Structural Basis for the Inhibition of the RNA-Dependent RNA Polymerase from SARS-CoV-2 by Remdesivir

Yin, Wanchao; Mao, Chunyou; Luan, Xiaodong; Shen, Dan‐Dan; Shen, Qingya; Su, Haixia; Wang, Xiaoxi; Zhou, Fulai; Zhao, Wenfeng; Gao, Minqi; Chang, Shenghai; Xie, Yuanchao; Tian, Guanghui; Jiang, He‐wei; Tao, Sheng-Ce; Shen, Jingshan; Jiang, Yi; Jiang, Hualiang; Xu, Yechun; Zhang, Shuyang; Zhang, Yan; Xu, Hao

doi:10.1101/2020.04.08.032763

Cited by 58 publications

(50 citation statements)

References 43 publications

(34 reference statements)

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“…Moreover, protein concentrations in the in vitro reactions may be higher than in cell culture systems. Together, these points mean that RNA synthesis inhibitors can show better efficacy in vivo than in vitro ; for example, the nucleotide analogue remdesivir-triphosphate requires a concentration of 100 µM to inhibit SARS-CoV-2 nsp7/8/12 activity in vitro , but remdesivir has an IC 50 of 0.77µM in cell culture(15, 20).…”

Section: Discussionmentioning

confidence: 99%

“…However, due to the SARS-CoV-2 RTC possessing error correcting exonuclease activity, the potential susceptibility of nsp12 to existing nucleoside analogues may not be sufficient to inhibit the SARS-CoV-2 RTC(13). Remdesivir has been shown to inhibit the SARS-CoV-2 nsp7/8/12 complex and not be excised by the nsp14 exonuclease, and other nucleoside analogue drugs have been suggested as therapeutic candidates(14, 15). However, there are currently no drugs licensed to treat SARS-CoV-2 infection, or any small molecule inhibitors known that could circumvent the nsp14 exonuclease activity.…”

Section: Introductionmentioning

confidence: 99%

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Enisamium is a small molecule inhibitor of the influenza A virus and SARS-CoV-2 RNA polymerases

Walker

Fan

Keown

et al. 2020

Preprint

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Influenza A virus and coronavirus strains cause a mild to severe respiratory disease that can result in death. Although vaccines exist against circulating influenza A viruses, such vaccines are ineffective against emerging pandemic influenza A viruses. Currently, no vaccine exists against coronavirus infections, including pandemic SARS-CoV-2, the causative agent of the Coronavirus Disease 2019 (COVID-19). To combat these RNA virus infections, alternative antiviral strategies are needed. A key drug target is the viral RNA polymerase, which is responsible for viral RNA synthesis. In January 2020, the World Health Organisation identified enisamium as a candidate therapeutic against SARS-CoV-2. Enisamium is an isonicotinic acid derivative that is an inhibitor of multiple influenza B and A virus strains in cell culture and clinically approved in 11 countries. Here we show using in vitro assays that enisamium and its putative metabolite, VR17-04, inhibit the activity of the influenza virus and the SARS-CoV-2 RNA polymerase. VR17-04 displays similar efficacy against the SARS-CoV-2 RNA polymerase as the nucleotide analogue remdesivir triphosphate. These results suggest that enisamium is a broad-spectrum small molecule inhibitor of RNA virus RNA synthesis, and implicate it as a possible therapeutic option for treating SARS-CoV-2 infection. Unlike remdesivir, enisamium does not require intravenous administration which may be advantageous for the development of COVID-19 treatments outside a hospital setting.ImportanceInfluenza A virus and SARS-CoV-2 are respiratory viruses capable of causing pandemics, and the latter is responsible for the Coronavirus Disease 2019 (COVID-19) pandemic. Both viruses encode RNA polymerases which transcribe their RNA genomes and are important targets for antiviral drugs including remdesivir. Here, we show that the antiviral drug enisamium inhibits the RNA polymerases of both influenza A virus and SARS-CoV-2. Furthermore, we show that a putative metabolite of enisamium is a more potent inhibitor, inhibiting the SARS-CoV-2 RNA polymerase with similar efficiency to remdesivir. Our data offer insight into the mechanism of action for enisamium, and implicate it as a broad-spectrum antiviral which could be used in the treatment of SARS-CoV-2 infection.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Enisamium is a small molecule inhibitor of the influenza A virus and SARS-CoV-2 RNA polymerases

Walker

Fan

Keown

et al. 2020

Preprint

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“…We tested 136 BSAAs against SARS-CoV-2 in VERO-E6 cells. Remdesivir was included as a positive control (Yin et al, 2020). Seven different concentrations of the compounds were added to virus-infected cells.…”

Section: Repurposing Safe-in-man Bsaasmentioning

confidence: 99%

Potential antiviral options against SARS-CoV-2 infection

Ianevski

Yao

Fenstad

et al. 2020

Preprint

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As of May 2020, the number of people infected with SARS-CoV-2 continues to skyrocket, with more than 4,5 million cases worldwide. Both the World Health Organization (WHO) and United Nations (UN) has highlighted the need for better control of SARS-CoV-2 infections. Developing novel virus-specific vaccines, monoclonal antibodies and antiviral drugs against SARS-CoV-2 can be time-consuming and costly. Convalescent plasma and safe-in-man broad-spectrum antivirals (BSAAs) are readily available treatment options. Here we developed a neutralization assay using SARS-CoV-2 virus and monkey Vero-E6 cells. We identified most potent sera from recovered patients for treatment of SARS-CoV-2-infected patients. We also screened 136 safe-in-man broad-spectrum antivirals against SARS-CoV-2 infection in Vero-E6 cells and identified antiviral activity of nelfinavir, salinomycin, amodiaquine, obatoclax, emetine and homoharringtonine. We found that combinations of virus-directed drug nelfinavir with host-directed drugs, such as salinomycin, amodiaquine, obatoclax, emetine and homoharringtonine exhibit synergistic effect against SARS-CoV-2 in vitro. Finally, we developed a website to disseminate the knowledge on available and emerging treatments of COVID-19.

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“…Whereas the core structures appear to be very similar, we additionally observe exiting RNA and novel nsp8 extensions that are implicated in enzyme processivity. The other study suggested that remdesivir functions as an immediate RNA chain terminator 24 . However, this contradicts previous biochemistry 10, 25 that showed that remdesivir causes delayed chain termination after the addition of several more nucleotides.…”

mentioning

confidence: 93%

“…When our study was about to be completed, a manuscript became available that also describes a structure of a SARS-CoV-2 RdRp-RNA complex 24 . Whereas the core structures appear to be very similar, we additionally observe exiting RNA and novel nsp8 extensions that are implicated in enzyme processivity.…”

mentioning

confidence: 99%

Structure of replicating SARS-CoV-2 polymerase

Hillen

Kokić

Farnung

et al. 2020

Preprint

191

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The coronavirus SARS-CoV-2 uses an RNA-dependent RNA polymerase (RdRp) for the replication of its genome and the transcription of its genes. Here we present the cryo-electron microscopic structure of the SARS-CoV-2 RdRp in its replicating form. The structure comprises the viral proteins nsp12, nsp8, and nsp7, and over two turns of RNA template-product duplex. The active site cleft of nsp12 binds the first turn of RNA and mediates RdRp activity with conserved residues. Two copies of nsp8 bind to opposite sides of the cleft and position the RNA duplex as it exits. Long helical extensions in nsp8 protrude along exiting RNA, forming positively charged 'sliding poles' that may enable processive replication of the long coronavirus genome. Our results will allow for a detailed analysis of the inhibitory mechanisms used by antivirals such as remdesivir, which is currently in clinical trials for the treatment of coronavirus disease 2019 (COVID-19).

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Structural Basis for the Inhibition of the RNA-Dependent RNA Polymerase from SARS-CoV-2 by Remdesivir

Cited by 58 publications

References 43 publications

Enisamium is a small molecule inhibitor of the influenza A virus and SARS-CoV-2 RNA polymerases

Enisamium is a small molecule inhibitor of the influenza A virus and SARS-CoV-2 RNA polymerases

Potential antiviral options against SARS-CoV-2 infection

Structure of replicating SARS-CoV-2 polymerase

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