IRES-targeting small molecule inhibits enterovirus 71 replication via allosteric stabilization of a ternary complex

Jesse Davila-Calderon,Neeraj N Patwardhan,Zhengguo Cai,Gary Brewer,Andrew Sugarman,Liang-Yuan Chiu,Srinivasa R Penutmutchu,Blanton S Tolbert,Mei-Ling Li,Amanda E Hargrove

doi:10.1038/s41467-020-18594-3

Jesse Davila-Calderon, Neeraj N Patwardhan + Show 8 more

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https://doi.org/10.1038/s41467-020-18594-3

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Enterovirus 71 (EV71) poses serious threats to human health, particularly in Southeast Asia, and no drugs or vaccines are available. Previous work identified the stem loop II structure of the EV71 internal ribosomal entry site as vital to viral translation and a potential target. After screening an RNA-biased library using a peptide-displacement assay, we identify DMA-135 as a dose-dependent inhibitor of viral translation and replication with no significant toxicity in cell-based studies. Structural, biophysical, and biochemical characterization support an allosteric mechanism in which DMA-135 induces a conformational change in the RNA structure that stabilizes a ternary complex with the AUF1 protein, thus repressing translation. This mechanism is supported by pull-down experiments in cell culture. These detailed studies establish enterovirus RNA structures as promising drug targets while revealing an approach and mechanism of action that should be broadly applicable to functional RNA targeting.

Highlights

Enterovirus 71 (EV71) poses serious threats to human health, in Southeast Asia, and no drugs or vaccines are available
To identify ligands for the EV71 SLII domain, a panel of RNAtargeted small molecule (SM) was screened against the native EV71 SLII domain using a fluorescent indicator displacement (FID) assay
We report a comprehensive study that combined SM screening, biophysics, and virological assays to successfully identify a SM (DMA-135) that targets the internal ribosome entry site (IRES) domain of EV71 to inhibit its replication in cell culture

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Enterovirus 71 (EV71) poses serious threats to human health, in Southeast Asia, and no drugs or vaccines are available. DMA-135 binds through the bulge of SLII and induces a change in the local stacking patterns at positions 133–135 such that the bases are unstacked and dynamic within the context of the complex (Fig. 5a, b). This difference is consistent with the observation that DMA-135 changes the local stacking interactions of the bulge (Fig. 5a) such that this leads to a reorientation of the SLII helices within the complex.

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