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Development of a Novel B-Cell Lymphoma 6 (BCL6) PROTAC To Provide Insight into Small Molecule Targeting of BCL6

  • William McCoull*
    William McCoull
    Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, 310 Cambridge Science Park, Milton Road, Cambridge CB4 0WG, U.K.
    *E-mail: [email protected]
  • Tony Cheung
    Tony Cheung
    Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gatehouse Park, Waltham, Massachusetts 02451, United States
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  • Erica Anderson
    Erica Anderson
    Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gatehouse Park, Waltham, Massachusetts 02451, United States
  • Peter Barton
    Peter Barton
    Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, 310 Cambridge Science Park, Milton Road, Cambridge CB4 0WG, U.K.
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  • Jonathan Burgess
    Jonathan Burgess
    Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, 310 Cambridge Science Park, Milton Road, Cambridge CB4 0WG, U.K.
  • Kate Byth
    Kate Byth
    Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gatehouse Park, Waltham, Massachusetts 02451, United States
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  • Qing Cao
    Qing Cao
    Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gatehouse Park, Waltham, Massachusetts 02451, United States
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  • M. Paola Castaldi
    M. Paola Castaldi
    Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gatehouse Park, Waltham, Massachusetts 02451, United States
  • Huawei Chen
    Huawei Chen
    Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gatehouse Park, Waltham, Massachusetts 02451, United States
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  • Elisabetta Chiarparin
    Elisabetta Chiarparin
    Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, 310 Cambridge Science Park, Milton Road, Cambridge CB4 0WG, U.K.
  • Rodrigo J. Carbajo
    Rodrigo J. Carbajo
    Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, 310 Cambridge Science Park, Milton Road, Cambridge CB4 0WG, U.K.
  • Erin Code
    Erin Code
    Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gatehouse Park, Waltham, Massachusetts 02451, United States
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  • Suzanna Cowan
    Suzanna Cowan
    Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, 310 Cambridge Science Park, Milton Road, Cambridge CB4 0WG, U.K.
  • Paul R. Davey
    Paul R. Davey
    Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, 310 Cambridge Science Park, Milton Road, Cambridge CB4 0WG, U.K.
  • Andrew D. Ferguson
    Andrew D. Ferguson
    Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gatehouse Park, Waltham, Massachusetts 02451, United States
  • Shaun Fillery
    Shaun Fillery
    Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, 310 Cambridge Science Park, Milton Road, Cambridge CB4 0WG, U.K.
  • Nathan O. Fuller
    Nathan O. Fuller
    Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gatehouse Park, Waltham, Massachusetts 02451, United States
  • Ning Gao
    Ning Gao
    Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gatehouse Park, Waltham, Massachusetts 02451, United States
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  • David Hargreaves
    David Hargreaves
    Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, 310 Cambridge Science Park, Milton Road, Cambridge CB4 0WG, U.K.
  • Martin R. Howard
    Martin R. Howard
    Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, 310 Cambridge Science Park, Milton Road, Cambridge CB4 0WG, U.K.
  • Jun Hu
    Jun Hu
    Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gatehouse Park, Waltham, Massachusetts 02451, United States
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  • Aarti Kawatkar
    Aarti Kawatkar
    Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gatehouse Park, Waltham, Massachusetts 02451, United States
  • Paul D. Kemmitt
    Paul D. Kemmitt
    Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, 310 Cambridge Science Park, Milton Road, Cambridge CB4 0WG, U.K.
  • Elisabetta Leo
    Elisabetta Leo
    Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, 310 Cambridge Science Park, Milton Road, Cambridge CB4 0WG, U.K.
  • Daniel M. Molina
    Daniel M. Molina
    Pelago Bioscience AB, Banvaktsvägen 20, 17148 Solna, Sweden
  • Nichole O’Connell
    Nichole O’Connell
    Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gatehouse Park, Waltham, Massachusetts 02451, United States
  • Philip Petteruti
    Philip Petteruti
    Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gatehouse Park, Waltham, Massachusetts 02451, United States
  • Timothy Rasmusson
    Timothy Rasmusson
    Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gatehouse Park, Waltham, Massachusetts 02451, United States
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    Piotr Raubo
    Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, 310 Cambridge Science Park, Milton Road, Cambridge CB4 0WG, U.K.
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  • Philip B. Rawlins
    Philip B. Rawlins
    Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, 310 Cambridge Science Park, Milton Road, Cambridge CB4 0WG, U.K.
  • Piero Ricchiuto
    Piero Ricchiuto
    Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, 310 Cambridge Science Park, Milton Road, Cambridge CB4 0WG, U.K.
  • Graeme R. Robb
    Graeme R. Robb
    Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, 310 Cambridge Science Park, Milton Road, Cambridge CB4 0WG, U.K.
  • Monica Schenone
    Monica Schenone
    Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, Massachusetts 02142, United States
  • Michael J. Waring
    Michael J. Waring
    Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, 310 Cambridge Science Park, Milton Road, Cambridge CB4 0WG, U.K.
  • Michael Zinda
    Michael Zinda
    Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gatehouse Park, Waltham, Massachusetts 02451, United States
  • Stephen Fawell
    Stephen Fawell
    Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gatehouse Park, Waltham, Massachusetts 02451, United States
  • , and 
  • David M. Wilson
    David M. Wilson
    Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, 310 Cambridge Science Park, Milton Road, Cambridge CB4 0WG, U.K.
Cite this: ACS Chem. Biol. 2018, 13, 11, 3131–3141
Publication Date (Web):October 17, 2018
https://doi.org/10.1021/acschembio.8b00698
Copyright © 2018 American Chemical Society

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    Abstract

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    B-cell lymphoma 6 (BCL6) inhibition is a promising mechanism for treating hematological cancers but high quality chemical probes are necessary to evaluate its therapeutic potential. Here we report potent BCL6 inhibitors that demonstrate cellular target engagement and exhibit exquisite selectivity for BCL6 based on mass spectrometry analyses following chemical proteomic pull down. Importantly, a proteolysis-targeting chimera (PROTAC) was also developed and shown to significantly degrade BCL6 in a number of diffuse large B-cell lymphoma (DLBCL) cell lines, but neither BCL6 inhibition nor degradation selectively induced marked phenotypic response. To investigate, we monitored PROTAC directed BCL6 degradation in DLBCL OCI-Ly1 cells by immunofluorescence and discovered a residual BCL6 population. Analysis of subcellular fractions also showed incomplete BCL6 degradation in all fractions despite having measurable PROTAC concentrations, together providing a rationale for the weak antiproliferative response seen with both BCL6 inhibitor and degrader. In summary, we have developed potent and selective BCL6 inhibitors and a BCL6 PROTAC that effectively degraded BCL6, but both modalities failed to induce a significant phenotypic response in DLBCL despite achieving cellular concentrations.

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    The Supporting Information is available free of charge on the ACS Publications website at DOI: 10.1021/acschembio.8b00698.

    • Detailed descriptions of the experimental material and methods applied in this study, kinase inhibition profiles for 4 and 6, crystallographic data, subcellular fractionation details, BCL6 degradation by 15, conformational analysis, CETSA data, MS proteomics data, PROTAC degradation of BCL6, BCL6 protein levels across cell lines, affect of BCL6 degradation on antiproliferative activity, qPCR and immunofluorescence analysis of MDA-MB-468 cell line, cell subfraction analysis, 2D NMR, BCL6 degradation by PROTACs with alternative linkers (PDF)

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    The structures of BCL6 BTB domain bound to compounds 1, 2, and 9 have been deposited in the Protein Data Bank with PDB accession codes 6ew6, 6ew7, and 6ew8, respectively.

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    Most electronic Supporting Information files are available without a subscription to ACS Web Editions. Such files may be downloaded by article for research use (if there is a public use license linked to the relevant article, that license may permit other uses). Permission may be obtained from ACS for other uses through requests via the RightsLink permission system: http://pubs.acs.org/page/copyright/permissions.html.

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