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Structure-guided design of a selective BCL-XL inhibitor

Nature Chemical Biology volume 9, pages 390–397 (2013)Cite this article

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Abstract

The prosurvival BCL-2 family protein BCL-XL is often overexpressed in solid tumors and renders malignant tumor cells resistant to anticancer therapeutics. Enhancing apoptotic responses by inhibiting BCL-XL will most likely have widespread utility in cancer treatment and, instead of inhibiting multiple prosurvival BCL-2 family members, a BCL-XL–selective inhibitor would be expected to minimize the toxicity to normal tissues. We describe the use of a high-throughput screen to discover a new series of small molecules targeting BCL-XL and their structure-guided development by medicinal chemistry. The optimized compound, WEHI-539 (7), has high affinity (subnanomolar) and selectivity for BCL-XL and potently kills cells by selectively antagonizing its prosurvival activity. WEHI-539 will be an invaluable tool for distinguishing the roles of BCL-XL from those of its prosurvival relatives, both in normal cells and notably in malignant tumor cells, many of which may prove to rely upon BCL-XL for their sustained growth.

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Figure 1: Compounds from the benzothiazole series adopt a unique binding mode in BCL-XL hydrophobic pocket P2.
Figure 2: Core optimization and extension toward P4 augment affinity.
Figure 3: WEHI-539 interacts with residues in the P4 pocket and adopts a distinct binding mode compared to ABT-737.
Figure 4: Decreased dissociation rate of the benzothiazole compounds from BCL-XL underpins their increase in binding potency.
Figure 5: WEHI-539 kills MEFs only when MCL-1 is absent or blocked.
Figure 6: WEHI-539 provokes BAK-mediated apoptosis in BCL-XL–dependent cells.

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Acknowledgements

The authors thank J. Blyth, D. Buczek, A. Georgiou, H. Ierino, C. Rye, G. Siciliano, G. Thompson and A. Wardak for outstanding technical assistance; S. Cory (Walter and Eliza Hall Institute of Medical Research (WEHI)), L. Chen (WEHI), V. Dixit (Genentech (GNE)), M. Hijnen (GE Healthcare), S. Hymowitz (GNE), D. Segal (WEHI), V. Tsui (GNE), M.F. van Delft (WEHI), A.H. Wei (WEHI) and I. Wertz (GNE) for discussions and suggestions; P. Bouillet and A. Strasser (both from WEHI) for mice; W.D. Fairlie and E. Lee (both from WEHI) for expression constructs; W. Welch (University of California–San Francisco) for anti-HSP70; P. Pilling, V. Streltsov (both from Commonwealth Scientific and Industrial Research Organisation, Australia) and staff at the photon Factory BL6 for their help with collecting data for 2; and AbbVie for providing ABT-737. This work was supported by fellowships and grants from the Australian Research Council (fellowship to P.E.C.), the National Health and Medical Research Council (NHMRC) (fellowships to J.M.A., J.B.B., P.M.C. and D.C.S.H.; development grant 305536 and program grants 257502, 461221 and 1016701), the Leukemia and Lymphoma Society (specialized center of research grant nos. 7015 and 7413), the Cancer Council of Victoria (fellowship to P.M.C.; grant-in-aid 461239) and the Australian Cancer Research Foundation. Infrastructure support from the NHMRC Independent Research Institutes Infrastructure Support Scheme grant no. 361646 and a Victorian State Government OIS grant are gratefully acknowledged.

Author information

Author notes

  1. Jonathan B Baell, Sanji Kulasegaram, John P Parisot & Brian J Smith

    Present address: Present addresses: Monash Institute of Pharmaceutical Sciences, Parkville, Victoria, Australia (J.B.B.); Chemistry Department, Monash University, Clayton, Victoria, Australia (S.K.); Peter McCallum Cancer Centre, East Melbourne, Victoria, Australia (J.P.P.); Department of Chemistry, La Trobe Institute of Molecular Sciences, La Trobe University, Bundoora, Victoria, Australia (B.J.S.).,

  2. Peter E Czabotar and Brad E Sleebs: These authors contributed equally to this work.

Authors and Affiliations

  1. Chemical Biology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia

    Guillaume Lessene, Brad E Sleebs, Kym N Lowes, Jonathan B Baell, Wilhelmus J A Kersten, Sanji Kulasegaram, Rebecca M Moss, John P Parisot, Brian J Smith, Ian P Street, Hong Yang, David C S Huang & Keith G Watson

  2. Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia

    Guillaume Lessene, Peter E Czabotar, Brad E Sleebs, Kym N Lowes, Jerry M Adams, Jonathan B Baell, Peter M Colman, Wilhelmus J A Kersten, Sanji Kulasegaram, Rebecca M Moss, John P Parisot, Brian J Smith, Ian P Street, Hong Yang, David C S Huang & Keith G Watson

  3. Structural Biology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia

    Peter E Czabotar & Peter M Colman

  4. Department of Early Discovery Biochemistry, Genentech, Inc., San Francisco, California, USA

    Kerry Zobel, Kurt Deshayes & Wayne J Fairbrother

  5. Molecular Genetics of Cancer Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia

    Jerry M Adams

  6. Department of Discovery Chemistry, Genentech, Inc., San Francisco, California, USA

    John A Flygare & Paul Gibbons

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  1. Guillaume Lessene
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Contributions

G.L. devised synthetic strategies, synthesized compounds, supervised the chemistry team and wrote the manuscript. P.E.C. performed X-ray crystallization and solved and analyzed structures. B.E.S., K.Z., W.J.A.K., S.K. and K.D. designed and synthesized compounds. J.M.A. conceived the study and analyzed data and results. J.B.B., K.D., J.A.F. and K.G.W. designed synthetic strategies and oversaw chemistry efforts. P.M.C. conceived the study and designed and oversaw structural studies. K.N.L. performed biological experiments. P.G. and B.J.S. performed computational modeling. W.J.F. and J.A.F. designed studies and data analysis. R.M.M., J.P.P. and I.P.S. performed the high-throughput chemical screening campaign. H.Y. performed Biacore experiments. D.C.S.H. conceived the study, designed and oversaw biological experiments and wrote the manuscript.

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Correspondence to Guillaume Lessene.

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Competing interests

G.L., P.E.C., B.E.S., K.N.L., J.M.A., J.B.B., P.M.C., W.J.A.K., S.K., R.M.M., J.P.P., B.J.S., I.P.S., H.Y., D.C.S.H. and K.G.W. are or were employees of WEHI, which received commercial income and research funding from Genentech, Inc. for part of this work. W.J.F., J.A.F., K.D., P.G. and K.Z. are employees of Genentech, Inc., a member of the Roche group, and are stockholders of Roche Holding.

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Lessene, G., Czabotar, P., Sleebs, B. et al. Structure-guided design of a selective BCL-XL inhibitor. Nat Chem Biol 9, 390–397 (2013). https://doi.org/10.1038/nchembio.1246

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