Structural basis for the inhibition of SARS-CoV-2 main protease by antineoplastic drug carmofur

Abstract

The antineoplastic drug carmofur is shown to inhibit the SARS-CoV-2 main protease (Mpro). Here, the X-ray crystal structure of Mpro in complex with carmofur reveals that the carbonyl reactive group of carmofur is covalently bound to catalytic Cys145, whereas its fatty acid tail occupies the hydrophobic S2 subsite. Carmofur inhibits viral replication in cells (EC50 = 24.30 μM) and is a promising lead compound to develop new antiviral treatment for COVID-19.

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Fig. 1: SARS-CoV-2 Mpro in complex with carmofur.
Fig. 2: Inhibition of SARS-CoV-2 by carmofur in Vero E6 cells.

Data availability

Coordinates and structure factors for SARS-CoV-2 Mpro in complex with carmofur have been deposited in the Protein Data Bank (PDB) under accession code 7BUY. Source data for Fig. 2 are available with the paper online.

References

  1. 1.

    Wu, F. et al. A new coronavirus associated with human respiratory disease in China. Nature 579, 265–269 (2020).

  2. 2.

    Zhou, P. et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature 579, 270–273 (2020).

  3. 3.

    Hegyi, A. & Ziebuhr, J. Conservation of substrate specificities among coronavirus main proteases. J. Gen. Virol. 83, 595–599 (2002).

  4. 4.

    Anand, K. et al. Structure of coronavirus main proteinase reveals combination of a chymotrypsin fold with an extra α-helical domain. EMBO J. 21, 3213–3224 (2002).

  5. 5.

    Yang, H. et al. The crystal structures of severe acute respiratory syndrome virus main protease and its complex with an inhibitor. Proc. Natl Acad. Sci. USA 100, 13190–13195 (2003).

  6. 6.

    Pillaiyar, T., Manickam, M., Namasivayam, V., Hayashi, Y. & Jung, S. H. An overview of severe acute respiratory syndrome-coronavirus (SARS-CoV) 3CL protease inhibitors: peptidomimetics and small molecule chemotherapy. J. Med. Chem. 59, 6595–6628 (2016).

  7. 7.

    Jin, Z. et al. Structure of Mpro from COVID-19 virus and discovery of its inhibitors. Nature https://doi.org/10.1038/s41586-020-2223-y (2020).

  8. 8.

    Sakamoto, J. et al. An individual patient data meta-analysis of adjuvant therapy with carmofur in patients with curatively resected colon cancer. Jpn J. Clin. Oncol. 35, 536–544 (2005).

  9. 9.

    Morimoto, K. & Koh, M. Postoperative adjuvant use of carmofur for early breast cancer. Osaka City Med. J. 49, 77–83 (2003).

  10. 10.

    Gröhn, P. et al. Oral carmofur in advanced gastrointestinal cancer. Am. J. Clin. Oncol. 13, 477–479 (1990).

  11. 11.

    Nishio, S. et al. Study on effectiveness of carmofur (Mifurol) in urogenital carcinoma, especially bladder cancer, as a post-operative adjuvant chemotherapeutic agent. Hinyokika Kiyo 33, 295–303 (1987).

  12. 12.

    Ooi, A. et al. Plasma, intestine and tumor levels of 5-fluorouracil in mice bearing L1210 ascites tumor following oral administration of 5-fluorouracil, UFT (mixed compound of tegafur and uracil), carmofur and 5′-deoxy-5-fluorouridine. Biol. Pharm. Bull. 24, 1329–1331 (2001).

  13. 13.

    Sato, S., Ueyama, T., Fukui, H., Miyazaki, K. & Kuwano, M. Anti-tumor effects of carmofur on human 5-FU resistant cells. Gan To Kagaku Ryoho 26, 1613–1616 (1999).

  14. 14.

    Nguyen, H. S., Awad, A. J., Shabani, S. & Doan, N. Molecular targeting of acid ceramidase in glioblastoma: a review of its role, potential treatment and challenges. Pharmaceutics 10, E45 (2018).

  15. 15.

    Dementiev, A. et al. Molecular mechanism of inhibition of acid ceramidase by carmofur. J. Med. Chem. 62, 987–992 (2019).

  16. 16.

    Xue, X. et al. Structures of two coronavirus main proteases: implications for substrate binding and antiviral drug design. J. Virol. 82, 2515–2527 (2008).

  17. 17.

    Ren, Z. et al. The newly emerged SARS-like coronavirus HCoV-EMC also has an ‘Achilles’ heel’: current effective inhibitor targeting a 3C-like protease. Protein Cell 4, 248–250 (2013).

  18. 18.

    Wang, F., Chen, C., Tan, W., Yang, K. & Yang, H. Structure of main protease from human coronavirus NL63: insights for wide spectrum anti-coronavirus drug design. Sci. Rep. 6, 22677 (2016).

  19. 19.

    Yang, H. et al. Design of wide-spectrum inhibitors targeting coronavirus main proteases. PLoS Biol. 3, e324 (2005).

  20. 20.

    Wang, M. et al. Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro. Cell Res. 30, 269–271 (2020).

  21. 21.

    Kabsch, W. XDS. Acta Crystallogr. D Biol. Crystallogr. 66, 125–132 (2010).

  22. 22.

    McCoy, A. J. et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658–674 (2007).

  23. 23.

    Liebschner, D. et al. Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Acta Crystallogr. D Struct. Biol. 75, 861–877 (2019).

  24. 24.

    Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 66, 486–501 (2010).

  25. 25.

    Afonine, P. V. et al. Towards automated crystallographic structure refinement with phenix.refine. Acta Crystallogr. D Biol. Crystallogr. 68, 352–367 (2012).

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Acknowledgements

We are grateful to the staff at beamlines BL17U1, BL18U1 and BL19U1 at Shanghai Synchrotron Radiation Facility (SSRF, China), where data were collected. This work was supported by grants from the National Key R&D Program of China (grant no. 2017YFC0840300 to Z.R. and 2020YFA0707500.), the Project of International Cooperation and Exchanges NSFC (grant no. 81520108019 to Z.R.), the Science and Technology Commission of Shanghai Municipality (grant no. 20431900200), the Department of Science and Technology of Guangxi Zhuang Autonomous Region (grant no. 2020AB40007) and the Natural Science Foundation of China (grant no. 31970165).

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Contributions

H.Y. and Z.R. conceived the project. Z.J., Y. Zhao, H.Y. and Z.R. designed the experiments. Z.J., Y. Zhao, H.W., Y. Zhu, C.Z., X.D., J.Y. and Xiuna Yang cloned, expressed, purified and crystallized proteins. Y. Zhao, Z.J., B.Z. and T.H. collected the diffraction data. Y. Zhao, B.Z. and X.L. solved the crystal structure. Y.S. and Y.W. performed cell-based antiviral and cytotoxicity assays. Y.D. and L.Z. performed qRT-PCR and cytotoxicity assay analysis. Y. Zhao, Z.J., Y.D., Xiaobao Yang, K.Y., X.L., L.W.G., G.X., L.Z., H.Y. and Z.R. analyzed and discussed the data. Y. Zhao, Z.J., K.Y., L.W.G., L.Z., H.Y. and Z.R. wrote the manuscript.

Corresponding authors

Correspondence to Leike Zhang or Haitao Yang.

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The authors declare no competing interests.

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Peer review information Inês Chen was the primary editor on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.

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Extended data

Extended Data Fig. 1 Overall structure of SARS-CoV-2 Mpro in complex with carmofur.

a, The overall structure of SARS-CoV-2 Mpro in complex with carmofur. The salmon and green represent the different protomers. The carmofur atoms are shown as solid spheres. b, The side view of the complex. c, The first serine participate in the formation of the dimer.

Extended Data Fig. 2 Inhibition of Mpro by carmofur.

a, Putative inhibition mechanism. Red curve represents Mpro polypeptide and the black sphere represent the Cα of C145. b, Schematic diagram of Mpro-carmofur interactions. Black spheres represent Cα atoms.

Extended Data Fig. 3 Binding mode of carmofur and N3 to Mpro.

a, Overall structural comparison between the Mpro-carmofur and Mpro-N3 complexes. The salmon cartoon represents the carmofur bound structure and the light cyan represents the N3 bound structure. Carmofur, N3 and DMSO are represented by the purple, yellow and green balls and sticks, respectively. b, The binding pocket of Mpro. Carmofur and N3 are represent in the same way as in panel a. c, Schematic diagram of carmofur and N3.

Supplementary information

Source data

Source Data Fig. 2

Statistical source data.

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Jin, Z., Zhao, Y., Sun, Y. et al. Structural basis for the inhibition of SARS-CoV-2 main protease by antineoplastic drug carmofur. Nat Struct Mol Biol (2020). https://doi.org/10.1038/s41594-020-0440-6

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