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)
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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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I04-1-Macromolecular Crystallography (fixed wavelength)
I04-Macromolecular Crystallography
I24-Microfocus Macromolecular Crystallography
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Paolo
Innocenti
,
Hannah L.
Woodward
,
Savade
Solanki
,
Sébastien
Naud
,
Isaac
Westwood
,
Nora
Cronin
,
Angela
Hayes
,
Jennie
Roberts
,
Alan T.
Henley
,
Ross
Baker
,
Amir
Faisal
,
Grace Wing-Yan
Mak
,
Gary
Box
,
Melanie
Valenti
,
Alexis
De Haven Brandon
,
Lisa
O’ Fee
,
Harry
Saville
,
Jessica
Schmitt
,
Berry
Matijssen
,
Rosemary
Burke
,
Rob
Van Montfort
,
Florence I.
Raynaud
,
Suzanne A.
Eccles
,
Spiros
Linardopoulos
,
Julian
Blagg
,
Swen
Hoelder
Open Access
Abstract: Monopolar spindle 1 (MPS1) plays a central role in the transition of cells from metaphase to anaphase and is one of the main components of the spindle assembly checkpoint. Chromosomally unstable cancer cells rely heavily on MPS1 to cope with the stress arising from abnormal numbers of chromosomes and centrosomes and are thus more sensitive to MPS1 inhibition than normal cells. We report the discovery and optimization of a series of new pyrido[3,4-d]pyrimidine based inhibitors via a structure-based hybridization approach from our previously reported inhibitor CCT251455 and a modestly potent screening hit. Compounds in this novel series display excellent potency and selectivity for MPS1, which translates into biomarker modulation in an in vivo human tumor xenograft model.
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Apr 2016
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I02-Macromolecular Crystallography
I04-1-Macromolecular Crystallography (fixed wavelength)
I04-Macromolecular Crystallography
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M. D.
Gurden
,
Isaac
Westwood
,
A.
Faisal
,
S.
Naud
,
K. M. J.
Cheung
,
C.
Mcandrew
,
A.
Wood
,
J.
Schmitt
,
K.
Boxall
,
G.
Mak
,
P.
Workman
,
R.
Burke
,
S.
Hoelder
,
J.
Blagg
,
Rob
Van Montfort
,
S.
Linardopoulos
Diamond Proposal Number(s):
[8015, 10088]
Abstract: Acquired resistance to therapy is perhaps the greatest challenge to effective clinical management of cancer. With several inhibitors of the mitotic checkpoint kinase MPS1 in preclinical development, we sought to investigate how resistance against these inhibitors may arise so that mitigation or bypass strategies could be addressed as early as possible. Toward this end, we modeled acquired resistance to the MPS1 inhibitors AZ3146, NMS-P715, and CCT251455, identifying five point mutations in the kinase domain of MPS1 that confer resistance against multiple inhibitors. Structural studies showed how the MPS1 mutants conferred resistance by causing steric hindrance to inhibitor binding. Notably, we show that these mutations occur in nontreated cancer cell lines and primary tumor specimens, and that they also preexist in normal lymphoblast and breast tissues. In a parallel piece of work, we also show that the EGFR p.T790M mutation, the most common mutation conferring resistance to the EGFR inhibitor gefitinib, also preexists in cancer cells and normal tissue. Our results therefore suggest that mutations conferring resistance to targeted therapy occur naturally in normal and malignant cells and these mutations do not arise as a result of the increased mutagenic plasticity of cancer cells.
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Aug 2015
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I02-Macromolecular Crystallography
I04-Macromolecular Crystallography
I24-Microfocus Macromolecular Crystallography
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Cris
Silva-santisteban
,
Isaac
Westwood
,
Kathy
Boxall
,
Nathan
Brown
,
Sam
Peacock
,
Craig
Mcandrews
,
Elaine
Barrie
,
Meirion
Richards
,
Amin
Mirza
,
Antony W.
Oliver
,
Rosemary
Burke
,
Swen
Hoelder
,
Keith
Jones
,
G. Wynne
Aherne
,
Julian
Blagg
,
Ian
Collins
,
Michelle D.
Garrett
,
Rob L.m.
Van Montfort
,
Qiming Jane
Wang
Open Access
Abstract: Checkpoint kinase 2 (CHK2) is an important serine/threonine kinase in the cellular response to DNA damage. A fragmentbased screening campaign using a combination of a high-concentration AlphaScreenTM kinase assay and a biophysical thermal shift assay, followed by X-ray crystallography, identified a number of chemically different ligand-efficient CHK2 hinge-binding scaffolds that have not been exploited in known CHK2 inhibitors. In addition, it showed that the use of these orthogonal techniques allowed efficient discrimination between genuine hit matter and false positives from each individual assay technology. Furthermore, the CHK2 crystal structures with a quinoxaline-based fragment and its follow-up compound highlight a hydrophobic area above the hinge region not previously explored in rat
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Jun 2013
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I24-Microfocus Macromolecular Crystallography
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Richard
Bayliss
,
Swen
Hoelder
,
Paulo
Innocent
,
K-m.
Cheung
,
S.
Solanki
,
C
Mas-droux
,
Fiona
Rowan
,
S.
Yeoh
,
K.
Boxall
,
M.
Westlake
,
L.
Pickard
,
T
Hardy
,
Joanne
Baxter
,
G. W.
Aherne
,
A.
Fry
Diamond Proposal Number(s):
[6388]
Abstract: We report herein a series of Nek2 inhibitors based on an aminopyridine scaffold. These compounds have been designed by combining key elements of two previously discovered chemical series. Structure based design led to aminopyridine (R)-21, a potent and selective inhibitor able to modulate Nek2 activity in cells.
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Apr 2012
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