I03-Macromolecular Crystallography
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Alice C.
Harnden
,
Owen A.
Davis
,
Gary M.
Box
,
Angela
Hayes
,
Louise D.
Johnson
,
Alan T.
Henley
,
Alexis K.
De Haven Brandon
,
Melanie
Valenti
,
Kwai-Ming J.
Cheung
,
Alfie
Brennan
,
Rosemary
Huckvale
,
Olivier A.
Pierrat
,
Rachel
Talbot
,
Michael D.
Bright
,
Hafize Aysin
Akpinar
,
Daniel S. J.
Miller
,
Dalia
Tarantino
,
Sharon
Gowan
,
Selby
De Klerk
,
Peter C.
Mcandrew
,
Yann-Vai
Le Bihan
,
Mirco
Meniconi
,
Rosemary
Burke
,
Vladimir
Kirkin
,
Rob
Van Montfort
,
Florence I.
Raynaud
,
Olivia W.
Rossanese
,
Benjamin R.
Bellenie
,
Swen
Hoelder
Diamond Proposal Number(s):
[24828]
Open Access
Abstract: B-cell lymphoma 6 (BCL6) is a transcriptional repressor and oncogenic driver of diffuse large B-cell lymphoma (DLBCL). Here, we report the optimization of our previously reported tricyclic quinolinone series for the inhibition of BCL6. We sought to improve the cellular potency and in vivo exposure of the non-degrading isomer, CCT373567, of our recently published degrader, CCT373566. The major limitation of our inhibitors was their high topological polar surface areas (TPSA), leading to increased efflux ratios. Reducing the molecular weight allowed us to remove polarity and decrease TPSA without considerably reducing solubility. Careful optimization of these properties, as guided by pharmacokinetic studies, led to the discovery of CCT374705, a potent inhibitor of BCL6 with a good in vivo profile. Modest in vivo efficacy was achieved in a lymphoma xenograft mouse model after oral dosing.
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Apr 2023
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I03-Macromolecular Crystallography
I04-1-Macromolecular Crystallography (fixed wavelength)
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Olivier A.
Pierrat
,
Manjuan
Liu
,
Gavin W.
Collie
,
Kartika N.
Shetty
,
Matthew J.
Rodrigues
,
Yann-Vai
Le Bihan
,
Emma A.
Gunnell
,
P. Craig
Mcandrew
,
Mark
Stubbs
,
Martin G.
Rowlands
,
Norhakim
Yahya
,
Erald
Shehu
,
Rachel
Talbot
,
Lisa
Pickard
,
Benjamin R.
Bellenie
,
Kwai-Ming J.
Cheung
,
Ludovic
Drouin
,
Paolo
Innocenti
,
Hannah
Woodward
,
Owen A.
Davis
,
Matthew G.
Lloyd
,
Ana
Varela
,
Rosemary
Huckvale
,
Fabio
Broccatelli
,
Michael
Carter
,
David
Galiwango
,
Angela
Hayes
,
Florence I.
Raynaud
,
Christopher
Bryant
,
Steven
Whittaker
,
Olivia W.
Rossanese
,
Swen
Hoelder
,
Rosemary
Burke
,
Rob L. M.
Van Montfort
Open Access
Abstract: By suppressing gene transcription through the recruitment of corepressor proteins, B-cell lymphoma 6 (BCL6) protein controls a transcriptional network required for the formation and maintenance of B-cell germinal centres. As BCL6 deregulation is implicated in the development of Diffuse Large B-Cell Lymphoma, we sought to discover novel small molecule inhibitors that disrupt the BCL6-corepressor protein–protein interaction (PPI). Here we report our hit finding and compound optimisation strategies, which provide insight into the multi-faceted orthogonal approaches that are needed to tackle this challenging PPI with small molecule inhibitors. Using a 1536-well plate fluorescence polarisation high throughput screen we identified multiple hit series, which were followed up by hit confirmation using a thermal shift assay, surface plasmon resonance and ligand-observed NMR. We determined X-ray structures of BCL6 bound to compounds from nine different series, enabling a structure-based drug design approach to improve their weak biochemical potency. We developed a time-resolved fluorescence energy transfer biochemical assay and a nano bioluminescence resonance energy transfer cellular assay to monitor cellular activity during compound optimisation. This workflow led to the discovery of novel inhibitors with respective biochemical and cellular potencies (IC50s) in the sub-micromolar and low micromolar range.
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Nov 2022
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I03-Macromolecular Crystallography
I04-1-Macromolecular Crystallography (fixed wavelength)
|
Owen A.
Davis
,
Kwai-Ming J.
Cheung
,
Alfie
Brennan
,
Matthew G.
Lloyd
,
Matthew J.
Rodrigues
,
Olivier A.
Pierrat
,
Gavin W.
Collie
,
Yann-Vai
Le Bihan
,
Rosemary
Huckvale
,
Alice C.
Harnden
,
Ana
Varela
,
Michael D.
Bright
,
Paul
Eve
,
Angela
Hayes
,
Alan T.
Henley
,
Michael D.
Carter
,
P. Craig
Mcandrew
,
Rachel
Talbot
,
Rosemary
Burke
,
Rob
Van Montfort
,
Florence I.
Raynaud
,
Olivia W.
Rossanese
,
Mirco
Meniconi
,
Benjamin R.
Bellenie
,
Swen
Hoelder
Open Access
Abstract: To identify new chemical series with enhanced binding affinity to the BTB domain of B-cell lymphoma 6 protein, we targeted a subpocket adjacent to Val18. With no opportunities for strong polar interactions, we focused on attaining close shape complementarity by ring fusion onto our quinolinone lead series. Following exploration of different sized rings, we identified a conformationally restricted core which optimally filled the available space, leading to potent BCL6 inhibitors. Through X-ray structure-guided design, combined with efficient synthetic chemistry to make the resulting novel core structures, a >300-fold improvement in activity was obtained by the addition of seven heavy atoms.
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Jun 2022
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I03-Macromolecular Crystallography
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Rosemary
Huckvale
,
Alice C.
Harnden
,
Kwai-Ming J.
Cheung
,
Olivier A.
Pierrat
,
Rachel
Talbot
,
Gary M.
Box
,
Alan T.
Henley
,
Alexis K.
De Haven Brandon
,
Albert E.
Hallsworth
,
Michael D.
Bright
,
Hafize Aysin
Akpinar
,
Daniel S. J.
Miller
,
Dalia
Tarantino
,
Sharon
Gowan
,
Angela
Hayes
,
Emma A.
Gunnell
,
Alfie
Brennan
,
Owen A.
Davis
,
Louise D.
Johnson
,
Selby
De Klerk
,
Craig
Mcandrew
,
Yann-Vai
Le Bihan
,
Mirco
Meniconi
,
Rosemary
Burke
,
Vladimir
Kirkin
,
Rob L. M.
Van Montfort
,
Florence I.
Raynaud
,
Olivia W.
Rossanese
,
Benjamin R.
Bellenie
,
Swen
Hoelder
Open Access
Abstract: The transcriptional repressor BCL6 is an oncogenic driver found to be deregulated in lymphoid malignancies. Herein, we report the optimization of our previously reported benzimidazolone molecular glue-type degrader CCT369260 to CCT373566, a highly potent probe suitable for sustained depletion of BCL6 in vivo. We observed a sharp degradation SAR, where subtle structural changes conveyed the ability to induce degradation of BCL6. CCT373566 showed modest in vivo efficacy in a lymphoma xenograft mouse model following oral dosing.
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Jun 2022
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I03-Macromolecular Crystallography
I04-1-Macromolecular Crystallography (fixed wavelength)
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Matthew G.
Lloyd
,
Rosemary
Huckvale
,
Kwai-Ming J.
Cheung
,
Matthew J.
Rodrigues
,
Gavin W.
Collie
,
Olivier A.
Pierrat
,
Mahad
Gatti Iou
,
Michael
Carter
,
Owen A.
Davis
,
P. Craig
Mcandrew
,
Emma
Gunnell
,
Yann-Vai
Le Bihan
,
Rachel
Talbot
,
Alan T.
Henley
,
Louise D.
Johnson
,
Angela T.
Hayes
,
Michael D.
Bright
,
Florence I.
Raynaud
,
Mirco
Meniconi
,
Rosemary
Burke
,
Rob L. M.
Van Montfort
,
Olivia W.
Rossanese
,
Benjamin R.
Bellenie
,
Swen
Hoelder
Diamond Proposal Number(s):
[14891, 20145]
Open Access
Abstract: We describe the optimization of modestly active starting points to potent inhibitors of BCL6 by growing into a subpocket, which was occupied by a network of five stably bound water molecules. Identifying potent inhibitors required not only forming new interactions in the subpocket but also perturbing the water network in a productive, potency-increasing fashion while controlling the physicochemical properties. We achieved this goal in a sequential manner by systematically probing the pocket and the water network, ultimately achieving a 100-fold improvement of activity. The most potent compounds displaced three of the five initial water molecules and formed hydrogen bonds with the remaining two. Compound 25 showed a promising profile for a lead compound with submicromolar inhibition of BCL6 in cells and satisfactory pharmacokinetic (PK) properties. Our work highlights the importance of finding productive ways to perturb existing water networks when growing into solvent-filled protein pockets.
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Nov 2021
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I03-Macromolecular Crystallography
I04-1-Macromolecular Crystallography (fixed wavelength)
|
Benjamin R.
Bellenie
,
Kwai-Ming J.
Cheung
,
Ana
Varela
,
Olivier A.
Pierrat
,
Gavin W.
Collie
,
Gary M.
Box
,
Michael D.
Bright
,
Sharon
Gowan
,
Angela
Hayes
,
Matthew J.
Rodrigues
,
Kartika N.
Shetty
,
Michael
Carter
,
Owen A.
Davis
,
Alan T.
Henley
,
Paolo
Innocenti
,
Louise D.
Johnson
,
Manjuan
Liu
,
Selby
De Klerk
,
Yann-Vai
Le Bihan
,
Matthew G.
Lloyd
,
P. Craig
Mcandrew
,
Erald
Shehu
,
Rachel
Talbot
,
Hannah L.
Woodward
,
Rosemary
Burke
,
Vladimir
Kirkin
,
Rob L. M.
Van Montfort
,
Florence I.
Raynaud
,
Olivia W.
Rossanese
,
Swen
Hoelder
Diamond Proposal Number(s):
[14891, 20145]
Open Access
Abstract: Deregulation of the transcriptional repressor BCL6 enables tumorigenesis of germinal center B-cells, and hence BCL6 has been proposed as a therapeutic target for the treatment of diffuse large B-cell lymphoma (DLBCL). Herein we report the discovery of a series of benzimidazolone inhibitors of the protein-protein interaction between BCL6 and its co-repressors. A subset of these inhibitors were found to cause rapid degradation of BCL6, and optimization of pharmacokinetic properties led to the discovery of 5-((5-chloro-2-((3R,5S)-4,4-difluoro-3,5-dimethylpiperidin-1-yl)pyrimidin-4-yl)amino)-3-(3-hydroxy-3-methylbutyl)-1-methyl-1,3-dihydro-2H-benzo[d]imidazol-2-one (CCT369260), which reduces BCL6 levels in a lymphoma xenograft mouse model following oral dosing.
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Apr 2020
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I04-1-Macromolecular Crystallography (fixed wavelength)
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Hannah L.
Woodward
,
Paolo
Innocenti
,
Kwai-Ming J.
Cheung
,
Angela
Hayes
,
Jennie
Roberts
,
Alan T.
Henley
,
Amir
Faisal
,
Grace Wing-Yan
Mak
,
Gary
Box
,
Isaac M.
Westwood
,
Nora
Cronin
,
Michael
Carter
,
Melanie
Valenti
,
Alexis
De Haven Brandon
,
Lisa
O’fee
,
Harry
Saville
,
Jessica
Schmitt
,
Rosemary
Burke
,
Fabio
Broccatelli
,
Rob L. M.
Van Montfort
,
Florence I.
Raynaud
,
Suzanne A.
Eccles
,
Spiros
Linardopoulos
,
Julian
Blagg
,
Swen
Hoelder
Diamond Proposal Number(s):
[10088]
Open Access
Abstract: Monopolar spindle 1 (MPS1) occupies a central role in mitosis and is one of the main components of the spindle assembly checkpoint. The MPS1 kinase is an attractive cancer target, and herein, we report the discovery of the clinical candidate BOS172722. The starting point for our work was a series of pyrido[3,4-d]pyrimidine inhibitors that demonstrated excellent potency and kinase selectivity but suffered from rapid turnover in human liver microsomes (HLM). Optimizing HLM stability proved challenging since it was not possible to identify a consistent site of metabolism and lowering lipophilicity proved unsuccessful. Key to overcoming this problem was the finding that introduction of a methyl group at the 6-position of the pyrido[3,4-d]pyrimidine core significantly improved HLM stability. Met ID studies suggested that the methyl group suppressed metabolism at the distant aniline portion of the molecule, likely by blocking the preferred pharmacophore through which P450 recognized the compound. This work ultimately led to the discovery of BOS172722 as a Phase 1 clinical candidate.
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Sep 2018
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I02-Macromolecular Crystallography
I03-Macromolecular Crystallography
I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[10619]
Open Access
Abstract: Structure–activity relationship and crystallographic data revealed that quinazolinone-containing fragments flip between two distinct modes of binding to activin receptor-like kinase-2 (ALK2). We explored both binding modes to discover potent inhibitors and characterized the chemical modifications that triggered the flip in binding mode. We report kinase selectivity and demonstrate that compounds of this series modulate ALK2 in cancer cells. These inhibitors are attractive starting points for the discovery of more advanced ALK2 inhibitors.
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Aug 2018
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I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[14891, 6385, 8015, 10088]
Open Access
Abstract: TLE1 is an oncogenic transcriptional co-repressor that exerts its repressive effects through binding of transcription factors. Inhibition of this protein-protein interaction represents a putative cancer target but no small molecule inhibitors have been published for this challenging interface. In this manuscript, we report the structure enabled design and synthesis of a constrained peptide inhibitor of TLE1. Our design featured introduction of a four carbon atom linker into the peptide epitope found in many TLE1 binding partners. We developed a concise synthetic route to a proof of concept peptide cycFWRPW. Biophysical testing by ITC and thermal shift assays showed that whilst the constrained peptide bound potently, it had an approximately five fold higher Kd than the unconstrained peptide. Our co-crystal structure suggested that the reduced affinity is likely due to a small shift of one side-chain compared to the otherwise well conserved conformation of the acyclic peptide. Our work describes a constrained peptide inhibitor that may serve as the basis for improved inhibitors.
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Mar 2017
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I03-Macromolecular Crystallography
I04-Macromolecular Crystallography
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Dominic
Tisi
,
Elisabetta
Chiarparin
,
Emiliano
Tamanini
,
Puja
Pathuri
,
Joseph E.
Coyle
,
Adam
Hold
,
Finn P.
Holding
,
Nader
Amin
,
Agnes C. L.
Martin
,
Sharna J.
Rich
,
Valerio
Berdini
,
Jeff
Yon
,
Paul
Acklam
,
Rosemary
Burke
,
Ludovic
Drouin
,
Jenny E.
Harmer
,
Fiona
Jeganathan
,
Rob
Van Montfort
,
Yvette
Newbatt
,
Marcello
Tortorici
,
Maura
Westlake
,
Amy
Wood
,
Swen
Hoelder
,
Tom D.
Heightman
Abstract: The members of the NSD subfamily of lysine methyl transferases are compelling oncology targets due to the recent characterization of gain-of-function mutations and translocations in several hematological cancers. To date, these proteins have proven intractable to small molecule inhibition. Here, we present initial efforts to identify inhibitors of MMSET (aka NSD2 or WHSC1) using solution phase and crystal structural methods. On the basis of 2D NMR experiments comparing NSD1 and MMSET structural mobility, we designed an MMSET construct with five point mutations in the N-terminal helix of its SET domain for crystallization experiments and elucidated the structure of the mutant MMSET SET domain at 2.1 Å resolution. Both NSD1 and MMSET crystal systems proved resistant to soaking or cocrystallography with inhibitors. However, use of the close homologue SETD2 as a structural surrogate supported the design and characterization of N-alkyl sinefungin derivatives, which showed low micromolar inhibition against both SETD2 and MMSET.
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Nov 2016
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