Protein-primed RNA synthesis in SARS-CoVs and structural basis for inhibition by AT-527

Shannon, Ashleigh; Fattorini, Véronique; Sama, Bhawna; Selisko, Barbara; Feracci, Mikaël; Falcou, Camille; Gauffre, Pierre; Kazzi, Priscila El; Decroly, Étienne; Rabah, Nadia; Alvarez, Karine; Eydoux, Cécilia; Guillemot, Jean‐Claude; Debart, Françoise; Vasseur, Jean‐Jacques; Noël, Mathieu; Moussa, Adel; Good, Steven S.; Lin, Kai; Sommadossi, Jean‐Pierre; Zhu, Y.; Yan, Xiaodong; Shi, Hui; Ferrón, François; Canard, Bruno

doi:10.1101/2021.03.23.436564

Cited by 19 publications

(29 citation statements)

References 42 publications

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“…The active triphosphate form of AT-527 is structurally similar to that of Sofosbuvir with the only difference being that it has a guanine base in place of uracil. AT-527 inhibits SARS-CoV-2 by targeting both the RdRp activity and the Nidovirus RdRp-associated nucleotidyltransferase (NiRAN) activity of nsp12, which are essential for viral RNA replication and transcription 47 . AT-527 is currently in COVID-19 clinical trials.…”

Section: Discussionmentioning

confidence: 99%

Combination of Antiviral Drugs to Inhibit SARS-CoV-2 Polymerase and Exonuclease as Potential COVID-19 Therapeutics

Wang

Sacramento

Jockusch

et al. 2021

Preprint

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SARS-CoV-2 has an exonuclease-based proofreader, which removes nucleotide inhibitors such as Remdesivir that are incorporated into the viral RNA during replication, reducing the efficacy of these drugs for treating COVID-19. Combinations of inhibitors of both the viral RNA-dependent RNA polymerase and the exonuclease could overcome this deficiency. Here we report the identification of hepatitis C virus NS5A inhibitors Pibrentasvir and Ombitasvir as SARS-CoV-2 exonuclease inhibitors. In the presence of Pibrentasvir, RNAs terminated with the active forms of the prodrugs Sofosbuvir, Remdesivir, Favipiravir, Molnupiravir and AT-527 were largely protected from excision by the exonuclease, while in the absence of Pibrentasvir, there was rapid excision. Due to its unique structure, Tenofovir-terminated RNA was highly resistant to exonuclease excision even in the absence of Pibrentasvir. Viral cell culture studies also demonstrate significant synergy using this combination strategy. This study supports the use of combination drugs that inhibit both the SARS-CoV-2 polymerase and exonuclease for effective COVID-19 treatment.

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Section: Discussionmentioning

confidence: 99%

Combination of Antiviral Drugs to Inhibit SARS-CoV-2 Polymerase and Exonuclease as Potential COVID-19 Therapeutics

Wang

Sacramento

Jockusch

et al. 2021

Preprint

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“…One major similarity is already known between these virus groups: namely, the main protease and 3 C protease in enteroviruses. In addition, very recently, it was discovered that there may be similarities in the mechanisms to initiate viral RNA synthesis by covalently modifying selected non-structural proteins [ 40 , 41 ]. We thus focus in the next chapter on these similarities, and what is known from wet lab studies with potential drugs targeting both groups.…”

Section: Similarities Between Coronaviruses and Enterovirusesmentioning

confidence: 99%

Enteroviruses and coronaviruses: similarities and therapeutic targets

Marjomäki

Kalander

Hellman

et al. 2021

Expert Opinion on Therapeutic Targets

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Introduction : Enteroviruses are common viruses causing a huge number of acute and chronic infections and producing towering economic costs. Similarly, coronaviruses cause seasonal mild infections, epidemics, and even pandemics and can lead to severe respiratory symptoms. It is important to develop broadly acting antiviral molecules to efficiently tackle the infections caused by thes. Areas covered : This review illuminates the differences and similarities between enteroviruses and coronaviruses and examines the most appealing therapeutic targets to combat both virus groups. Publications of both virus groups and deposited structures discovered through PubMed to March 2021 for viral proteases have been evaluated. Expert opinion : The main protease of coronaviruses and enteroviruses share similarities in their structure and function. These proteases process their viral polyproteins and thus drugs that bind to the active site have potential to target both virus groups. It is important to develop drugs that target more evolutionarily conserved processes and proteins. Moreover, it is a wise strategy to concentrate on processes that are similar between several virus families.

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“…The NiRAN has been previously shown to mediate the covalent transfer of NMPs (13) to various cofactor proteins (15)(16)(17). UTP is the preferred substrate for cofactor labeling.…”

Section: At-9010 Inhibits Nsp9 and Nsp8 Umpylationmentioning

confidence: 99%

“…When provided at equimolar concentrations to UTP, nsp9-UMPylation is inhibited ~85-90% by both STP and AT-9010 for the SARS-CoV-2 complex, showing both drugs outcompete UTP for NiRAN-binding. Nsp8 has additionally been shown to act as a substrate for NiRAN-mediated UMPylation by the CoV RTC (15,17). Interestingly, AT-9010 is ~4-5-fold more efficient at blocking nsp8 labeling than the uracil equivalent STP (Extended Data Fig.…”

Section: At-9010 Inhibits Nsp9 and Nsp8 Umpylationmentioning

confidence: 99%

“…Among these is the Nidovirus RdRp-Associated Nucleotidyltransferase (NiRAN) N-terminus domain of nsp12, just upstream of the RdRp (13). The NiRAN is structurally related to the pseudo-kinase family of enzymes (14), and has been shown to mediate the covalent transfer of nucleoside monophosphates (NMP) to viral cofactor proteins nsp7, nsp8 and nsp9 (15)(16)(17). However, the role of this activity in the viral life-cycle remains unknown.…”

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confidence: 99%

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A dual mechanism of action of AT-527 against SARS-CoV-2 polymerase

Canard

Shannon

Fattorini

et al. 2021

Preprint

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A worldwide effort is ongoing to discover drugs against the Severe Acute Respiratory Syndrome coronavirus type 2 (SARS-CoV-2), which has so far caused >3.5 million fatalities (https://covid19.who.int/). The virus essential RNA-dependent RNA polymerase complex is targeted by several nucleoside/tide analogues whose mechanisms of action and clinical potential are currently evaluated. The guanosine analogue AT-527, a double prodrug of its 5'-triphosphate AT-9010, is currently in phase III clinical trials as a COVID19 treatment. Here we report the cryo-EM structure at 2.98 Å resolution of the SARS-CoV-2 nsp12-nsp7-(nsp8)2 complex with RNA showing AT-9010 bound at three sites of nsp12. At the RdRp active-site, one AT-9010 is incorporated into the RNA product. Its 2'-methyl group prevents correct alignment of a second AT-9010 occupying the incoming NTP pocket. The 2'-F, 2'-methyl 3'-OH ribose scaffold explains the non-obligate RNA chain-termination potency of this NA series for both HCV NS5 and SARS-CoV RTCs. A third AT-9010 molecule 5'-diphosphate binds to a coronavirus-specific pocket in the nsp12 N-terminus NiRAN domain, a SelO pseudo-kinase structural and functional homologue. This unique binding mode impedes NiRAN-mediated UMPylation of SARS-CoV-2 nsp8 and nsp9 proteins. Our results suggest a mechanism of action for AT-527 in line with a therapeutic use for COVID19.

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Protein-primed RNA synthesis in SARS-CoVs and structural basis for inhibition by AT-527

Cited by 19 publications

References 42 publications

Combination of Antiviral Drugs to Inhibit SARS-CoV-2 Polymerase and Exonuclease as Potential COVID-19 Therapeutics

Combination of Antiviral Drugs to Inhibit SARS-CoV-2 Polymerase and Exonuclease as Potential COVID-19 Therapeutics

Enteroviruses and coronaviruses: similarities and therapeutic targets

A dual mechanism of action of AT-527 against SARS-CoV-2 polymerase

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