Nucleoside analogues for the treatment of coronavirus infections

Andrea J Pruijssers, Mark R Denison, Andrea J Pruijssers, Mark R Denison

Abstract

Recent outbreaks of SARS-Coronavirus and MERS-Coronavirus (CoV) have heightened awareness about the lack of vaccines or antiviral compounds approved for prevention or treatment of human or potential zoonotic CoVs. Anti-CoV drug development has long been challenged by the activity of a 3' to 5' proofreading exoribonuclease unique to CoVs. Recently, a promising nucleoside analogue with broad-spectrum activity against CoVs has been identified. This review will discuss progress made in the development of antiviral nucleoside and nucleotide analogues targeting viral RNA synthesis as effective therapeutics against CoV infections and propose promising strategies for combination therapy.

Copyright © 2019. Published by Elsevier B.V.

Figures

Figure 1
Figure 1
Mechanisms of inhibition by nucleoside and nucleotide analogues. Schematic representation illustrates normal replication by the RdRp (blue sphere), premature chain termination caused by an obligate chain terminator, reduced replication fidelity due to mutagen incorporation, and depletion of pools of naturally occurring nucleotides.

References

    1. Su S., Wong G., Shi W., Liu J., Lai A.C.K., Zhou J., Liu W., Bi Y., Gao G.F. Epidemiology, genetic recombination, and pathogenesis of coronaviruses. Trends Microbiol. 2016;24:490–502.
    1. Revised U.S. Surveillance Case Definition for Severe Acute Respiratory Syndrome (SARS) and Update on SARS Cases — United States and Worldwide, December 2003. [date unknown].
    1. WHO | Middle East respiratory syndrome coronavirus (MERS-CoV).WHO [date unknown.
    1. Arabi Y.M., Balkhy H.H., Hayden F.G., Bouchama A., Luke T., Baillie J.K., Al-Omari A., Hajeer A.H., Senga M., Denison M.R. Middle east respiratory syndrome. N Engl J Med. 2017;376:584–594.
    1. Luo C.-M., Wang N., Yang X.-L., Liu H.-Z., Zhang W., Li B., Hu B., Peng C., Geng Q.-B., Zhu G.-J. Discovery of novel bat coronaviruses in South China that use the same receptor as middle east respiratory syndrome coronavirus. J Virol. 2018;92
    1. Chu H., Chan C.-M., Zhang X., Wang Y., Yuan S., Zhou J., Au-Yeung R.K.-H., Sze K.-H., Yang D., Shuai H. Middle east respiratory syndrome coronavirus and bat coronavirus HKU9 both can utilize GRP78 for attachment onto host cells. J Biol Chem. 2018;293:11709–11726.
    1. Modjarrad K., Moorthy V.S., Ben Embarek P., Van Kerkhove M., Kim J., Kieny M.-P. A roadmap for MERS-CoV research and product development: report from a world health organization consultation. Nat Med. 2016;22:701–705.
    1. Brende B., Farrar J., Gashumba D., Moedas C., Mundel T., Shiozaki Y., Vardhan H., Wanka J., Røttingen J.-A. CEPI-a new global R&D organisation for epidemic preparedness and response. Lancet Lond Engl. 2017;389:233–235.
    1. Mehand M.S., Al-Shorbaji F., Millett P., Murgue B. The WHO R&D blueprint: 2018 review of emerging infectious diseases requiring urgent research and development efforts. Antiviral Res. 2018:63–67.
    1. Perales C., Domingo E. Antiviral strategies based on lethal mutagenesis and error threshold. Curr Top Microbiol Immunol. 2016;392:323–339.
    1. Eckerle L.D., Lu X., Sperry S.M., Choi L., Denison M.R. High fidelity of murine hepatitis virus replication is decreased in nsp14 exoribonuclease mutants. J Virol. 2007;81:12135–12144.
    1. Smith E.C., Blanc H., Vignuzzi M., Denison M.R. Coronaviruses lacking exoribonuclease activity are susceptible to lethal mutagenesis: evidence for proofreading and potential therapeutics. PLoS Pathog. 2013;9
    1. Ferron F., Subissi L., Silveira De Morais A.T., Le N.T.T., Sevajol M., Gluais L., Decroly E., Vonrhein C., Bricogne G., Canard B. Structural and molecular basis of mismatch correction and ribavirin excision from coronavirus RNA. Proc Natl Acad Sci U S A. 2018;115:E162–E171.
    1. Tejero H., Montero F., Nuño J.C. Theories of lethal mutagenesis: from error catastrophe to lethal defection. In: Domingo E., Schuster P., editors. Quasispecies: From Theory to Experimental Systems. Springer International Publishing; 2016. pp. 161–179.
    1. Te H.S., Randall G., Jensen D.M. Mechanism of action of ribavirin in the treatment of chronic hepatitis C. Gastroenterol Hepatol. 2007;3:218–225.
    1. Jordan P.C., Stevens S.K., Deval J. Nucleosides for the treatment of respiratory RNA virus infections. Antivir Chem Chemother. 2018;26
    1. Sheahan T.P., Sims A.C., Graham R.L., Menachery V.D., Gralinski L.E., Case J.B., Leist S.R., Pyrc K., Feng J.Y., Trantcheva I. Broad-spectrum antiviral GS-5734 inhibits both epidemic and zoonotic coronaviruses. Sci Transl Med. 2017;9
    2. Although nucleoside analogs have been shown effective against many RNA viruses, many do not potently inhibit CoVs. This study demonstrates potent activity of nucleoside analogue GS-5734 against a diverse spectrum of human and zoonotic CoV in human airway epithelial cultures and in mouse models of SARS-CoV and MERS-CoV disease. This is the first study to demonstrate activity of GS-5734 against CoVs.

    1. Saijo M., Morikawa S., Fukushi S., Mizutani T., Hasegawa H., Nagata N., Iwata N., Kurane I. Inhibitory effect of mizoribine and ribavirin on the replication of severe acute respiratory syndrome (SARS)-associated coronavirus. Antiviral Res. 2005;66:159–163.
    1. Feld J.J., Hoofnagle J.H. Mechanism of action of interferon and ribavirin in treatment of hepatitis C. Nature. 2005;436:967–972.
    1. Cameron C.E., Castro C. The mechanism of action of ribavirin: lethal mutagenesis of RNA virus genomes mediated by the viral RNA-dependent RNA polymerase. Curr Opin Infect Dis. 2001;14:757–764.
    1. Chan J.F.W., Chan K.-H., Kao R.Y.T., To K.K.W., Zheng B.-J., Li C.P.Y., Li P.T.W., Dai J., Mok F.K.Y., Chen H. Broad-spectrum antivirals for the emerging Middle East respiratory syndrome coronavirus. J Infect. 2013;67:606–616.
    1. Barnard D.L., Day C.W., Bailey K., Heiner M., Montgomery R., Lauridsen L., Winslow S., Hoopes J., JK-K Li, Lee J. Enhancement of the infectivity of SARS-CoV in BALB/c mice by IMP dehydrogenase inhibitors, including ribavirin. Antiviral Res. 2006;71:53–63.
    1. Booth C.M., Matukas L.M., Tomlinson G.A., Rachlis A.R., Rose D.B., Dwosh H.A., Walmsley S.L., Mazzulli T., Avendano M., Derkach P. Clinical features and short-term outcomes of 144 patients with SARS in the greater Toronto area. JAMA. 2003;289:2801–2809.
    1. Gross A.E., Bryson M.L. Oral Ribavirin for the treatment of noninfluenza respiratory viral infections: a systematic review. Ann Pharmacother. 2015;49:1125–1135.
    1. Falzarano D., de Wit E., Rasmussen A.L., Feldmann F., Okumura A., Scott D.P., Brining D., Bushmaker T., Martellaro C., Baseler L. Treatment with interferon-α2b and ribavirin improves outcome in MERS-CoV-infected rhesus macaques. Nat Med. 2013;19:1313–1317.
    1. Falzarano D., de Wit E., Martellaro C., Callison J., Munster V.J., Feldmann H. Inhibition of novel β coronavirus replication by a combination of interferon-α2b and ribavirin. Sci Rep. 2013;3
    1. Al-Tawfiq J.A., Momattin H., Dib J., Memish Z.A. Ribavirin and interferon therapy in patients infected with the middle east respiratory syndrome coronavirus: an observational study. Int J Infect Dis. 2014;20:42–46.
    1. Omrani A.S., Saad M.M., Baig K., Bahloul A., Abdul-Matin M., Alaidaroos A.Y., Almakhlafi G.A., Albarrak M.M., Memish Z.A., Albarrak A.M. Ribavirin and interferon alfa-2a for severe middle east respiratory syndrome coronavirus infection: a retrospective cohort study. Lancet Infect Dis. 2014;14:1090–1095.
    1. Shalhoub S., Farahat F., Al-Jiffri A., Simhairi R., Shamma O., Siddiqi N., Mushtaq A. IFN-α2a or IFN-β1a in combination with ribavirin to treat Middle East respiratory syndrome coronavirus pneumonia: a retrospective study. J Antimicrob Chemother. 2015;70:2129–2132.
    1. Lo M.K., Jordan R., Arvey A., Sudhamsu J., Shrivastava-Ranjan P., Hotard A.L., Flint M., McMullan L.K., Siegel D., Clarke M.O. GS-5734 and its parent nucleoside analog inhibit Filo-, Pneumo-, and Paramyxoviruses. Sci Rep. 2017;7
    1. Warren T.K., Wells J., Panchal R.G., Stuthman K.S., Garza N.L., Van Tongeren S.A., Dong L., Retterer C.J., Eaton B.P., Pegoraro G. Protection against filovirus diseases by a novel broad-spectrum nucleoside analogue BCX4430. Nature. 2014;508:402–405.
    1. Agostini M.L., Andres E.L., Sims A.C., Graham R.L., Sheahan T.P., Lu X., Smith E.C., Case J.B., Feng J.Y., Jordan R. Coronavirus susceptibility to the antiviral remdesivir (GS-5734) is mediated by the viral polymerase and the proofreading exoribonuclease. mBio. 2018;9
    2. Low level resistance against the potent, broad-spectrum anti-CoV nucleoside analog GS-5734 (remdesivir) was selected by serial passage and is associated with two mutations in the viral RdRP. Remdesivir resistance decreased fitness of MHV and attenuated pathogenesis of SARS-CoV in a mouse model of SARS-CoV disease, supporting further development of remdesivir as a pan-CoV antiviral and raising important questions about the mechanism by which remdesivir overcomes CoV nsp14-ExoN activity.

    1. Urakova N., Kuznetsova V., Crossman D.K., Sokratian A., Guthrie D.B., Kolykhalov A.A., Lockwood M.A., Natchus M.G., Crowley M.R., Painter G.R. β-d-N4-hydroxycytidine is a potent anti-alphavirus compound that induces a high level of mutations in the viral genome. J Virol. 2018;92
    1. Ehteshami M., Tao S., Zandi K., Hsiao H.-M., Jiang Y., Hammond E., Amblard F., Russell O.O., Merits A., Schinazi R.F. Characterization of β-d-N4-hydroxycytidine as a novel inhibitor of chikungunya virus. Antimicrob Agents Chemother. 2017;61
    1. Yoon J.-J., Toots M., Lee S., Lee M.-E., Ludeke B., Luczo J.M., Ganti K., Cox R.M., Sticher Z.M., Edpuganti V. Orally efficacious broad-spectrum ribonucleoside analog inhibitor of influenza and respiratory syncytial viruses. Antimicrob Agents Chemother. 2018;62
    2. This study identifies the modified cytidine ribonucleoside analogue β-d-N4-hydroxycytidine as a potent broad-spectrum inhibitor of respiratory viruses including respiratory syncytial virus, influenza B virus, and influenza A viruses of human, avian, and swine origins and has a high resistance barrier. This compound also is a candidate for the treatment of CoV infection.

    1. Pyrc K., Bosch B.J., Berkhout B., Jebbink M.F., Dijkman R., Rottier P., van der Hoek L. Inhibition of human coronavirus NL63 infection at early stages of the replication cycle. Antimicrob Agents Chemother. 2006;50:2000–2008.
    1. Stuyver L.J., Whitaker T., McBrayer T.R., Hernandez-Santiago B.I., Lostia S., Tharnish P.M., Ramesh M., Chu C.K., Jordan R., Shi J. Ribonucleoside analogue that blocks replication of bovine viral diarrhea and hepatitis C viruses in culture. Antimicrob Agents Chemother. 2003;47:244–254.
    1. Barnard D.L., Hubbard V.D., Burton J., Smee D.F., Morrey J.D., Otto M.J., Sidwell R.W. Inhibition of severe acute respiratory syndrome-associated coronavirus (SARSCoV) by calpain inhibitors and beta-d-N4-hydroxycytidine. Antivir Chem Chemother. 2004;15:15–22.
    1. Taylor R., Kotian P., Warren T., Panchal R., Bavari S., Julander J., Dobo S., Rose A., El-Kattan Y., Taubenheim B. BCX4430 – a broad-spectrum antiviral adenosine nucleoside analog under development for the treatment of Ebola virus disease. J Infect Public Health. 2016;9:220–226.
    1. Dyall J., Coleman C.M., Hart B.J., Venkataraman T., Holbrook M.R., Kindrachuk J., Johnson R.F., Olinger G.G., Jahrling P.B., Laidlaw M. Repurposing of clinically developed drugs for treatment of middle east respiratory syndrome coronavirus infection. Antimicrob Agents Chemother. 2014;58:4885–4893.
    1. Peters H.L., Jochmans D., de Wilde A.H., Posthuma C.C., Snijder E.J., Neyts J., Seley-Radtke K.L. Design, synthesis and evaluation of a series of acyclic fleximer nucleoside analogues with anti-coronavirus activity. Bioorg Med Chem Lett. 2015;25:2923–2926.
    1. Deval J., Fung A., Stevens S.K., Jordan P.C., Gromova T., Taylor J.S., Hong J., Meng J., Wang G., Dyatkina N. Biochemical effect of resistance mutations against synergistic inhibitors of RSV RNA polymerase. PLoS One. 2016;11
    1. Eyer L., Kondo H., Zouharova D., Hirano M., Valdés J.J., Muto M., Kastl T., Kobayashi S., Haviernik J., Igarashi M. Escape of tick-borne flavivirus from 2′-C-methylated nucleoside antivirals is mediated by a single conservative mutation in NS5 that has a dramatic effect on viral fitness. J Virol 91. 2017:e01028-17.
    2. This study demonstrates that the nucleoside analog 7-deaza-2′-C-methyladenosine (7-deaza-2′-CMA) demonstrates potent antiviral activity against tick-borne encephalitis virus. Resistance generated by serial passaging in the presence of 7-deaza-2′-CMA was associated with a single mutation in the polymerase and resulted in resistance against a broad spectrum of derivative compounds. This finding highlights the importance combination therapy to reduce the emergence of resistant virus.

    1. Diphoko T., Gaseitsiwe S., Kasvosve I., Moyo S., Okatch H., Musonda R., Wainberg M., Makhema J., Marlink R., Novitsky V. Prevalence of rilpivirine and etravirine resistance mutations in HIV-1 subtype C-infected patients failing nevirapine or efavirenz-based combination antiretroviral therapy in botswana. AIDS Res Hum Retroviruses. 2018;34:667–671.
    1. Valdés J.J., Butterill P.T., Růžek D. Flaviviridae viruses use a common molecular mechanism to escape nucleoside analogue inhibitors. Biochem Biophys Res Commun. 2017;492:652–658.
    1. Zumla A., Chan J.F.W., Azhar E.I., Hui D.S.C., Yuen K.-Y. Coronaviruses - drug discovery and therapeutic options. Nat Rev Drug Discov. 2016;15:327–347.
    1. Liang R., Wang L., Zhang N., Deng X., Su M., Su Y., Hu L., He C., Ying T., Jiang S. Development of small-molecule MERS-CoV inhibitors. Viruses. 2018;10:721.
    2. Comprehensive review of small-molecule inhibitors targeting viral proteins at different stages of the MERS-CoV viral replication cycle. Illustrates chemical structure formulas of inhibitors and summarizes potency, cytotoxicity, and testing model of each inhibitor in a table.

    1. Huang K.-W., Hsu K.-C., Chu L.-Y., Yang J.-M., Yuan H.S., Hsiao Y.-Y. Identification of inhibitors for the DEDDh family of exonucleases and a unique inhibition mechanism by Crystal structure analysis of CRN-4 bound with 2-Morpholin-4-ylethanesulfonate (MES) J Med Chem. 2016;59:8019–8029.
    1. Gralinski L.E., Baric R.S. Molecular pathology of emerging coronavirus infections. J Pathol. 2015;235:185–195.
    1. Arabi Y.M., Alothman A., Balkhy H.H., Al-Dawood A., AlJohani S., Al Harbi S., Kojan S., Al Jeraisy M., Deeb A.M., Assiri A.M. Treatment of Middle East Respiratory Syndrome with a combination of lopinavir-ritonavir and interferon-β1b (MIRACLE trial): study protocol for a randomized controlled trial. Trials. 2018;19:81.
    1. Chen F., Chan K.H., Jiang Y., Kao R.Y.T., Lu H.T., Fan K.W., Cheng V.C.C., Tsui W.H.W., Hung I.F.N., Lee T.S.W. In vitro susceptibility of 10 clinical isolates of SARS coronavirus to selected antiviral compounds. J Clin Virol. 2004;31:69–75.

Source: PubMed

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