The ProTide Prodrug Technology: Where Next?

Alanazi, Ashwag S.; James, Edward; Mehellou, Youcef

doi:10.1021/acsmedchemlett.8b00586

Cited by 51 publications

(59 citation statements)

References 11 publications

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“…In summary, these results demonstrate that the nucleotide analogues 2'-F,Me-UTP, 3'-F-dTTP, 3'-N 3 -dTTP, and TFV-DP are permanent terminators for the SARS-CoV-2 RdRp. Their prodrug versions (Sofosbuvir, 3'-F-5'-O-phosphoramidate dT nucleoside, 3'-N 3 -5'-O-phosphoramidate dT nucleoside, and TAF) are available or can be readily synthesized using the ProTide prodrug approach, 18 as shown in Fig. 1 a-d, and can be developed as therapeutics for COVID-19.…”

Section: Resultsmentioning

confidence: 99%

Nucleotide Analogues as Inhibitors of SARS-CoV-2 Polymerase

Chien

Anderson

Jockusch

et al. 2020

Preprint

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SARS-CoV-2, a member of the coronavirus family, is responsible for the current COVID-19 pandemic. Based on our analysis of hepatitis C virus and coronavirus replication, and the molecular structures and activities of viral inhibitors, we previously demonstrated that three nucleotide analogues inhibit the SARS-CoV RNA-dependent RNA polymerase (RdRp). Here, using polymerase extension experiments, we have demonstrated that the active triphosphate form of Sofosbuvir (a key component of the FDA approved hepatitis C drug EPCLUSA), is incorporated by SARS-CoV-2 RdRp, and blocks further incorporation. Using the same molecular insight, we selected the active triphosphate forms of three other anti-viral agents, Alovudine, AZT (an FDA approved HIV/AIDS drug) and Tenofovir alafenamide (TAF, an FDA approved drug for HIV and hepatitis B) for evaluation as inhibitors of SARS-CoV-2 RdRp. We demonstrated the ability of these three viral polymerase inhibitors, 3'-fluoro-3'-deoxythymidine triphosphate, 3'-azido-3'deoxythymidine triphosphate and Tenofovir diphosphate (the active triphosphate forms of Alovudine, AZT and TAF, respectively) to be incorporated by SARS-CoV-2 RdRp, where they also terminate further polymerase extension. These results offer a strong molecular basis for these nucleotide analogues to be evaluated as potential therapeutics for COVID-19.

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Section: Resultsmentioning

confidence: 99%

Nucleotide Analogues as Inhibitors of SARS-CoV-2 Polymerase

Chien

Anderson

Jockusch

et al. 2020

Preprint

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“…2 and S1. The phosphoramidate forms of prodrugs can be readily synthesized using the ProTide approach (Alanazi et al 2019). The RdRp of these coronaviruses, referred to as nsp12, and its two protein cofactors, nsp7 and nsp8, have been shown to be required for the processive polymerase activity of nsp12 in SARS-CoV (Subissi et al 2014;Kirchdoerfer and Ward 2019).…”

Section: Resultsmentioning

confidence: 99%

“…Their prodrug versions (shown in Fig. 2 and S1) are available or can be readily synthesized using the ProTide approach (Alanazi et al 2019). The prodrugs of several of these nucleoside triphosphate analogues (Ganciclovir/Valganciclovir, Cidofovir/Brincidofovir, Abacavir, Stavudine, and Entecavir) have been FDA approved for treatment of other viral infections and their toxicity profile is well established.…”

Section: Resultsmentioning

confidence: 99%

A Library of Nucleotide Analogues Terminate RNA Synthesis Catalyzed by Polymerases of Coronaviruses Causing SARS and COVID-19

Jockusch

Tao

et al. 2020

Preprint

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SARS-CoV-2, a member of the coronavirus family, is responsible for the current COVID-19 worldwide pandemic. We previously demonstrated that five nucleotide analogues inhibit the SARS-CoV-2 RNAdependent RNA polymerase (RdRp), including the active triphosphate forms of Sofosbuvir, Alovudine, Zidovudine, Tenofovir alafenamide and Emtricitabine. We report here the evaluation of a library of additional nucleoside triphosphate analogues with a variety of structural and chemical features as inhibitors of the RdRps of SARS-CoV and SARS-CoV-2. These features include modifications on the sugar (2' or 3' modifications, carbocyclic, acyclic, or dideoxynucleotides) or on the base. The goal is to identify nucleotide analogues that not only terminate RNA synthesis catalyzed by these coronavirus RdRps, but also have the potential to resist the viruses' exonuclease activity. We examined these nucleotide analogues with regard to their ability to be incorporated by the RdRps in the polymerase reaction and then prevent further incorporation. While all 11 molecules tested displayed incorporation, 6 exhibited immediate termination of the polymerase reaction (Carbovir triphosphate, Ganciclovir triphosphate, Stavudine triphosphate, Entecavir triphosphate, 3'-O-methyl UTP and Biotin-16-dUTP), 2 showed delayed termination (Cidofovir diphosphate and 2'-O-methyl UTP), and 3 did not terminate the polymerase reaction (2'-fluoro-dUTP, 2'-amino-dUTP and Desthiobiotin-16-UTP). The coronavirus genomes encode an exonuclease that apparently requires a 2'-OH group to excise mismatched bases at the 3'-terminus. In this study, all of the nucleoside triphosphate analogues we evaluated form Watson-Cricklike base pairs. All the nucleotide analogues which demonstrated termination either lack a 2'-OH, have a blocked 2'-OH, or show delayed termination. These nucleotides may thus have the potential to resist exonuclease activity, a property that we will investigate in the future. Furthermore, prodrugs of five of these nucleotide analogues (Brincidofovir/Cidofovir, Abacavir, Valganciclovir/Ganciclovir, Stavudine and Entecavir) are FDA approved for other viral infections, and their safety profile is well known. Thus, they can be evaluated rapidly as potential therapies for COVID-19.

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“…2b) are unmodified, but a cyano group at the 1' position serves to inhibit the RdRp in the active triphosphate form. In addition to the use of hydrophobic groups to mask the phosphate in the Protide-based prodrug strategy, 17 as with Sofosbuvir and Remdesivir, there are other classes of nucleoside prodrugs including those based on ester derivatives of the ribose hydroxyl groups to enhance cellular delivery. 18,19 The replication cycle of HCV 4 is very similar to that of the coronaviruses.…”

mentioning

confidence: 99%

Nucleotide Analogues as Inhibitors of SARS-CoV Polymerase

Kumar

et al. 2020

Preprint

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SARS-CoV-2, a member of the coronavirus family, has caused a global public health emergency. 1 Based on our analysis of hepatitis C virus and coronavirus replication, and the molecular structures and activities of viral inhibitors, we previously reasoned that the FDA-approved heptatitis C drug EPCLUSA (Sofosbuvir/Velpatasvir) should inhibit coronaviruses, including SARS-CoV-2. 2 Here, using model polymerase extension experiments, we demonstrate that the activated triphosphate form of Sofosbuvir is incorporated by low-fidelity polymerases and SARS-CoV RNA-dependent RNA polymerase (RdRp), and blocks further incorporation by these polymerases; the activated triphosphate form of Sofosbuvir is not incorporated by a host-like high-fidelity DNA polymerase. Using the same molecular insight, we selected two other anti-viral agents, Alovudine and AZT (an FDA approved HIV/AIDS drug) for evaluation as inhibitors of SARS-CoV RdRp. We demonstrate the ability of two HIV reverse transcriptase inhibitors, 3'fluoro-3'-deoxythymidine triphosphate and 3'-azido-3'-deoxythymidine triphosphate (the active triphosphate forms of Alovudine and AZT), to be incorporated by SARS-CoV RdRp where they also terminate further polymerase extension. Given the 98% amino acid similarity of the SARS-CoV and SARS-CoV-2 RdRps, we expect these nucleotide analogues would also inhibit the SARS-CoV-2 polymerase. These results offer guidance to further modify these nucleotide analogues to generate more potent broad-spectrum anticoronavirus agents.The recent appearance of a new coronaviral infection, COVID-19, in Wuhan, China, and its worldwide spread, has made international headlines. Already more than 3,000 deaths have been ascribed to this virus, and COVID-19 has reached near pandemic status. The virus has been isolated from the lower respiratory tracts of patients with pneumonia, sequenced and visualized by electron microscopy. 1 The virus, designated SARS-CoV-2, is a new member of the subgenus Sarbecovirus, in the Orthocoronavirinae subfamily, but is distinct from MERS-CoV and SARS-CoV. 1 The coronaviruses are single strand RNA viruses, sharing properties with other single-stranded RNA viruses such as hepatitis C virus (HCV), West Nile virus, Marburg virus, HIV virus, Ebola virus, dengue virus, and rhinoviruses. In particular, coronaviruses and HCV are both positive-sense single-strand RNA viruses, 3,4 and thus have a similar replication mechanism requiring a RNA-dependent RNA polymerase (RdRp).The coronavirus life cycle has been described. 3 Briefly, the virus enters the cell by endocytosis, is uncoated, and ORF1a and ORF1b of the positive strand RNA is translated to produce nonstructural protein precursors, including a cysteine protease and a serine protease; these further cleave the precursors to form mature, functional helicase and RNA-dependent RNA polymerase. A replication-transcription complex is then . CC-BY-NC

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The ProTide Prodrug Technology: Where Next?

Cited by 51 publications

References 11 publications

Nucleotide Analogues as Inhibitors of SARS-CoV-2 Polymerase

Nucleotide Analogues as Inhibitors of SARS-CoV-2 Polymerase

A Library of Nucleotide Analogues Terminate RNA Synthesis Catalyzed by Polymerases of Coronaviruses Causing SARS and COVID-19

Nucleotide Analogues as Inhibitors of SARS-CoV Polymerase

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