Nucleoside analogues for the treatment of coronavirus infections

Pruijssers, Andrea J.; Denison, Mark R.

doi:10.1016/j.coviro.2019.04.002

Cited by 174 publications

(185 citation statements)

References 49 publications

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“…S2B). In cell culture, these inhibitors often show EC 50 values in the higher micromolar range depending on the nature of the RNA virus (26,41,42). High concentrations of favipiravir and ribavirin were also required to reduce infection with SARS-CoV-2 (EC 50 ϭ 109.50 M and EC 50 ϭ 61.88 M, respectively) (33).…”

Section: Discussionmentioning

confidence: 99%

Remdesivir is a direct-acting antiviral that inhibits RNA-dependent RNA polymerase from severe acute respiratory syndrome coronavirus 2 with high potency

Gordon

Tchesnokov

Woolner

et al. 2020

Journal of Biological Chemistry

846

1,070

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Effective treatments for coronavirus disease 2019 (COVID-19) are urgently needed to control this current pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Replication of SARS-CoV-2 depends on the viral RNA-dependent RNA polymerase (RdRp), which is the likely target of the investigational nucleotide analogue remdesivir (RDV). RDV shows broad-spectrum antiviral activity against RNA viruses, and previous studies with RdRps from Ebola virus and Middle East respiratory syndrome coronavirus (MERS-CoV) have revealed that delayed chain termination is RDV's plausible mechanism of action. Here, we expressed and purified active SARS-CoV-2 RdRp composed of the nonstructural proteins nsp8 and nsp12. Enzyme kinetics indicated that this RdRp efficiently incorporates the active triphosphate form of RDV (RDV-TP) into RNA. Incorporation of RDV-TP at position i caused termination of RNA synthesis at position i؉3. We obtained almost identical results with SARS-CoV, MERS-CoV, and SARS-CoV-2 RdRps. A unique property of RDV-TP is its high selectivity over incorporation of its natural nucleotide counterpart ATP. In this regard, the triphosphate forms of 2-Cmethylated compounds, including sofosbuvir, approved for the management of hepatitis C virus infection, and the broad-acting antivirals favipiravir and ribavirin, exhibited significant deficits. Furthermore, we provide evidence for the target specificity of RDV, as RDV-TP was less efficiently incorporated by the distantly related Lassa virus RdRp, and termination of RNA synthesis was not observed. These results collectively provide a unifying, refined mechanism of RDV-mediated RNA synthesis inhibition in coronaviruses and define this nucleotide analogue as a direct-acting antiviral.

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Section: Discussionmentioning

confidence: 99%

Remdesivir is a direct-acting antiviral that inhibits RNA-dependent RNA polymerase from severe acute respiratory syndrome coronavirus 2 with high potency

Gordon

Tchesnokov

Woolner

et al. 2020

Journal of Biological Chemistry

846

1,070

View full text Add to dashboard Cite

show abstract

“…CoV RdRps are able to accommodate a wide variety of different chemical modifications of NAs (e.g., on the ribose, on the base, on both) 30 highlighting the A-G motifs. All structural models were made using Chimera 44 .…”

Section: Discussionmentioning

confidence: 99%

“…Remdesivir (GS-5734) is one of the few nucleotide analogues reported to be active against SARS-CoV (reviewed in 30 ). It carries a cyano group on the 1' position of the ribose (1'-CN) and a 4-aza-7,9dideazaadenosine nucleobase (pseudo-adenine) linked to the ribose by a C-C bond (Fig.…”

Section: Gs-441524-tp At the Nsp12 Active-sitementioning

confidence: 99%

Remdesivir and SARS-CoV-2: Structural requirements at both nsp12 RdRp and nsp14 Exonuclease active-sites

et al. 2020

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The rapid global emergence of SARS-CoV-2 has been the cause of significant health concern, highlighting the immediate need for antivirals. Viral RNA-dependent RNA polymerases (RdRp) play essential roles in viral RNA synthesis, and thus remains the target of choice for the prophylactic or curative treatment of several viral diseases, due to high sequence and structural conservation. To date, the most promising broad-spectrum class of viral RdRp inhibitors are nucleoside analogues (NAs), with over 25 approved for the treatment of several medically important viral diseases. However, Coronaviruses stand out as a particularly challenging case for NA drug design due to the presence of an exonuclease (ExoN) domain capable of excising incorporated NAs and thus providing resistance to many of these available antivirals. Here we use the available structures of the SARS-CoV RdRp and ExoN proteins, as well as Lassa virus N exonuclease to derive models of catalytically competent SARS-CoV-2 enzymes. We then map a promising NA candidate, GS-441524 (the active metabolite of Remdesivir) to the nucleoside active site of both proteins, identifying the residues important for nucleotide recognition, discrimination, and excision. Interestingly, GS-441524 addresses both enzyme active sites in a manner consistent with significant incorporation, delayed chain termination, and altered excision due to the ribose 1'-CN group, which may account for the increased antiviral effect compared to other available analogues. Additionally, we propose structural and function implications of two previously identified RdRp resistance mutations in relation to resistance against Remdesivir.This study highlights the importance of considering the balance between incorporation and excision properties of NAs between the RdRp and ExoN.

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“…4b, Supplementary Table 5). Coronavirus replication depends on availability of cellular nucleotide pools 20 . Compounds interfering with nucleic acid metabolism, such as ribavirin, have been used in the past to inhibit viral replication 21 .…”

Section: Kinetic Infection Proteome Profilingmentioning

confidence: 99%

Proteomics of SARS-CoV-2-infected host cells reveals therapy targets

Bojkova

Klann

Koch

et al. 2020

Nature

927

1,151

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A novel coronavirus was recently discovered and termed SARS-CoV-2. Human infection can cause coronavirus disease 2019 , which has been rapidly spreading around the globe 1,2 . SARS-CoV-2 shows some similarities to other coronaviruses. However, treatment options and a cellular understanding of SARS-CoV-2 infection are lacking. Here we identify the host cell pathways modulated by SARS-CoV-2 infection and show that inhibition of these pathways prevent viral replication in human cells. We established a human cell culture model for infection with SARS-CoV-2 clinical isolate. Employing this system, we determined the SARS-CoV-2 infection profile by translatome 3 and proteome proteomics at different times after infection. These analyses revealed that SARS-CoV-2 reshapes central cellular pathways, such as translation, splicing, carbon metabolism and nucleic acid metabolism. Small molecule inhibitors targeting these pathways prevented viral replication in cells. Our results reveal the cellular infection profile of SARS-CoV-2 and led to the identification of drugs inhibiting viral replication. We anticipate our results to guide efforts to understand the molecular mechanisms underlying host cell modulation upon SARS-CoV-2 infection. Furthermore, our findings provide insight for the development of therapy options for COVID-19.

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Nucleoside analogues for the treatment of coronavirus infections

Cited by 174 publications

References 49 publications

Remdesivir is a direct-acting antiviral that inhibits RNA-dependent RNA polymerase from severe acute respiratory syndrome coronavirus 2 with high potency

Remdesivir is a direct-acting antiviral that inhibits RNA-dependent RNA polymerase from severe acute respiratory syndrome coronavirus 2 with high potency

Remdesivir and SARS-CoV-2: Structural requirements at both nsp12 RdRp and nsp14 Exonuclease active-sites

Proteomics of SARS-CoV-2-infected host cells reveals therapy targets

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