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.

Chemical inhibition of prometastatic lysyl-tRNA synthetase–laminin receptor interaction

Abstract

Lysyl-tRNA synthetase (KRS), a protein synthesis enzyme in the cytosol, relocates to the plasma membrane after a laminin signal and stabilizes a 67-kDa laminin receptor (67LR) that is implicated in cancer metastasis; however, its potential as an antimetastatic therapeutic target has not been explored. We found that the small compound BC-K-YH16899, which binds KRS, impinged on the interaction of KRS with 67LR and suppressed metastasis in three different mouse models. The compound inhibited the KRS-67LR interaction in two ways. First, it directly blocked the association between KRS and 67LR. Second, it suppressed the dynamic movement of the N-terminal extension of KRS and reduced membrane localization of KRS. However, it did not affect the catalytic activity of KRS. Our results suggest that specific modulation of a cancer-related KRS-67LR interaction may offer a way to control metastasis while avoiding the toxicities associated with inhibition of the normal functions of KRS.

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

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Effects of KRS on cancer metastasis.
Figure 2: Identification of YH16899 inhibiting KRS–LR interaction and cell invasion.
Figure 3: Mapping and validation of an YH16899 docking site.
Figure 4: Effects of YH16899 binding on the KRS structure.
Figure 5: A schematic model for the mode of action of YH16899.

Accession codes

Accessions

Protein Data Bank

References

  1. Steeg, P.S. Tumor metastasis: mechanistic insights and clinical challenges. Nat. Med. 12, 895–904 (2006).

    Article  CAS  PubMed  Google Scholar 

  2. Berno, V. et al. The 67 kDa laminin receptor increases tumor aggressiveness by remodeling laminin-1. Endocr. Relat. Cancer 12, 393–406 (2005).

    Article  CAS  PubMed  Google Scholar 

  3. Givant-Horwitz, V., Davidson, B. & Reich, R. Laminin-induced signaling in tumor cells. Cancer Lett. 223, 1–10 (2005).

    Article  CAS  PubMed  Google Scholar 

  4. Kim, D.G. et al. Interaction of two translational components, lysyl-tRNA synthetase and p40/37LRP, in plasma membrane promotes laminin-dependent cell migration. FASEB J. 26, 4142–4159 (2012).

    Article  CAS  PubMed  Google Scholar 

  5. Scheiman, J., Tseng, J.C., Zheng, Y. & Meruelo, D. Multiple functions of the 37/67-kD laminin receptor make it a suitable target for novel cancer gene therapy. Mol. Ther. 18, 63–74 (2010).

    Article  CAS  PubMed  Google Scholar 

  6. van den Brûle, F.A. et al. Expression of the 67-kD laminin receptor, galectin-1, and galectin-3 in advanced human uterine adenocarcinoma. Hum. Pathol. 27, 1185–1191 (1996).

    Article  PubMed  Google Scholar 

  7. Sanjuán, X. et al. Overexpression of the 67-kD laminin receptor correlates with tumour progression in human colorectal carcinoma. J. Pathol. 179, 376–380 (1996).

    Article  PubMed  Google Scholar 

  8. Martignone, S. et al. Prognostic significance of the 67-kilodalton laminin receptor expression in human breast carcinomas. J. Natl. Cancer Inst. 85, 398–402 (1993).

    Article  CAS  PubMed  Google Scholar 

  9. Fontanini, G. et al. 67-Kilodalton laminin receptor expression correlates with worse prognostic indicators in non-small cell lung carcinomas. Clin. Cancer Res. 3, 227–231 (1997).

    CAS  PubMed  Google Scholar 

  10. Li, D. et al. 67-kDa laminin receptor in human bile duct carcinoma. Eur. Surg. Res. 42, 168–173 (2009).

    Article  CAS  PubMed  Google Scholar 

  11. Batissoco, A.C., Auricchio, M.T., Kimura, L., Tabith-Junior, A. & Mingroni-Netto, R.C. A novel missense mutation p.L76P in the GJB2 gene causing nonsyndromic recessive deafness in a Brazilian family. Braz. J. Med. Biol. Res. 42, 168–171 (2009).

    Article  CAS  PubMed  Google Scholar 

  12. Morris, G.M. et al. AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. J. Comput. Chem. 30, 2785–2791 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Allen, B. Jr. Is CMS's requirement for age-specific clinical evidence before considering coverage for CT colonography reasonable and necessary? J. Am. Coll. Radiol. 6, 606–608 (2009).

    Article  PubMed  Google Scholar 

  14. Guo, M., Ignatov, M., Musier-Forsyth, K., Schimmel, P. & Yang, X.L. Crystal structure of tetrameric form of human lysyl-tRNA synthetase: implications for multisynthetase complex formation. Proc. Natl. Acad. Sci. USA 105, 2331–2336 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Ofir-Birin, Y. et al. Structural switch of lysyl-tRNA synthetase between translation and transcription. Mol. Cell 49, 30–42 (2013).

    Article  CAS  PubMed  Google Scholar 

  16. Park, S.G. et al. Human lysyl-tRNA synthetase is secreted to trigger proinflammatory response. Proc. Natl. Acad. Sci. USA 102, 6356–6361 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Kim, J.Y. et al. p38 is essential for the assembly and stability of macromolecular tRNA synthetase complex: implications for its physiological significance. Proc. Natl. Acad. Sci. USA 99, 7912–7916 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Kwon, N.H. et al. Dual role of methionyl-tRNA synthetase in the regulation of translation and tumor suppressor activity of aminoacyl-tRNA synthetase-interacting multifunctional protein-3. Proc. Natl. Acad. Sci. USA 108, 19635–19640 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Nam, J.S. et al. Transforming growth factor β subverts the immune system into directly promoting tumor growth through interleukin-17. Cancer Res. 68, 3915–3923 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Sevenich, L. et al. Transgenic expression of human cathepsin B promotes progression and metastasis of polyoma-middle-T–induced breast cancer in mice. Oncogene 30, 54–64 (2011).

    Article  CAS  PubMed  Google Scholar 

  21. Arguello, F. et al. Incidence and distribution of experimental metastases in mutant mice with defective organ microenvironments (genotypes Sl/Sld and W/Wv). Cancer Res. 52, 2304–2309 (1992).

    CAS  PubMed  Google Scholar 

  22. Pérot, S., Sperandio, O., Miteva, M.A., Camproux, A.C. & Villoutreix, B.O. Druggable pockets and binding site centric chemical space: a paradigm shift in drug discovery. Drug Discov. Today 15, 656–667 (2010).

    Article  PubMed  CAS  Google Scholar 

  23. Cheng, A.C. et al. Structure-based maximal affinity model predicts small-molecule druggability. Nat. Biotechnol. 25, 71–75 (2007).

    Article  PubMed  CAS  Google Scholar 

  24. Fang, P. et al. Structural context for mobilization of a human tRNA synthetase from its cytoplasmic complex. Proc. Natl. Acad. Sci. USA 108, 8239–8244 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Omar, A., Reusch, U., Knackmuss, S., Little, M. & Weiss, S.F. Anti-LRP/LR-specific antibody IgG1-iS18 significantly reduces adhesion and invasion of metastatic lung, cervix, colon and prostate cancer cells. J. Mol. Biol. 419, 102–109 (2012).

    Article  CAS  PubMed  Google Scholar 

  26. Zuber, C. et al. Invasion of tumorigenic HT1080 cells is impeded by blocking or downregulating the 37-kDa/67-kDa laminin receptor. J. Mol. Biol. 378, 530–539 (2008).

    Article  CAS  PubMed  Google Scholar 

  27. Lukk, M. et al. A global map of human gene expression. Nat. Biotechnol. 28, 322–324 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Hippo, Y. et al. Global gene expression analysis of gastric cancer by oligonucleotide microarrays. Cancer Res. 62, 233–240 (2002).

    CAS  PubMed  Google Scholar 

  29. Hura, G.L. et al. Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS). Nat. Methods 6, 606–612 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Young, I.S. & Nicholls, D.P. Lipid metabolism. Curr. Opin. Lipidol. 21, 550–551 (2010).

    Article  CAS  PubMed  Google Scholar 

  31. Pettersen, E.F. et al. UCSF Chimera—a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).

    Article  CAS  PubMed  Google Scholar 

  32. Soares, M.R., de Paula, F.O., Chaves, M., Assis, N.M. & Chaves Filho, H.D. Patient with Down syndrome and implant therapy: a case report. Braz. Dent. J. 21, 550–554 (2010).

    Article  PubMed  Google Scholar 

  33. Schmidlin, K. et al. Complication and failure rates in patients treated for chronic periodontitis and restored with single crowns on teeth and/or implants. Clin. Oral Implants Res. 21, 550–557 (2010).

    Article  PubMed  Google Scholar 

  34. Otani, A. et al. A fragment of human TrpRS as a potent antagonist of ocular angiogenesis. Proc. Natl. Acad. Sci. USA 99, 178–183 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Cardin, V., Friston, K.J. & Zeki, S. Top-down modulations in the visual form pathway revealed with dynamic causal modeling. Cereb. Cortex 21, 550–562 (2011).

    Article  PubMed  Google Scholar 

  36. Ford, C.L., Randal-Whitis, L. & Ellis, S.R. Yeast proteins related to the p40/laminin receptor precursor are required for 20S ribosomal RNA processing and the maturation of 40S ribosomal subunits. Cancer Res. 59, 704–710 (1999).

    CAS  PubMed  Google Scholar 

  37. Kawamata, H., Magrane, J., Kunst, C., King, M.P. & Manfredi, G. Lysyl-tRNA synthetase is a target for mutant SOD1 toxicity in mitochondria. J. Biol. Chem. 283, 28321–28328 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Kim, E.S. et al. Sphingosine 1-phosphate regulates matrix metalloproteinase-9 expression and breast cell invasion through S1P3-Gαq coupling. J. Cell Sci. 124, 2220–2230 (2011).

    Article  CAS  PubMed  Google Scholar 

  39. Nyberg, P. et al. Endostatin inhibits human tongue carcinoma cell invasion and intravasation and blocks the activation of matrix metalloprotease-2, -9, and -13. J. Biol. Chem. 278, 22404–22411 (2003).

    Article  CAS  PubMed  Google Scholar 

  40. Shenkarev, Z.O. et al. Lipid-protein nanodiscs: possible application in high-resolution NMR investigations of membrane proteins and membrane-active peptides. Biochemistry (Mosc.) 74, 756–765 (2009).

    Article  CAS  Google Scholar 

  41. Delaglio, F. et al. NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J. Biomol. NMR 6, 277–293 (1995).

    Article  CAS  PubMed  Google Scholar 

  42. Vranken, W.F. et al. The CCPN data model for NMR spectroscopy: development of a software pipeline. Proteins 59, 687–696 (2005).

    Article  CAS  PubMed  Google Scholar 

  43. Kim, K.A. et al. Structure of human PRL-3, the phosphatase associated with cancer metastasis. FEBS Lett. 565, 181–187 (2004).

    Article  CAS  PubMed  Google Scholar 

  44. Putnam, C.D., Hammel, M., Hura, G.L. & Tainer, J.A. X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution. Q. Rev. Biophys. 40, 191–285 (2007).

    Article  CAS  PubMed  Google Scholar 

  45. Konarev, P.V., Volkov, V.V., Sokolova, A.V., Koch, M.H.J. & Svergun, D.I. PRIMUS: a Windows PC-based system for small-angle scattering data analysis. J. Appl. Crystallogr. 36, 1277–1282 (2003).

    Article  CAS  Google Scholar 

  46. Svergun, D.I. Determination of the regularization parameter in indirect-transform methods using perceptual criteria. J. Appl. Crystallogr. 25, 495–503 (1992).

    Article  CAS  Google Scholar 

  47. Franke, D. & Svergun, D.I. DAMMIF, a program for rapid ab-initio shape determination in small-angle scattering. J. Appl. Crystallogr. 42, 342–346 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Zhang, H.M. et al. Enhanced digestion efficiency, peptide ionization efficiency, and sequence resolution for protein hydrogen/deuterium exchange monitored by Fourier transform ion cyclotron resonance mass spectrometry. Anal. Chem. 80, 9034–9041 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Zhang, H.M., Bou-Assaf, G.M., Emmett, M.R. & Marshall, A.G. Fast reversed-phase liquid chromatography to reduce back exchange and increase throughput in H/D exchange monitored by FT-ICR mass spectrometry. J. Am. Soc. Mass Spectrom. 20, 520–524 (2009).

    Article  CAS  PubMed  Google Scholar 

  50. Zhang, H.M. et al. Simultaneous reduction and digestion of proteins with disulfide bonds for hydrogen/deuterium exchange monitored by mass spectrometry. Anal. Chem. 82, 1450–1454 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Schaub, T.M. et al. High-performance mass spectrometry: Fourier transform ion cyclotron resonance at 14.5 Tesla. Anal. Chem. 80, 3985–3990 (2008).

    Article  CAS  PubMed  Google Scholar 

  52. Kazazic, S. et al. Automated data reduction for hydrogen/deuterium exchange experiments, enabled by high-resolution Fourier transform ion cyclotron resonance mass spectrometry. J. Am. Soc. Mass Spectrom. 21, 550–558 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Zhang, Z., Li, W., Logan, T.M., Li, M. & Marshall, A.G. Human recombinant [C22A] FK506-binding protein amide hydrogen exchange rates from mass spectrometry match and extend those from NMR. Protein Sci. 6, 2203–2217 (1997).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Beebe, K., Waas, W., Druzina, Z., Guo, M. & Schimmel, P. A universal plate format for increased throughput of assays that monitor multiple aminoacyl transfer RNA synthetase activities. Anal. Biochem. 368, 111–121 (2007).

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

This work was supported by the Global Frontier Project (grants NRF-M1AXA002-2010-0029785 (S.K.), NRF-M1AXA002-2010-0029765 (Y.H.J.), NRF-2012M3A6A4054271 (J.W.L.) and NRF- 2012-054237 (B.W.H.)), the World Class University (grant R31-2008-000-10086-0 (G.H.)), the Proteogenomic Research Program (2012M3A9B9036679 (C.L.)) and by the National Research Foundation funded by the Ministry of Education, Science and Technology of Korea (grant ROA-2012-0006262 (A.M.)). This study was also funded by the Ministry for Health and Welfare Affairs of Korea through the Korea Healthcare Technology Research and Development Project (A092255 (D.-H.N.)) and by a grant from Gyeonggi Research Development Program (S.K.). This work was supported in part by grants from the US National Institutes of Health (GM100136 (M.G.)); the US National Science Foundation Division of Materials Research through DMR-11-57490 (A.G. Marshall, Florida State University); by the state of Florida (M.G.) and by a Kimmel Scholar Award for Cancer Research (M.G.). We appreciate A.G. Marshall for supporting the HDX-MS program and facility, M.-S. Seok (Korea University) for the preparation of the nanodisc and S.W. Lee (Sungkyunkwan University) for X-ray analysis.

Author information

Authors and Affiliations

Authors

Contributions

D.G.K., J.Y.L. and S.K. designed experiments. D.G.K., J.Y.L., P.F., Q.Z., J.W., H.Y.C., A.U.M., J.W.C., H.W.K., J.E.J., W.K., H.Y., M.-S.L., E.-S.K., E.J.K., J.S.Y., W.S.Y. and J.S.Y. performed experiments. D.G.K., J.Y.L., N.H.K., N.L.Y., M.G., Y.H.J., H.W.K., Y.H., D.-H.N., J.W.L., A.M., J.M.H., G.H., C.L. and S.K. analyzed the data. Y.H., K.K., Y.M., D.K., K.H.R. and B.W.H. provided materials and supported experiments. D.G.K., N.H.K., M.G., Y.H.J., Y.H. and S.K. wrote the manuscript. D.G.K., J.Y.L., N.H.K., M.G., Y.H.J., H.W.K., Y.H., D.-H.N. and S.K. reviewed the manuscript. D.G.K., J.Y.L., N.H.K., M.G., Y.H.J., G.H., M.W.W. and S.K. discussed the results and commented.

Corresponding author

Correspondence to Sunghoon Kim.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Results, Supplementary Tables 1–4, Supplementary Figures 1–24 and Supplementary Note. (PDF 14418 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Kim, D., Lee, J., Kwon, N. et al. Chemical inhibition of prometastatic lysyl-tRNA synthetase–laminin receptor interaction. Nat Chem Biol 10, 29–34 (2014). https://doi.org/10.1038/nchembio.1381

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nchembio.1381

This article is cited by

Search

Quick links

Nature Briefing: Translational Research

Sign up for the Nature Briefing: Translational Research newsletter — top stories in biotechnology, drug discovery and pharma.

Get what matters in translational research, free to your inbox weekly. Sign up for Nature Briefing: Translational Research