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Synthesis facilitates an understanding of the structural basis for translation inhibition by the lissoclimides

Abstract

The lissoclimides are unusual succinimide-containing labdane diterpenoids that were reported to be potent cytotoxins. Our short semisynthesis and analogue-oriented synthesis approaches provide a series of lissoclimide natural products and analogues that expand the structure–activity relationships (SARs) in this family. The semisynthesis approach yielded significant quantities of chlorolissoclimide (CL) to permit an evaluation against the National Cancer Institute's 60-cell line panel and allowed us to obtain an X-ray co-crystal structure of the synthetic secondary metabolite with the eukaryotic 80S ribosome. Although it shares a binding site with other imide-based natural product translation inhibitors, CL engages in a particularly interesting and novel face-on halogen–π interaction between the ligand's alkyl chloride and a guanine residue. Our analogue-oriented synthesis provides many more lissoclimide compounds, which were tested against aggressive human cancer cell lines and for protein synthesis inhibitory activity. Finally, computational modelling was used to explain the SARs of certain key compounds and set the stage for the structure-guided design of better translation inhibitors.

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Figure 1: Natural product inhibitors of the eukaryotic translation are important as potential drugs and biochemical tools.
Figure 2: The X-ray co-crystal structure of CL with the eukaryotic 80S ribosome reveals the molecular basis of translation inhibition.
Figure 3: Our two synthesis approaches to the lissoclimides are designed to access a broad range of structurally perturbed analogues for a better understanding of SARs.
Figure 4: Our analogue-oriented synthesis approaches to the lissoclimides and congeners are designed to access point changes in the natural product structures at key positions.
Figure 5: Crystallographically derived binding arrangement of CL in the 80S ribosome and predicted binding poses of three analogue structures to rationalize aspects of the experimentally determined SAR.

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Acknowledgements

Preliminary studies in the Vanderwal laboratory were supported by grants from the National Institutes of Health (NIH) and the University of California (UC) Cancer Research Coordinating Committee (GM-086483 and UCCRCC-55179, respectively, to C.D.V.). We acknowledge the Developmental Therapeutics Program of the National Cancer Institute for the evaluations of CL in the NCI-60 cell line panel. The work in the Yusupov laboratory was supported by the French National Research Agency ANR-15-CE11-0021-01 (to G.Y.), and by a European Research Council advanced grant 294312 (to S.P., M.M. and M.Y.). M.Y. thanks the Russian Government Program of Competitive Growth of Kazan Federal University. The Yusupov group is grateful to the staff of the PROXIMA 1 beamline at the synchrotron SOLEIL (France) and, in particular, to L. Chavas and P. Legrand for providing a rapid access and assisting with data collection. D.L.M. and C.Z. appreciate support from the NIH (GM-108889), and C.Z. was supported by a Brazilian Science Without Borders fellowship administered by Capes/LASPAU. The results from the Horne laboratory reported in this publication derived from work performed in the Drug Discovery and Structural Biology Core of City of Hope Comprehensive Cancer Center supported by the National Cancer Institute of the NIH under award number P30CA033572. The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH. Work in the Pelletier lab is supported by a Canadian Institutes of Health Research (CIHR) grant (FDN-148366). The work of V.O.V. from the laboratory of F. Furche (University of California Irvine Department of Chemistry) was supported by the National Science Foundation (CHE-1464828).

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C.D.V. and M.Y. designed the research with assistance from Z.A.K., G.Y., D.L.M., J.P. and D.A.H. All the synthetic chemistry was performed by Z.A.K., A.R.S. and S.E.M. M.M. purified and crystallized the yeast 80S ribosome. S.P. and M.M. performed the data collection at the synchrotron source. S.P. carried out the data processing, structure determination and interpretation of the CL/80S structure, with inputs from M.M., G.Y. and M.Y. Computational studies were carried out by C.Z. and V.O.V., cytotoxicity experiments were performed by S.N. and translation-inhibition data were obtained by R.C. C.D.V. wrote the manuscript with contributions from all the authors; all the authors helped to refine the manuscript and approved the final version.

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Correspondence to Marat Yusupov or Christopher D. Vanderwal.

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Könst, Z., Szklarski, A., Pellegrino, S. et al. Synthesis facilitates an understanding of the structural basis for translation inhibition by the lissoclimides. Nature Chem 9, 1140–1149 (2017). https://doi.org/10.1038/nchem.2800

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