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Allosteric non-bisphosphonate FPPS inhibitors identified by fragment-based discovery

Nature Chemical Biology volume 6, pages 660–666 (2010)Cite this article

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Abstract

Bisphosphonates are potent inhibitors of farnesyl pyrophosphate synthase (FPPS) and are highly efficacious in the treatment of bone diseases such as osteoporosis, Paget's disease and tumor-induced osteolysis. In addition, the potential for direct antitumor effects has been postulated on the basis of in vitro and in vivo studies and has recently been demonstrated clinically in early breast cancer patients treated with the potent bisphosphonate zoledronic acid. However, the high affinity of bisphosphonates for bone mineral seems suboptimal for the direct treatment of soft-tissue tumors. Here we report the discovery of the first potent non-bisphosphonate FPPS inhibitors. These new inhibitors bind to a previously unknown allosteric site on FPPS, which was identified by fragment-based approaches using NMR and X-ray crystallography. This allosteric and druggable pocket allows the development of a new generation of FPPS inhibitors that are optimized for direct antitumor effects in soft tissue.

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Figure 1: Identification of fragments with binding affinity to FPPS.
Figure 2: Crystal structures of FPPS complexed with inhibitors.
Figure 3: Cellular activity of 10 in a plasma membrane translocation assay. (a) eGFP tagged with the prenylation motif of human H-Ras.
Figure 4: Mechanism of FPPS inhibition by allosteric ligands.

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Acknowledgements

We thank G. Hofmann for help with the plasma membrane translocation assay, A. Schmid for help with the scintillation proximity assay, R. Denay for recording the 13C NMR spectra, W. Breitenstein for help in preparing the manuscript and B. Faller for useful discussions. X-ray data collections of the FPPS complexes with 1 to 4, 8 and 10 were performed at the Swiss Light Source, Paul Scherrer Institut, Villigen, Switzerland. We are grateful to the machine and beamline groups whose outstanding efforts have made these experiments possible.

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Authors and Affiliations

  1. Center for Proteomic Chemistry and Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Basel, Switzerland

    Wolfgang Jahnke, Jean-Michel Rondeau, Simona Cotesta, Andreas Marzinzik, Xavier Pellé, Martin Geiser, André Strauss, Marjo Götte, Francis Bitsch, René Hemmig, Chrystèle Henry, Sylvie Lehmann, J Fraser Glickman, Thomas P Roddy, Steven J Stout & Jonathan R Green

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  1. Wolfgang Jahnke
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  2. Jean-Michel Rondeau
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Contributions

W.J. initiated the project, led the project team and performed NMR studies together with C.H. J.-M.R. and S.L. performed crystallographic studies. S.C. performed molecular modeling studies. A.M. and X.P. synthesized chemical compounds. M. Geiser, A.S. and R.H. cloned, expressed and purified protein. M. Götte performed the cellular assay, F.B. performed ITC experiments, J.F.G., T.P.R. and S.J.S. performed the biochemical assay. W.J., J.-M.R. and J.R.G. wrote the paper with input from all coauthors.

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Correspondence to Wolfgang Jahnke.

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All authors are past or present full-time employees of Novartis AG and hold stock in the company.

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Supplementary Figures 1–7, Supplementary Tables 1 & 2 and Supplementary Methods (PDF 479 kb)

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Jahnke, W., Rondeau, JM., Cotesta, S. et al. Allosteric non-bisphosphonate FPPS inhibitors identified by fragment-based discovery. Nat Chem Biol 6, 660–666 (2010). https://doi.org/10.1038/nchembio.421

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