1887

Abstract

Rapid repurposing of existing drugs as new therapeutics for COVID-19 has been an important strategy in the management of disease severity during the ongoing SARS-CoV-2 pandemic. Here, we used high-throughput docking to screen 6000 compounds within the DrugBank library for their potential to bind and inhibit the SARS-CoV-2 3 CL main protease, a chymotrypsin-like enzyme that is essential for viral replication. For 19 candidate hits, parallel fluorescence-based protease-inhibition assays and Vero-CCL81 cell-based SARS-CoV-2 replication-inhibition assays were performed. One hit, diclazuril (an investigational anti-protozoal compound), was validated as a SARS-CoV-2 3 CL main protease inhibitor (IC value of 29 µM) and modestly inhibited SARS-CoV-2 replication in Vero-CCL81 cells. Another hit, lenvatinib (approved for use in humans as an anti-cancer treatment), could not be validated as a SARS-CoV-2 3 CL main protease inhibitor , but serendipitously exhibited a striking functional synergy with the approved nucleoside analogue remdesivir to inhibit SARS-CoV-2 replication, albeit this was specific to Vero-CCL81 cells. Lenvatinib is a broadly-acting host receptor tyrosine kinase (RTK) inhibitor, but the synergistic effect with remdesivir was not observed with other approved RTK inhibitors (such as pazopanib or sunitinib), suggesting that the mechanism-of-action is independent of host RTKs. Furthermore, time-of-addition studies revealed that lenvatinib/remdesivir synergy probably targets SARS-CoV-2 replication subsequent to host-cell entry. Our work shows that combining computational and cellular screening is a means to identify existing drugs with repurposing potential as antiviral compounds. Future studies could be aimed at understanding and optimizing the lenvatinib/remdesivir synergistic mechanism as a therapeutic option.

Funding
This study was supported by the:
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Award 310030B_189363)
    • Principle Award Recipient: AmedeoCaflisch
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Award 31003A_182464)
    • Principle Award Recipient: BenjaminG Hale
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Award 31003A_176170)
    • Principle Award Recipient: SilkeStertz
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. The Microbiology Society waived the open access fees for this article.
Loading

Article metrics loading...

/content/journal/jgv/10.1099/jgv.0.001625
2021-07-28
2024-12-03
Loading full text...

Full text loading...

/deliver/fulltext/jgv/102/7/jgv001625.html?itemId=/content/journal/jgv/10.1099/jgv.0.001625&mimeType=html&fmt=ahah

References

  1. Dong E, Du H, Gardner L. An interactive web-based dashboard to track COVID-19 in real time. Lancet Infect Dis 2020; 20:533–534 [View Article] [PubMed]
    [Google Scholar]
  2. Zhu N, Zhang D, Wang W, Li X, Yang B et al. A novel coronavirus from patients with pneumonia in China, 2019. N Engl J Med 2020; 382:727–733 [View Article] [PubMed]
    [Google Scholar]
  3. Wu Z, McGoogan JM. Characteristics of and important lessons from the coronavirus disease 2019 (COVID-19) outbreak in China: summary of a report of 72314 cases from the Chinese center for disease control and prevention. JAMA 2020; 323:1239–1242 [View Article] [PubMed]
    [Google Scholar]
  4. Huang C, Wang Y, Li X, Ren L, Zhao J et al. Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. Lancet 2020; 395:497–506 [View Article] [PubMed]
    [Google Scholar]
  5. Stertz S, Hale BG. Interferon system deficiencies exacerbating severe pandemic virus infections. Trends Microbiol 2021 [View Article] [PubMed]
    [Google Scholar]
  6. Polack FP, Thomas SJ, Kitchin N, Absalon J, Gurtman A et al. Safety and efficacy of the BNT162b2 mRNA Covid-19 Vaccine. N Engl J Med 2020; 383:2603–2615 [View Article] [PubMed]
    [Google Scholar]
  7. Baden LR, El Sahly HM, Essink B, Kotloff K, Frey S et al. Efficacy and safety of the mRNA-1273 SARS-CoV-2 Vaccine. N Engl J Med 2021; 384:403–416 [View Article] [PubMed]
    [Google Scholar]
  8. Voysey M, Clemens SAC, Madhi SA, Weckx LY, Folegatti PM et al. Safety and efficacy of the chadox1 NCOV-19 vaccine (AZD1222) against SARS-COV-2: An interim analysis of four randomised controlled trials in Brazil, South Africa, and the UK. Lancet 2021; 397:99–111 [View Article] [PubMed]
    [Google Scholar]
  9. Krammer F. SARS-CoV-2 vaccines in development. Nature 2020; 586:516–527 [View Article] [PubMed]
    [Google Scholar]
  10. Consortium WHOST Pan H, Peto R, Henao-Restrepo AM, Preziosi MP et al. repurposed antiviral drugs for covid-19 - interim WHO solidarity trial results. N Engl J Med 2021; 384:497–511
    [Google Scholar]
  11. Beigel JH, Tomashek KM, Dodd LE, Mehta AK, Zingman BS et al. Remdesivir for the treatment of Covid-19. N Engl J Med 2020; 383:1813–1826 [View Article] [PubMed]
    [Google Scholar]
  12. Riva L, Yuan S, Yin X, Martin-Sancho L, Matsunaga N et al. Discovery of SARS-CoV-2 antiviral drugs through large-scale compound repurposing. Nature 2020; 586:113–119 [View Article] [PubMed]
    [Google Scholar]
  13. Gordon DE, Hiatt J, Bouhaddou M, Rezelj VV, Ulferts S et al. Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms. Science 2020; 370:6521 [View Article]
    [Google Scholar]
  14. V’Kovski P, Kratzel A, Steiner S, Stalder H, Thiel V. Coronavirus biology and replication: implications for SARS-CoV-2. Nat Rev Microbiol 2020; 19:155–170 [View Article] [PubMed]
    [Google Scholar]
  15. Anand K, Ziebuhr J, Wadhwani P, Mesters JR, Hilgenfeld R. Coronavirus main proteinase (3CLpro) structure: basis for design of anti-SARS drugs. Science 2003; 300:1763–1767 [View Article] [PubMed]
    [Google Scholar]
  16. Zhang L, Lin D, Sun X, Curth U, Drosten C et al. Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved alpha-ketoamide inhibitors. Science 2020; 368:409–412 [View Article] [PubMed]
    [Google Scholar]
  17. Douangamath A, Fearon D, Gehrtz P, Krojer T, Lukacik P et al. Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease. Nat Commun 2020; 11:5047 [View Article] [PubMed]
    [Google Scholar]
  18. Farnik H, Zeuzem S. New antiviral therapies in the management of HCV infection. Antivir Ther 2012; 17:771–783 [View Article] [PubMed]
    [Google Scholar]
  19. Wensing AM, van Maarseveen NM, Nijhuis M. Fifteen years of HIV Protease Inhibitors: raising the barrier to resistance. Antiviral Res 2010; 85:59–74 [View Article] [PubMed]
    [Google Scholar]
  20. Drayman N, Jones KA, Azizi SA, Froggatt HM, Tan K et al. Drug repurposing screen identifies masitinib as a 3CLpro inhibitor that blocks replication of SARS-CoV-2 in vitro. bioRxiv 2020 [View Article] [PubMed]
    [Google Scholar]
  21. Hung HC, YY K, Huang SY, Huang PN, Kung YA et al. Discovery of M protease inhibitors encoded by SARS-CoV-2. Antimicrob Agents Chemother 2020; 64:
    [Google Scholar]
  22. Fu L, Ye F, Feng Y, Yu F, Wang Q et al. Both Boceprevir and GC376 efficaciously inhibit SARS-CoV-2 by targeting its main protease. Nat Commun 2020; 11:4417
    [Google Scholar]
  23. Vuong W, Khan MB, Fischer C, Arutyunova E, Lamer T et al. Feline coronavirus drug inhibits the main protease of SARS-CoV-2 and blocks virus replication. Nat Commun 2020; 11:4282
    [Google Scholar]
  24. Wishart DS, Feunang YD, Guo AC, EJ L, Marcu A et al. DrugBank 5.0: a major update to the DrugBank database for 2018. Nucleic Acids Res 2018; 46:D1074–D1082
    [Google Scholar]
  25. Pohl MO, Busnadiego I, Kufner V, Glas I, Karakus U et al. SARS-CoV-2 variants reveal features critical for replication in primary human cells. PLoS Biol 2021; 19:e3001006 [View Article] [PubMed]
    [Google Scholar]
  26. Pruijssers AJ, George AS, Schafer A, Leist SR, Gralinksi LE et al. Remdesivir Inhibits SARS-CoV-2 in Human Lung Cells and Chimeric SARS-CoV Expressing the SARS-CoV-2 RNA Polymerase in Mice. Cell Rep 2020; 32:107940 [View Article] [PubMed]
    [Google Scholar]
  27. Capozzi M, De Divitiis C, Ottaiano A, von Arx C, Scala S et al. Lenvatinib, a molecule with versatile application: from preclinical evidence to future development in anti-cancer treatment. Cancer Manag Res 2019; 11:3847–3860 [View Article] [PubMed]
    [Google Scholar]
  28. Suyama K, Iwase H. Lenvatinib: A promising molecular targeted agent for multiple cancers. Cancer Control 2018; 25:1073274818789361 [View Article]
    [Google Scholar]
  29. Kneller DW, Phillips G, O’Neill HM, Jedrzejczak R, Stols L et al. Structural plasticity of SARS-CoV-2 3CL M(pro) active site cavity revealed by room temperature X-ray crystallography. Nat Commun 2020; 11:3202 [View Article] [PubMed]
    [Google Scholar]
  30. Majeux N, Scarsi M, Caflisch A. Efficient electrostatic solvation model for protein-fragment docking. Proteins 2001; 42:256–268 [View Article] [PubMed]
    [Google Scholar]
  31. Majeux N, Scarsi M, Apostolakis J, Ehrhardt C, Caflisch A. Exhaustive docking of molecular fragments with electrostatic solvation. Proteins 1999; 37:88–105 [View Article] [PubMed]
    [Google Scholar]
  32. Scarsi M, Apostolakis J, Caflisch A. Continuum electrostatic energies of macromolecules in aqueous solutions. J Phys Chem A 1997; 101:8098–8106 [View Article]
    [Google Scholar]
  33. MacKerell AD, Bashford D, Bellott M, Dunbrack RL, Evanseck JD et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 1998; 102:3586–3616 [View Article]
    [Google Scholar]
  34. MacKerell AD, Feig M, Brooks CL. Improved treatment of the protein backbone in empirical force fields. J Am Chem Soc 2004; 126:698–699 [View Article] [PubMed]
    [Google Scholar]
  35. Vanommeslaeghe K, Hatcher E, Acharya C, Kundu S, Zhong S et al. CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. J Comput Chem 2010; 31:671–690 [View Article] [PubMed]
    [Google Scholar]
  36. Zhao HT, Huang DZ. Hydrogen bonding penalty upon ligand binding. Plos One 2011; 6:
    [Google Scholar]
  37. Busnadiego I, Fernbach S, Pohl MO, Karakus U, Huber M et al. Antiviral activity of type I, II, and III interferons counterbalances ACE2 inducibility and restricts SARS-CoV-2. mBio 2020; 11: [View Article] [PubMed]
    [Google Scholar]
  38. Konig R, Chiang CY, BP T, Yan SF, DeJesus PD et al. A probability-based approach for the analysis of large-scale RNAI screens. Nat Methods 2007; 4:847–849 [View Article]
    [Google Scholar]
/content/journal/jgv/10.1099/jgv.0.001625
Loading
/content/journal/jgv/10.1099/jgv.0.001625
Loading

Data & Media loading...

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error