d Natural amino acid substitutions found in Aglaia eIF4As provide self-resistance to RocA

Cited by 144 publications

References 66 publications

Crystal structure of a novel ATPase RadD from Escherichia coli

Crystal structure of a novel ATPase RadD from Escherichia coli

Comparison of broad-spectrum antiviral activities of the synthetic rocaglate CR-31-B (−) and the eIF4A-inhibitor Silvestrol

Challenges for the Discovery of Non‐Covalent WRN Helicase Inhibitors

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