Amilorides inhibit SARS-CoV-2 replication in vitro by targeting RNA structures

Zafferani, Martina; Haddad, Christina; Luo, Le; Davila‐Calderon, Jesse; Yuan-Chiu, Liang; Mugisha, Christian Shema; Monaghan, Adeline G; Kennedy, Andrew; Yesselman, Joseph D.; Gifford, Robert R; Tai, Andrew W.; Kutluay, Sebla B.; Li, Meiling; Brewer, Gary; Tolbert, Blanton S.; Hargrove, Amanda E.

doi:10.1101/2020.12.05.409821

“…Since early 2020, enormous scientific efforts are geared structured RNAe lements in SCoV-2 have been reported. [8,21,22] Here,w er eport ah olistic NMR-based screening campaign investigating previously identified structured RNA elements. [23] We determine the druggability of these regulatory RNAe lements by NMR-based screening, [24] using ap reviously implemented workflow.…”

Section: Introductionmentioning

confidence: 99%

Exploring the Druggability of Conserved RNA Regulatory Elements in the SARS‐CoV‐2 Genome

Sreeramulu

¹

,

Richter

²

,

Berg

³

et al. 2021

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SARS‐CoV‐2 contains a positive single‐stranded RNA genome of approximately 30 000 nucleotides. Within this genome, 15 RNA elements were identified as conserved between SARS‐CoV and SARS‐CoV‐2. By nuclear magnetic resonance (NMR) spectroscopy, we previously determined that these elements fold independently, in line with data from in vivo and ex‐vivo structural probing experiments. These elements contain non‐base‐paired regions that potentially harbor ligand‐binding pockets. Here, we performed an NMR‐based screening of a poised fragment library of 768 compounds for binding to these RNAs, employing three different 1H‐based 1D NMR binding assays. The screening identified common as well as RNA‐element specific hits. The results allow selection of the most promising of the 15 RNA elements as putative drug targets. Based on the identified hits, we derive key functional units and groups in ligands for effective targeting of the RNA of SARS‐CoV‐2.

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“…[19,20] Currently,h owever,o nly few experimental screenings for ligands directly targeting the structured RNAe lements in SCoV-2 have been reported. [8,21,22] Here,w er eport ah olistic NMR-based screening campaign investigating previously identified structured RNA elements. [23] We determine the druggability of these regulatory RNAe lements by NMR-based screening, [24] using ap reviously implemented workflow.…”

Section: Introductionmentioning

confidence: 99%

Exploring the Druggability of Conserved RNA Regulatory Elements in the SARS‐CoV‐2 Genome

Sreeramulu

¹

,

Richter

²

,

Berg

³

et al. 2021

View full text Add to dashboard Cite

SARS‐CoV‐2 contains a positive single‐stranded RNA genome of approximately 30 000 nucleotides. Within this genome, 15 RNA elements were identified as conserved between SARS‐CoV and SARS‐CoV‐2. By nuclear magnetic resonance (NMR) spectroscopy, we previously determined that these elements fold independently, in line with data from in vivo and ex‐vivo structural probing experiments. These elements contain non‐base‐paired regions that potentially harbor ligand‐binding pockets. Here, we performed an NMR‐based screening of a poised fragment library of 768 compounds for binding to these RNAs, employing three different 1H‐based 1D NMR binding assays. The screening identified common as well as RNA‐element specific hits. The results allow selection of the most promising of the 15 RNA elements as putative drug targets. Based on the identified hits, we derive key functional units and groups in ligands for effective targeting of the RNA of SARS‐CoV‐2.

show abstract

De novo3D models of SARS-CoV-2 RNA elements from consensus experimental secondary structures

Rangan

¹

,

Watkins

²

,

Chacón

³

et al. 2021

Nucleic Acids Research

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The rapid spread of COVID-19 is motivating development of antivirals targeting conserved SARS-CoV-2 molecular machinery. The SARS-CoV-2 genome includes conserved RNA elements that offer potential small-molecule drug targets, but most of their 3D structures have not been experimentally characterized. Here, we provide a compilation of chemical mapping data from our and other labs, secondary structure models, and 3D model ensembles based on Rosetta's FARFAR2 algorithm for SARS-CoV-2 RNA regions including the individual stems SL1-8 in the extended 5′ UTR; the reverse complement of the 5′ UTR SL1-4; the frameshift stimulating element (FSE); and the extended pseudoknot, hypervariable region, and s2m of the 3′ UTR. For eleven of these elements (the stems in SL1–8, reverse complement of SL1–4, FSE, s2m and 3′ UTR pseudoknot), modeling convergence supports the accuracy of predicted low energy states; subsequent cryo-EM characterization of the FSE confirms modeling accuracy. To aid efforts to discover small molecule RNA binders guided by computational models, we provide a second set of similarly prepared models for RNA riboswitches that bind small molecules. Both datasets (‘FARFAR2-SARS-CoV-2’, https://github.com/DasLab/FARFAR2-SARS-CoV-2; and ‘FARFAR2-Apo-Riboswitch’, at https://github.com/DasLab/FARFAR2-Apo-Riboswitch’) include up to 400 models for each RNA element, which may facilitate drug discovery approaches targeting dynamic ensembles of RNA molecules.

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Amilorides inhibit SARS-CoV-2 replication in vitro by targeting RNA structures

Cited by 6 publications

References 51 publications

Exploring the Druggability of Conserved RNA Regulatory Elements in the SARS‐CoV‐2 Genome

Exploring the Druggability of Conserved RNA Regulatory Elements in the SARS‐CoV‐2 Genome

Exploring the Druggability of Conserved RNA Regulatory Elements in the SARS‐CoV‐2 Genome

De novo3D models of SARS-CoV-2 RNA elements from consensus experimental secondary structures

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