Skip to main content
PMC home page
Springer Nature - PMC COVID-19 Collection logoLink to Springer Nature - PMC COVID-19 Collection
. 2021 Dec 24;65(6):1181–1197. doi: 10.1007/s11427-021-2031-7

Discovery of potential anti-SARS-CoV-2 drugs based on large-scale screening in vitro and effect evaluation in vivo

Haoran Peng 1,#, Cuiling Ding 1,#, Liangliang Jiang 1,#, Wanda Tang 1, Yan Liu 1, Lanjuan Zhao 1, Zhigang Yi 2, Hao Ren 1, Chong Li 3, Yanhua He 1, Xu Zheng 1, Hailin Tang 1, Zhihui Chen 4,✉, Zhongtian Qi 1,✉, Ping Zhao 1,✉
PMCID: PMC8713546  PMID: 34962614

Abstract

The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a global crisis. Clinical candidates with high efficacy, ready availability, and that do not develop resistance are in urgent need. Despite that screening to repurpose clinically approved drugs has provided a variety of hits shown to be effective against SARS-CoV-2 infection in cell culture, there are few confirmed antiviral candidates in vivo. In this study, 94 compounds showing high antiviral activity against SARS-CoV-2 in Vero E6 cells were identified from 2,580 FDA-approved small-molecule drugs. Among them, 24 compounds with low cytotoxicity were selected, and of these, 17 compounds also effectively suppressed SARS-CoV-2 infection in HeLa cells transduced with human ACE2. Six compounds disturb multiple processes of the SARS-CoV-2 life cycle. Their prophylactic efficacies were determined in vivo using Syrian hamsters challenged with SARS-CoV-2 infection. Seven compounds reduced weight loss and promoted weight regain of hamsters infected not only with the original strain but also the D614G variant. Except for cisatracurium, six compounds reduced hamster pulmonary viral load, and IL-6 and TNF-α mRNA when assayed at 4 d postinfection. In particular, sertraline, salinomycin, and gilteritinib showed similar protective effects as remdesivir in vivo and did not induce antiviral drug resistance after 10 serial passages of SARS-CoV-2 in vitro, suggesting promising application for COVID-19 treatment.

Supporting Information

The supporting information is available online at 10.1007/s11427-021-2031-7. The supporting materials are published as submitted, without typesetting or editing. The responsibility for scientific accuracy and content remains entirely with the authors.

Keywords: SARS-CoV-2, drug repurposing, drug screening, hamster model, D614G variant, drug resistance

Electronic Supplementary Material

Appendix (478.5KB, pdf)

Acknowledgements

This work was supported by the National Natural Science Foundation of China (31570170) and the National Key Research and Development Program of China (2016YFC1200401).

Footnotes

Compliance and ethics

The author(s) declare that they have no conflict of interest.

Contributed equally to this work

Contributor Information

Zhihui Chen, Email: hchzhi@126.com.

Zhongtian Qi, Email: qizt@smmu.edu.cn.

Ping Zhao, Email: pnzhao@163.com.

References

  1. Abu-Farha M, Thanaraj TA, Qaddoumi MG, Hashem A, Abubaker J, Al-Mulla F. The role of lipid metabolism in COVID-19 virus infection and as a drug target. Int J Mol Sci. 2020;21:3544. doi: 10.3390/ijms21103544. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Ahmad J, Ikram S, Ahmad F, Rehman IU, Mushtaq M. SARS-CoV-2 RNA dependent RNA polymerase (RdRp)—a drug repurposing study. Heliyon. 2020;6:e04502. doi: 10.1016/j.heliyon.2020.e04502. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Balasubramanian A, Teramoto T, Kulkarni AA, Bhattacharjee AK, Padmanabhan R. Antiviral activities of selected antimalarials against dengue virus type 2 and Zika virus. Antiviral Res. 2017;137:141–150. doi: 10.1016/j.antiviral.2016.11.015. [DOI] [PubMed] [Google Scholar]
  4. Berber B, Doluca O. A comprehensive drug repurposing study for COVID19 treatment: novel putative dihydroorotate dehydrogenase inhibitors show association to serotonin-dopamine receptors. Brief Bioinform. 2021;22:1023–1037. doi: 10.1093/bib/bbaa379. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Bouhaddou M, Memon D, Meyer B, White KM, Rezelj VV, Correa Marrero M, Polacco BJ, Melnyk JE, Ulferts S, Kaake RM, et al. The global phosphorylation landscape of SARS-CoV-2 infection. Cell. 2020;182:685–712. doi: 10.1016/j.cell.2020.06.034. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Carpinteiro A, Edwards MJ, Hoffmann M, Kochs G, Gripp B, Weigang S, Adams C, Carpinteiro E, Gulbins A, Keitsch S, et al. Pharmacological inhibition of acid sphingomyelinase prevents uptake of SARS-CoV-2 by epithelial cells. Cell Rep Med. 2020;1:100142. doi: 10.1016/j.xcrm.2020.100142. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Chen Y, Lear TB, Evankovich JW, Larsen MB, Lin B, Alfaras I, Kennerdell JR, Salminen L, Camarco DP, Lockwood KC, et al. A high-throughput screen for TMPRSS2 expression identifies FDA-approved compounds that can limit SARS-CoV-2 entry. Nat Commun. 2021;12:3907. doi: 10.1038/s41467-021-24156-y. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Cheung YY, Chen KC, Chen H, Seng EK, Chu JJH. Antiviral activity of lanatoside C against dengue virus infection. Antiviral Res. 2014;111:93–99. doi: 10.1016/j.antiviral.2014.09.007. [DOI] [PubMed] [Google Scholar]
  9. Dittmar M, Lee JS, Whig K, Segrist E, Li M, Kamalia B, Castellana L, Ayyanathan K, Cardenas-Diaz FL, Morrisey EE, et al. Drug repurposing screens reveal cell-type-specific entry pathways and FDA-approved drugs active against SARS-CoV-2. Cell Rep. 2021;35:108959. doi: 10.1016/j.celrep.2021.108959. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Drayman N, DeMarco JK, Jones KA, Azizi SA, Froggatt HM, Tan K, Maltseva NI, Chen S, Nicolaescu V, Dvorkin S, et al. Masitinib is a broad coronavirus 3CL inhibitor that blocks replication of SARS-CoV-2. Science. 2021;373:931–936. doi: 10.1126/science.abg5827. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Eberle RJ, Olivier DS, Amaral MS, Gering I, Willbold D, Arni R K, Coronado MA. The repurposed drugs suramin and quinacrine cooperatively inhibit SARS-CoV-2 3CLproin vitro. Viruses. 2021;13:873. doi: 10.3390/v13050873. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Farsalinos K, Eliopoulos E, Leonidas DD, Papadopoulos GE, Tzartos S, Poulas K. Nicotinic cholinergic system and COVID-19: in silico identification of an interaction between SARS-CoV-2 and nicotinic receptors with potential therapeutic targeting implications. Int J Mol Sci. 2020;21:5807. doi: 10.3390/ijms21165807. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Finch CL, Dyall J, Xu S, Nelson EA, Postnikova E, Liang JY, Zhou H, DeWald LE, Thomas CJ, Wang A, et al. Formulation, stability, pharmacokinetic, and modeling studies for tests of synergistic combinations of orally available approved drugs against ebola virus in vivo. Microorganisms. 2021;9:566. doi: 10.3390/microorganisms9030566. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Francis ME, Goncin U, Kroeker A, Swan C, Ralph R, Lu Y, Etzioni AL, Falzarano D, Gerdts V, Machtaler S, et al. SARS-CoV-2 infection in the syrian hamster model causes inflammation as well as type I interferon dysregulation in both respiratory and non-respiratory tissues including the heart and kidney. PLoS Pathog. 2021;17:e1009705. doi: 10.1371/journal.ppat.1009705. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Gao K, Nguyen DD, Chen J, Wang R, Wei GW. Repositioning of 8565 existing drugs for COVID-19. J Phys Chem Lett. 2020;11:5373–5382. doi: 10.1021/acs.jpclett.0c01579. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Gao M, Yang L, Chen X, Deng Y, Yang S, Xu H, Chen Z, Gao X. A study on infectivity of asymptomatic SARS-CoV-2 carriers. Respir Med. 2020;169:106026. doi: 10.1016/j.rmed.2020.106026. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Gehring G, Rohrmann K, Atenchong N, Mittler E, Becker S, Dahlmann F, PÖhlmann S, Vondran FWR, David S, Manns MP, et al. The clinically approved drugs amiodarone, dronedarone and verapamil inhibit filovirus cell entry. J Antimicrob Chemother. 2014;69:2123–2131. doi: 10.1093/jac/dku091. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Geleris J, Sun Y, Platt J, Zucker J, Baldwin M, Hripcsak G, Labella A, Manson DK, Kubin C, Barr RG, et al. Observational study of hydroxychloroquine in hospitalized patients with COVID-19. N Engl J Med. 2020;382:2411–2418. doi: 10.1056/NEJMoa2012410. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Ginex T, Garaigorta U, Ramirez D, Castro V, Nozal V, Maestro I, García-Cárceles J, Campillo NE, Martinez A, Gastaminza P, et al. Host-directed FDA-approved drugs with antiviral activity against SARS-CoV-2 identified by hierarchical in silico/in vitro screening methods. Pharmaceuticals. 2021;14:332. doi: 10.3390/ph14040332. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Global report investigating novel coronavirus haplotypes. https://cov-lineages.org/global_report.html.
  21. Guan M, Wang W, Liu X, Tong Y, Liu Y, Ren H, Zhu S, Dubuisson J, Baumert TF, Zhu Y, et al. Three different functional microdomains in the hepatitis C virus hypervariable region 1 (HVR1) mediate entry and immune evasion. J Biol Chem. 2012;287:35631–35645. doi: 10.1074/jbc.M112.382341. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Han Y, Duan X, Yang L, Nilsson-Payant BE, Wang P, Duan F, Tang X, Yaron TM, Zhang T, Uhl S, et al. Identification of SARS-CoV-2 inhibitors using lung and colonic organoids. Nature. 2021;589:270–275. doi: 10.1038/s41586-020-2901-9. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Herring, S., Oda, J.M., Wagoner, J., Kirchmeier, D., O’Connor, A., Nelson, E.A., Huang, Q., Liang, Y., DeWald, L.E., Johansen, L.M., et al. (2021). Inhibition of arenaviruses by combinations of orally available approved drugs. Antimicrob Agents Chemother 65. [DOI] [PMC free article] [PubMed]
  24. Ianevski A, Yao R, Fenstad MH, Biza S, Zusinaite E, Reisberg T, Lysvand H, Løseth K, Landsem VM, Malmring JF, et al. Potential antiviral options against SARS-CoV-2 infection. Viruses. 2020;12:642. doi: 10.3390/v12060642. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Ju X, Zhu Y, Wang Y, Li J, Zhang J, Gong M, Ren W, Li S, Zhong J, Zhang L, et al. A novel cell culture system modeling the SARS-CoV-2 life cycle. PLoS Pathog. 2021;17:e1009439. doi: 10.1371/journal.ppat.1009439. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Li Q, Cui C, Xu F, Zhao J, Li N, Li H, Wang T, Zhang H, Liu N, Wei Y, et al. Evaluation of the efficacy and safety of hydroxychloroquine in comparison with chloroquine in moderate and severe patients with COVID-19. Sci China Life Sci. 2021;64:660–663. doi: 10.1007/s11427-020-1871-4. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Liu Z, Chu R, Gong L, Su B, Wu J. The assessment of transmission efficiency and latent infection period in asymptomatic carriers of SARS-CoV-2 infection. Int J Infect Dis. 2020;99:325–327. doi: 10.1016/j.ijid.2020.06.036. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Mahase E. COVID-19: molnupiravir reduces risk of hospital admission or death by 50% in patients at risk, MSD reports. BMJ. 2021;375:n2422. doi: 10.1136/bmj.n2422. [DOI] [PubMed] [Google Scholar]
  29. Mirabelli C, Wotring JW, Zhang CJ, McCarty SM, Fursmidt R, Pretto CD, Qiao Y, Zhang Y, Frum T, Kadambi NS, et al. Morphological cell profiling of SARS-CoV-2 infection identifies drug repurposing candidates for COVID-19. Proc Natl Acad Sci USA. 2021;118:e2105815118. doi: 10.1073/pnas.2105815118. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Mori M, Kaneko N, Ueno Y, Yamada M, Tanaka R, Saito R, Shimada I, Mori K, Kuromitsu S. Gilteritinib, a FLT3/AXL inhibitor, shows antileukemic activity in mouse models of FLT3 mutated acute myeloid leukemia. Invest New Drugs. 2017;35:556–565. doi: 10.1007/s10637-017-0470-z. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Naujokat C, Steinhart R. Salinomycin as a drug for targeting human cancer stem cells. J Biomed Biotechnol. 2012;2012:1–17. doi: 10.1155/2012/950658. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Nemerow GR, Cooper NR. Infection of B lymphocytes by a human herpesvirus, Epstein-Barr virus, is blocked by calmodulin antagonists. Proc Natl Acad Sci U S A. 1984;81:4955–4959. doi: 10.1073/pnas.81.15.4955. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Ochiai H, Kurokawa M, Niwayama S. Influence of trifluoperazine on the late stage of influenza virus infection in MDCK cells. Antiviral Res. 1991;15:149–160. doi: 10.1016/0166-3542(91)90032-M. [DOI] [PubMed] [Google Scholar]
  34. Otręba M, Kośmider L, Rzepecka-Stojko A. Antiviral activity of chlorpromazine, fluphenazine, perphenazine, prochlorperazine, and thioridazine towards RNA-viruses. A review. Eur J Pharmacol. 2020;887:173553. doi: 10.1016/j.ejphar.2020.173553. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Pandey A, Nikam AN, Shreya AB, Mutalik SP, Gopalan D, Kulkarni S, Padya BS, Fernandes G, Mutalik S, Prassl R. Potential therapeutic targets for combating SARS-CoV-2: drug repurposing, clinical trials and recent advancements. Life Sci. 2020;256:117883. doi: 10.1016/j.lfs.2020.117883. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Patten, J.J., Keiser, P.T., Gysi, D., Menichetti, G., Mori, H., Donahue, C.J., Gan, X., Do Valle, I., Geoghegan-Barek, K., Anantpadma, M. et al. (2021). Multidose evaluation of 6,710 drug repurposing library identifies potent SARS-CoV-2 infection inhibitors in vitro and in vivo. bioRxiv doi: 10.1101/2021.04.20.440626.
  37. Peng HR, Li CZ, Tang HL, Xue JY, Chen ZH, Liang XS, Zhu YM, Xia BH, Zhu YJ, Wu JJ, et al. Isolation and identification of two strains of severe acute respiratory syndrome coronavirus 2 from coronavirus disease 2019 patients in Shanghai (in Chinese) Acad J Sec Mil Med Univ. 2020;41:365–370. [Google Scholar]
  38. Plante JA, Liu Y, Liu J, Xia H, Johnson BA, Lokugamage KG, Zhang X, Muruato AE, Zou J, Fontes-Garfias CR, et al. Spike mutation d614g alters SARS-CoV-2 fitness. Nature. 2021;592:116–121. doi: 10.1038/s41586-020-2895-3. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Puhl AC, Fritch EJ, Lane TR, Tse LV, Yount BL, Sacramento C Q, Fintelman-Rodrigues N, Tavella TA, Maranhão Costa FT, Weston S, et al. Repurposing the Ebola and Marburg virus inhibitors tilorone, quinacrine, and pyronaridine: In vitro activity against SARS-CoV-2 and potential mechanisms. ACS Omega. 2021;6:7454–7468. doi: 10.1021/acsomega.0c05996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Rakedzon S, Neuberger A, Domb AJ, Petersiel N, Schwartz E. From hydroxychloroquine to ivermectin: what are the anti-viral properties of anti-parasitic drugs to combat SARS-CoV-2. J Travel Med. 2021;28:taab005. doi: 10.1093/jtm/taab005. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Riva L, Yuan S, Yin X, Martin-Sancho L, Matsunaga N, Pache L, Burgstaller-Muehlbacher S, De Jesus PD, Teriete P, Hull MV, et al. Discovery of SARS-CoV-2 antiviral drugs through large-scale compound repurposing. Nature. 2020;586:113–119. doi: 10.1038/s41586-020-2577-1. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Sharma G, Champalal Sharma D, Hwei Fen L, Pathak M, Bethur N, Pendharkar V, Peiris M, Altmeyer R. Reduction of influenza virus-induced lung inflammation and mortality in animals treated with a phosophodisestrase-4 inhibitor and a selective serotonin reuptake inhibitor. Emerg Microbes Infect. 2013;2:1–9. doi: 10.1038/emi.2013.52. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Ueno Y, Mori M, Kamiyama Y, Kaneko N, Isshiki E, Takeuchi M. Gilteritinib (ASP2215), a novel FLT3/AXL inhibitor: Preclinical evaluation in combination with azacitidine in acute myeloid leukemia. Blood. 2016;128:2830. doi: 10.1182/blood.V128.22.2830.2830. [DOI] [Google Scholar]
  44. Vagapova ER, Lebedev TD, Prassolov VS. Viral fibrotic scoring and drug screen based on MAPK activity uncovers EGFR as a key regulator of COVID-19 fibrosis. Sci Rep. 2021;11:11234. doi: 10.1038/s41598-021-90701-w. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Volz E, Hill V, McCrone JT, Price A, Jorgensen D, O’Toole Á, Southgate J, Johnson R, Jackson B, Nascimento FF, et al. Evaluating the effects of SARS-CoV-2 spike mutation D614G on transmissibility and pathogenicity. Cell. 2021;184:64–75. doi: 10.1016/j.cell.2020.11.020. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Wang M, Cao R, Zhang L, Yang X, Liu J, Xu M, Shi Z, Hu Z, Zhong W, Xiao G. Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro. Cell Res. 2020;30:269–271. doi: 10.1038/s41422-020-0282-0. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Wang S, Qiu Z, Hou Y, Deng X, Xu W, Zheng T, Wu P, Xie S, Bian W, Zhang C, et al. AXL is a candidate receptor for SARS-CoV-2 that promotes infection of pulmonary and bronchial epithelial cells. Cell Res. 2021;31:126–140. doi: 10.1038/s41422-020-00460-y. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Wilson AJ, Troy-Barnes E, Subhan M, Clark F, Gupta R, Fielding AK, Kottaridis P, Mansour MR, O’Nions J, Payne E, et al. Successful remission induction therapy with gilteritinib in a patient with de novo FLT3-mutated acute myeloid leukaemia and severe COVID-19. Br J Haematol. 2020;190:e189–e190. doi: 10.1111/bjh.16962. [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. Xiao X, Wang C, Chang D, Wang Y, Dong X, Jiao T, Zhao Z, Ren L, Dela Cruz CS, Sharma L, et al. Identification of potent and safe antiviral therapeutic candidates against SARS-CoV-2. Front Immunol. 2020;11:586572. doi: 10.3389/fimmu.2020.586572. [DOI] [PMC free article] [PubMed] [Google Scholar]
  50. Xing, J., Paithankar, S., Liu, K., Uhl, K., Li, X., Ko, M., Kim, S., Haskins, J., and Chen, B. (2021). Published anti-SARS-CoV-2 in vitro hits share common mechanisms of action that synergize with antivirals. Brief Bioinform 22. [DOI] [PMC free article] [PubMed]
  51. Yang CW, Peng TT, Hsu HY, Lee YZ, Wu SH, Lin WH, Ke Y Y, Hsu TA, Yeh TK, Huang WZ, et al. Repurposing old drugs as antiviral agents for coronaviruses. Biomed J. 2020;43:368–374. doi: 10.1016/j.bj.2020.05.003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  52. Yu B, Li C, Chen P, Li J, Jiang H, Wang DW. Beneficial effects exerted by hydroxychloroquine in treating COVID-19 patients via protecting multiple organs. Sci China Life Sci. 2021;64:330–333. doi: 10.1007/s11427-020-1782-1. [DOI] [PMC free article] [PubMed] [Google Scholar]
  53. Zhou S, Hill CS, Sarkar S, Tse LV, Woodburn BMD, Schinazi R F, Sheahan TP, Baric RS, Heise MT, Swanstrom R. p-d-N4-hydroxycytidine inhibits SARS-CoV-2 through lethal mutagenesis but is also mutagenic to mammalian cells. J Infect Dis. 2021;224:415–419. doi: 10.1093/infdis/jiab247. [DOI] [PMC free article] [PubMed] [Google Scholar]
  54. Zhou Y, Zhou B, Pache L, Chang M, Khodabakhshi AH, Tanaseichuk O, Benner C, Chanda SK. Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat Commun. 2019;10:1523. doi: 10.1038/s41467-019-09234-6. [DOI] [PMC free article] [PubMed] [Google Scholar]

Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Appendix (478.5KB, pdf)

Articles from Science China. Life Sciences are provided here courtesy of Nature Publishing Group

RESOURCES