I03-Macromolecular Crystallography
I04-1-Macromolecular Crystallography (fixed wavelength)
I04-Macromolecular Crystallography
I24-Microfocus Macromolecular Crystallography
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Diamond Proposal Number(s):
[22717, 15433, 19301]
Open Access
Abstract: SHIP1, an inositol 5-phosphatase, plays a central role in cellular signaling. As such, it has been implicated in many conditions. Exploiting SHIP1 as a drug target will require structural knowledge and the design of selective small molecules. We have determined apo, and magnesium and phosphate-bound structures of the phosphatase and C2 domains of SHIP1. The C2 domains of SHIP1 and the related SHIP2 modulate the activity of the phosphatase domain. To understand the mechanism, we performed activity assays, hydrogen-deuterium exchange mass spectrometry, and molecular dynamics on SHIP1 and SHIP2. Our findings demonstrate that the influence of the C2 domain is more pronounced for SHIP2 than SHIP1. We determined 91 structures of SHIP1 with fragments bound, with some near the interface between the two domains. We performed a mass spectrometry screen and determined four structures with covalent fragments. These structures could act as starting points for the development of potent, selective probes.
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Feb 2024
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Open Access
Abstract: The human dedicator of cytokinesis (DOCK) family consists of 11 structurally conserved proteins that serve as atypical RHO guanine nucleotide exchange factors (RHO GEFs). These regulatory proteins act as mediators in numerous cellular cascades that promote cytoskeletal remodelling, playing roles in various crucial processes such as differentiation, migration, polarisation and axon growth in neurons. At the molecular level, DOCK DHR2 domains facilitate nucleotide dissociation from small GTPases, a process which is otherwise too slow for rapid spatiotemporal control of cellular signalling. Here, we provide an overview of the biological and structural characteristics for the various DOCK proteins and describe how they differ from other RHO GEFs and between DOCK sub-families. The expression of the family varies depending on cell or tissue type, and they are consequently implicated in a broad range of disease phenotypes, particularly in the brain. A growing body of available structural information reveals the mechanism by which the catalytic DHR2 domain elicits nucleotide dissociation and also indicates strategies for the discovery and design of high-affinity small molecule inhibitors. Such compounds could serve as chemical probes to interrogate the cellular function and provide starting points for drug discovery of this important class of enzymes.
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Mar 2021
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I02-Macromolecular Crystallography
I03-Macromolecular Crystallography
I24-Microfocus Macromolecular Crystallography
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Vincent
Fagan
,
Catrine
Johansson
,
Carina
Gileadi
,
Octovia
Monteiro
,
James Edward
Dunford
,
Reshma
Nibhani
,
Martin
Philpott
,
Jessica
Malzahn
,
Graham
Wells
,
Ruth
Farham
,
Adam
Cribbs
,
Nadia
Halidi
,
Fengling
Li
,
Irene
Chau
,
Holger
Greschik
,
Srikannathasan
Velupillai
,
Abdellah
Allali-Hassani
,
James M.
Bennett
,
Thomas
Christott
,
Charline
Giroud
,
Andrew M.
Lewis
,
Kilian V. M.
Huber
,
Nick
Athanasou
,
Chas
Bountra
,
Manfred
Jung
,
Roland
Schüle
,
Masoud
Vedadi
,
Cheryl H.
Arrowsmith
,
Yan
Xiong
,
Jian
Jin
,
Oleg
Fedorov
,
Gillian
Farnie
,
Paul E.
Brennan
,
Udo C. T.
Oppermann
Diamond Proposal Number(s):
[10619, 15433]
Abstract: Modifications of histone tails, including lysine/arginine methylation, provide the basis of a 'chromatin or histone code'. Proteins that con-tain 'reader' domains can bind to these modifications and form specific effector complexes, which ultimately mediate chromatin function. The spindlin1 (SPIN1) protein contains three Tudor methyl-lysine/arginine reader domains and was identified as a putative onco-gene and transcriptional co-activator. Here we report a SPIN1 chemi-cal probe inhibitor with low nanomolar in vitro activity, exquisite selectivity on a panel of methyl reader and writer proteins, and with submicromolar cellular activity. X-ray crystallography showed that this Tudor domain chemical probe simultaneously engages Tudor domains 1 and 2 via a bidentate binding mode. Small molecule inhibition and siRNA knockdown of SPIN1, as well as chemoproteomic studies, iden-tified genes which are transcriptionally regulated by SPIN1 in squa-mous cell carcinoma and suggest that SPIN1 may have a roll in cancer related inflammation and/or cancer metastasis.
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Sep 2019
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I04-Macromolecular Crystallography
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Yan
Xiong
,
Holger
Greschik
,
Catrine
Johansson
,
Ludwig
Seifert
,
Johannes
Bacher
,
Kwang-Su
Park
,
Nicolas
Babault
,
Michael L.
Martini
,
Vincent
Fagan
,
Fengling
Li
,
Irene
Chau
,
Thomas
Christott
,
David
Dilworth
,
Dalia
Barsyte-Lovejoy
,
Masoud
Vedadi
,
Cheryl H.
Arrowsmith
,
Paul E.
Brennan
,
Oleg
Fedorov
,
Manfred
Jung
,
Gillian
Farnie
,
Jing
Liu
,
Udo C. T.
Oppermann
,
Roland
Schüle
,
Jian
Jin
Abstract: By screening an epigenetic compound library, we identified that UNC0638, a highly potent inhibitor of the histone methyltransferases G9a and GLP, was a weak inhibitor of SPIN1 (Spindlin 1), a methyllysine reader protein. Our optimization of this weak hit resulted in the discovery of a potent, selective and cell-active SPIN1 inhibitor, compound 3 (MS31). Compound 3 potently inhibited binding of trimethyllysine-containing peptides to SPIN1, displayed high binding affinity, was highly selective for SPIN1 over other epigenetic readers and writers, directly engaged SPIN1 in cells, and was not toxic to non-tumorigenic cells. The crystal structure of the SPIN1–compound 3 complex indicated that it selectively binds Tudor domain II of SPIN1. We also designed a structurally similar but inactive compound 4 (MS31N) as a negative control. Our results have demonstrated for the first time that potent, selective and cell-active fragment-like inhibitors can be generated by targeting a single Tudor domain.
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Jul 2019
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I03-Macromolecular Crystallography
I04-1-Macromolecular Crystallography (fixed wavelength)
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Efrat
Resnick
,
Anthony
Bradley
,
Jinrui
Gan
,
Alice
Douangamath
,
Tobias
Krojer
,
Ritika
Sethi
,
Paul P.
Geurink
,
Anthony
Aimon
,
Gabriel
Amitai
,
Dom
Bellini
,
James
Bennett
,
Michael
Fairhead
,
Oleg
Fedorov
,
Ronen
Gabizon
,
Jin
Gan
,
Jingxu
Guo
,
Alexander
Plotnikov
,
Nava
Reznik
,
Gian Filippo
Ruda
,
Laura
Diaz-Saez
,
Verena M.
Straub
,
Tamas
Szommer
,
Srikannathasan
Velupillai
,
Daniel
Zaidman
,
Yanling
Zhang
,
Alun R.
Coker
,
Christopher G.
Dowson
,
Haim
Barr
,
Chu
Wang
,
Kilian V. M.
Huber
,
Paul E.
Brennan
,
Huib
Ovaa
,
Frank
Von Delft
,
Nir
London
Open Access
Abstract: Covalent probes can display unmatched potency, selectivity and duration of action; however, their discovery is challenging. In principle, fragments that can irreversibly bind their target can overcome the low affinity that limits reversible fragment screening, but such electrophilic fragments were considered non-selective and were rarely screened. We hypothesized that mild electrophiles might overcome the selectivity challenge and constructed a library of 993 mildly electrophilic fragments. We characterized this library by a new high-throughput thiol-reactivity assay and screened them against ten cysteine-containing proteins. Highly reactive and promiscuous fragments were rare and could be easily eliminated. By contrast, we found hits for most targets. Combining our approach with high-throughput crystallography allowed rapid progression to potent and selective probes for two enzymes, the deubiquitinase OTUB2 and the pyrophosphatase NUDT7. No inhibitors were previously known for either. This study highlights the potential of electrophile-fragment screening as a practical and efficient tool for covalent-ligand discovery.
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May 2019
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I02-Macromolecular Crystallography
I03-Macromolecular Crystallography
I04-1-Macromolecular Crystallography (fixed wavelength)
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Yann-Vai
Le Bihan
,
Rachel M.
Lanigan
,
Butrus
Atrash
,
Mark G.
Mclaughlin
,
Srikannathasan
Velupillai
,
Andrew G.
Malcolm
,
Katherine S.
England
,
Gian Filippo
Ruda
,
N. Yi
Mok
,
Anthony
Tumber
,
Kathy
Tomlin
,
Harry
Saville
,
Erald
Shehu
,
Craig
Mcandrew
,
Leanne
Carmichael
,
James M.
Bennett
,
Fiona
Jeganathan
,
Paul
Eve
,
Adam
Donovan
,
Angela
Hayes
,
Francesca
Wood
,
Florence I.
Raynaud
,
Oleg
Fedorov
,
Paul
Brennan
,
Rosemary
Burke
,
Rob
Van Montfort
,
Olivia W.
Rossanese
,
Julian
Blagg
,
Vassilios
Bavetsias
Diamond Proposal Number(s):
[20145]
Open Access
Abstract: Residues in the histone substrate binding sites that differ between the KDM4 and KDM5 subfamilies were identified. Subsequently, a C8-substituted pyrido[3,4-d]pyrimidin-4(3H)-one series was designed to rationally exploit these residue differences between the histone substrate binding sites in order to improve affinity for the KDM4-subfamily over KDM5-subfamily enzymes. In particular, residues E169 and V313 (KDM4A numbering) were targeted. Additionally, the conformational restriction of the flexible pyridopyrimidinone C8-substituent was investigated. These approaches yielded potent and cell-penetrant dual KDM4/5-subfamily inhibitors including 19a (KDM4A and KDM5B Ki = 0.004 and 0.007 μM, respectively). Compound cellular profiling in two orthogonal target engagement assays revealed a significant reduction from biochemical to cell-based activity across multiple analogues; this decrease was shown to be consistent with 2OG competition, and suggest that sub-nanomolar biochemical potency will be required with C8-substituted pyrido[3,4-d]pyrimidin-4(3H)-one compounds to achieve sub-micromolar target inhibition in cells.
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May 2019
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I04-1-Macromolecular Crystallography (fixed wavelength)
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Open Access
Abstract: The Ras superfamily of small GTPases are guanine nucleotide dependent switches essential for numerous cellular processes. Mutations or dysregulation of these proteins are associated with many diseases, but unsuccessful attempts to target the small GTPases directly have resulted in them being classed as ‘undruggable’. The GTP dependent signaling of these proteins is controlled by their regulators; guanine nucleotide exchange factors (GEFs), GTPase activating proteins (GAPs), and in the Rho and Rab subfamilies, guanine nucleotide dissociation inhibitors (GDIs). This review covers the recent small molecule and biologics strategies to target the small GTPases through their regulators. It seeks to critically re‐evaluate recent chemical biology practice, such as the presence of PAINs motifs and the cell‐based readout using compounds that are weakly potent or of unknown specificity. It highlights the vast scope of potential approaches for targeting the small GTPases in the future through their regulatory proteins.
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Mar 2019
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I03-Macromolecular Crystallography
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Melissa
D'Ascenzio
,
Kathryn M.
Pugh
,
Rebecca
Konietzny
,
Georgina
Berridge
,
Cynthia
Tallant
,
Shaima
Hashem
,
Octovia
Monteiro
,
Jason R.
Thomas
,
Markus
Schirle
,
Stefan
Knapp
,
Brian
Marsden
,
Oleg
Fedorov
,
Chas
Bountra
,
Benedikt M.
Kessler
,
Paul E.
Brennan
Diamond Proposal Number(s):
[10619]
Open Access
Abstract: Bromodomain‐containing proteins are epigenetic modulators involved in a wide range of cellular processes, from recruitment of transcription factors to pathological disruption of gene regulation and cancer development. Since the druggability of these acetyl‐lysine reader domains was established, efforts were made to develop potent and selective inhibitors across the entire family. Here we report the development of a small molecule‐based approach to covalently modify recombinant and endogenous bromodomain‐containing proteins by targeting a conserved lysine and a tyrosine residue in the variable ZA or BC loops. Moreover, the addition of a reporter tag allowed in‐gel visualization and pull‐down of the desired bromodomains.
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Jan 2019
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I04-Macromolecular Crystallography
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Saleta
Vazquez-Rodriguez
,
Miranda
Wright
,
Catherine M.
Rogers
,
Adam P.
Cribbs
,
Srikannathasan
Velupillai
,
Martin
Philpott
,
Henry
Lee
,
James E.
Dunford
,
Kilian V. M.
Huber
,
Matthew B.
Robers
,
James D.
Vasta
,
Marie-Laetitia
Thezenas
,
Sarah
Bonham
,
Benedikt
Kessler
,
James
Bennett
,
Oleg
Fedorov
,
Florence
Raynaud
,
Adam
Donovan
,
Julian
Blagg
,
Vassilios
Bavetsias
,
Udo
Oppermann
,
Chas
Bountra
,
Akane
Kawamura
,
Paul E.
Brennan
Diamond Proposal Number(s):
[15433]
Open Access
Abstract: Histone lysine demethylases (KDMs) are involved in the dynamic regulation of gene expression and they play a critical role in several biological processes. Achieving selectivity over the different KDMs has been a major challenge for KDM inhibitor development. Here we report potent and selective KDM5 covalent inhibitors designed to target cysteine residues only present in the KDM5 sub‐family. The covalent binding to the targeted proteins was confirmed by MS and time‐dependent inhibition. Additional competition assays show that compounds were non 2‐OG competitive. Target engagement and ChIP‐seq analysis showed that the compounds inhibited the KDM5 members in cells at nano‐ to micromolar levels and induce a global increase of the H3K4me3 mark at transcriptional start sites.
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Jan 2019
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I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[105433]
Abstract: Lysine acetylation is an epigenetic mark that is principally recognized by bromodomains and recently structurally diverse YEATS domains also emerged as readers of lysine acetyl/acylations. Here we present a crystallography-based strategy and the discovery of fragments binding to the ENL YEATS domain, a potential drug target. Crystal structures combined with synthetic efforts led to the identification of a sub-micromolar binder, providing first starting points for the development of chemical probes for this reader domain family.
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Nov 2018
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