Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

ATP-directed capture of bioactive herbal-based medicine on human tRNA synthetase

Abstract

Febrifugine is the active component of the Chinese herb Chang Shan (Dichroa febrifuga Lour.)1,2, which has been used for treating malaria-induced fever for about 2,000 years. Halofuginone (HF), the halogenated derivative of febrifugine, has been tested in clinical trials for potential therapeutic applications in cancer and fibrotic disease3,4,5,6. Recently, HF was reported to inhibit TH17 cell differentiation by activating the amino acid response pathway7, through inhibiting human prolyl-transfer RNA synthetase (ProRS) to cause intracellular accumulation of uncharged tRNA8,9. Curiously, inhibition requires the presence of unhydrolysed ATP. Here we report an unusual 2.0 Å structure showing that ATP directly locks onto and orients two parts of HF onto human ProRS, so that one part of HF mimics bound proline and the other mimics the 3′ end of bound tRNA. Thus, HF is a new type of ATP-dependent inhibitor that simultaneously occupies two different substrate binding sites on ProRS. Moreover, our structure indicates a possible similar mechanism of action for febrifugine in malaria treatment. Finally, the elucidation here of a two-site modular targeting activity of HF raises the possibility that substrate-directed capture of similar inhibitors might be a general mechanism that could be applied to other synthetases.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Buy article

Get time limited or full article access on ReadCube.

$32.00

All prices are NET prices.

Figure 1: Structure of human ProRS with bound ligands.
Figure 2: Mechanistic basis for ATP-dependent inhibition of ProRS by halofuginone.
Figure 3: HF interacts with both the site for amino acid activation and the site for docking the 3′-end of tRNA.
Figure 4: Febrifugine blocks ProRS.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

Atomic coordinates and structure factors for the reported crystal structure have been deposited in the Protein Data Bank under accession code 4HVC.

References

  1. Koepfli, J. B., Mead, J. F. & Brockman, J. A., Jr An alkaloid with high antimalarial activity from Dichroa febrifuga . J. Am. Chem. Soc. 69, 1837 (1947)

    CAS  Article  Google Scholar 

  2. Coatney, G. R., Cooper, W. C., Culwell, W. B., White, W. C. & Imboden, C. A., Jr Studies in human malaria. XXV. Trial of febrifugine, an alkaloid obtained from Dichroa febrifuga Lour., against the Chesson strain of Plasmodium vivax . J. Natl. Malar. Soc. 9, 183–186 (1950)

    CAS  PubMed  Google Scholar 

  3. Pines, M., Snyder, D., Yarkoni, S. & Nagler, A. Halofuginone to treat fibrosis in chronic graft-versus-host disease and scleroderma. Biol. Blood Marrow Transplant. 9, 417–425 (2003)

    CAS  Article  Google Scholar 

  4. Pines, M. & Nagler, A. Halofuginone: a novel antifibrotic therapy. Gen. Pharmacol. 30, 445–450 (1998)

    CAS  Article  Google Scholar 

  5. de Jonge, M. J. et al. Phase I and pharmacokinetic study of halofuginone, an oral quinazolinone derivative in patients with advanced solid tumours. Eur. J. Cancer 42, 1768–1774 (2006)

    CAS  Article  Google Scholar 

  6. Koon, H. B. et al. Phase II AIDS Malignancy Consortium trial of topical halofuginone in AIDS-related Kaposi sarcoma. J. Acquir. Immune Defic. Syndr. 56, 64–68 (2011)

    CAS  Article  Google Scholar 

  7. Sundrud, M. S. et al. Halofuginone inhibits TH17 cell differentiation by activating the amino acid starvation response. Science 324, 1334–1338 (2009)

    ADS  CAS  Article  Google Scholar 

  8. Keller, T. L. et al. Halofuginone and other febrifugine derivatives inhibit prolyl-tRNA synthetase. Nature Chem. Biol. 8, 311–317 (2012)

    ADS  CAS  Article  Google Scholar 

  9. Kilberg, M. S., Pan, Y. X., Chen, H. & Leung-Pineda, V. Nutritional control of gene expression: how mammalian cells respond to amino acid limitation. Annu. Rev. Nutr. 25, 59–85 (2005)

    CAS  Article  Google Scholar 

  10. Schimmel, P., Tao, J. & Hill, J. Aminoacyl tRNA synthetases as targets for new anti-infectives. FASEB J. 12, 1599–1609 (1998)

    CAS  Article  Google Scholar 

  11. Hill, J. Aminoacyl sulfamides for the treatment of hyperproliferative disorders. US Patent 5,824. 657 (1998)

  12. Carter, C. W., Jr Cognition, mechanism, and evolutionary relationships in aminoacyl-tRNA synthetases. Annu. Rev. Biochem. 62, 715–748 (1993)

    CAS  Article  Google Scholar 

  13. Yaremchuk, A., Tukalo, M., Grotli, M. & Cusack, S. A succession of substrate induced conformational changes ensures the amino acid specificity of Thermus thermophilus prolyl-tRNA synthetase: comparison with histidyl-tRNA synthetase. J. Mol. Biol. 309, 989–1002 (2001)

    CAS  Article  Google Scholar 

  14. Zhu, S. et al. Synthesis and biological evaluation of febrifugine analogues as potential antimalarial agents. Bioorg. Med. Chem. 17, 4496–4502 (2009)

    CAS  Article  Google Scholar 

  15. Sankaranarayanan, R. et al. The structure of threonyl-tRNA synthetase-tRNAThr complex enlightens its repressor activity and reveals an essential zinc ion in the active site. Cell 97, 371–381 (1999)

    CAS  Article  Google Scholar 

  16. Heacock, D., Forsyth, C. J., Shiba, K. & Musier-Forsyth, K. Synthesis and aminoacyl-tRNA synthetase inhibitory activity of prolyl adenylate analogs. Bioorg. Chem. 24, 273–289 (1996)

    CAS  Article  Google Scholar 

  17. Nakama, T., Nureki, O. & Yokoyama, S. Structural basis for the recognition of isoleucyl-adenylate and an antibiotic, mupirocin, by isoleucyl-tRNA synthetase. J. Biol. Chem. 276, 47387–47393 (2001)

    CAS  Article  Google Scholar 

  18. Rock, F. L. et al. An antifungal agent inhibits an aminoacyl-tRNA synthetase by trapping tRNA in the editing site. Science 316, 1759–1761 (2007)

    ADS  CAS  Article  Google Scholar 

  19. Pantoliano, M. W. et al. High-density miniaturized thermal shift assays as general strategy for drug discovery. J. Biomol. Screen. 6, 429–440 (2001)

    CAS  Article  Google Scholar 

  20. Arnold, K., Bordoli, L., Kopp, J. & Schwede, T. The SWISS-MODEL workspace: a web-based environment for protein structure homology modeling. Bioinformatics 22, 195–201 (2006)

    CAS  Article  Google Scholar 

  21. Beebe, K. et al. A universal plate format for increased throughput of assays that monitor multiple aminoacyl transfer RNA synthetase activities. Anal. Biochem. 368, 111–121 (2007)

    CAS  Article  Google Scholar 

  22. Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326 (1997)

    CAS  Article  Google Scholar 

  23. Vagin, A. & Teplyakov, A. MOLREP: an automated program for molecular replacement. J. Appl. Crystallogr. 30, 1022–1025 (1997)

    CAS  Article  Google Scholar 

  24. Murshudov, G. N., Vagin, A. A. & Dodson, E. J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D 53, 240–255 (1997)

    CAS  Article  Google Scholar 

  25. Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D 66, 213–221 (2010)

    CAS  Article  Google Scholar 

  26. Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126–2132 (2004)

    Article  Google Scholar 

  27. Chen, V. B. et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D 66, 12–21 (2010)

    CAS  Article  Google Scholar 

  28. Corpet, F. Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res. 16, 10881–10890 (1988)

    CAS  Article  Google Scholar 

  29. Gouet, P., Courcelle, E., Stuart, D. I. & Metoz, F. ESPript: analysis of multiple sequence alignments in PostScript. Bioinformatics 15, 305–308 (1999)

    CAS  Article  Google Scholar 

  30. Shi, J. P. & Schimmel, P. Aminoacylation of alanine minihelices. ‘Discriminator’ base modulates transition state of single turnover reaction. J. Biol. Chem. 266, 2705–2708 (1991)

    CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We thank K. Musier-Forsyth for providing the ProRS gene plasmid and Pro-SA, staff at beamline 7-1 of Stanford Synchrotron Radiation Lightsource for assistance in X-ray diffraction data collection, and M. Guo for comments. This work was supported by National Institutes of Health grants GM15539, GM23562 and GM88278 and by a fellowship from the National Foundation for Cancer Research.

Author information

Authors and Affiliations

Authors

Contributions

H.Z., L.S., X.-L.Y. and P.S. designed the experiments. H.Z. and L.S. performed the experiments and all authors analysed the data. All authors discussed the results and H.Z. and P.S. wrote the manuscript.

Corresponding author

Correspondence to Paul Schimmel.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Figures 1-5 and Supplementary Table 1. (PDF 1223 kb)

PowerPoint slides

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Zhou, H., Sun, L., Yang, XL. et al. ATP-directed capture of bioactive herbal-based medicine on human tRNA synthetase. Nature 494, 121–124 (2013). https://doi.org/10.1038/nature11774

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature11774

Further reading

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing