I03-Macromolecular Crystallography
I04-Macromolecular Crystallography
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John
Liddle
,
Andrew C.
Pearce
,
Christopher
Arico-Muendel
,
Svetlana
Belyanskaya
,
Andrew
Brewster
,
Murray
Brown
,
Chun-Wa
Chung
,
Alexis
Denis
,
Nerina
Dodic
,
Anthony
Dossang
,
Peter
Eddershaw
,
Diana
Klimaszewska
,
Imran
Haq
,
Duncan S.
Holmes
,
Alistair
Jagger
,
Toral
Jakhria
,
Emilie
Jigorel
,
Ken
Lind
,
Jeff
Messer
,
Margaret
Neu
,
Allison
Olszewski
,
Riccardo
Ronzoni
,
James
Rowedder
,
Martin
Rüdiger
,
Steve
Skinner
,
Kathrine J.
Smith
,
Lionel
Trottet
,
Iain
Uings
,
Zhengrong
Zhu
,
James A.
Irving
,
David A.
Lomas
Diamond Proposal Number(s):
[23853, 17201]
Abstract: α1-antitrypsin deficiency is characterised by the misfolding and intracellular polymerisation of mutant α1-antitrypsin protein within the endoplasmic reticulum (ER) of hepatocytes. Small molecules that bind and stabilise Z α1-antitrypsin were identified via a DNA-encoded library screen. A subsequent structure based optimisation led to a series of highly potent, selective and cellular active α1-antitrypsin correctors.
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Jun 2021
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I02-Macromolecular Crystallography
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Diamond Proposal Number(s):
[14043]
Open Access
Abstract: Inosine-5′-monophosphate dehydrogenase (IMPDH) is a rate-limiting enzyme involved in nucleotide biosynthesis. Because of its critical role in purine biosynthesis, IMPDH is a drug design target for immunosuppressive, anticancer, antiviral and antimicrobial chemotherapy. In this study, we use mass spectrometry and X-ray crystallography to show that the inhibitor 6-Cl-purine ribotide forms a covalent adduct with the Cys-341 residue of Mycobacterium thermoresistibile IMPDH.
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Jan 2020
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I03-Macromolecular Crystallography
I24-Microfocus Macromolecular Crystallography
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Benjamin N.
Atkinson
,
David
Steadman
,
William
Mahy
,
Yuguang
Zhao
,
James
Sipthorp
,
Elliott D.
Bayle
,
Fredrik
Svensson
,
George
Papageorgiou
,
Fiona
Jeganathan
,
Sarah
Frew
,
Amy
Monaghan
,
Magda
Bictash
,
E.
Yvonne Jones
,
Paul V.
Fish
Diamond Proposal Number(s):
[14744]
Abstract: The carboxylesterase Notum is a key negative regulator of the Wnt signaling pathway by mediating the depalmitoleoylation of Wnt proteins. Our objective was to discover potent small molecule inhibitors of Notum suitable for exploring the regulation of Wnt signaling in the central nervous system. Scaffold-hopping from thienopyrimidine acids 1 and 2, supported by X-ray structure determination, identified 3-methylimidazolin-4-one amides 20-24 as potent inhibitors of Notum with activity across three orthogonal assay formats (biochemical, extra-cellular, occupancy). A preferred example 24 demonstrated good stability in mouse microsomes and plasma, and cell permeability in the MDCK-MDR1 assay albeit with modest P-gp mediated efflux. Pharmacokinetic studies with 24 were performed in vivo in mouse with single oral administration of 24 showing good plasma exposure and reasonable CNS penetration. We propose that 24 is a new chemical tool suitable for cellular studies to explore the fundamental biology of Notum.
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Oct 2019
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I04-Macromolecular Crystallography
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Ann L.
Walker
,
Alexis
Denis
,
Ryan P.
Bingham
,
Anne
Boulliot
,
Emma V.
Edgar
,
Alan
Ferrie
,
Duncan S.
Holmes
,
Alain
Laroze
,
John
Liddle
,
Marie-helene
Fouchet
,
Alexandre
Moquette
,
Pam
Nassau
,
Andrew C.
Pearce
,
Oxana
Polyakova
,
Kathrine J.
Smith
,
Pamela
Thomas
,
James H.
Thorpe
,
Lionel
Trottet
,
Yichen
Wang
,
Alain
Hovnanian
Diamond Proposal Number(s):
[5799]
Abstract: The connection between Netherton syndrome and overactivation of epidermal/dermal proteases, particularly Kallikrein 5 (KLK5) has been well established and it is expected that a KLK5 inhibitor would improve the dermal barrier and also reduce the pain and itch that afflict Netherton syndrome patients. One of the challenges of covalent protease inhibitors has been achieving selectivity over closely related targets. In this paper we describe the use of structural insight to design and develop a selective and highly potent reversibly covalent KLK5 inhibitor from an initial weakly binding fragment.
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Oct 2019
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I02-Macromolecular Crystallography
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Abstract: In silico virtual screening using the ligand-based ROCS approach and the commercially purchasable compound collection from the ZINC database resulted in the identification of distinctly different and novel acetamide core frameworks with series representatives 1a and 2a exhibiting nanomolar affinity in the kinase domain only hTrkA HTRF biochemical assay. Additional experimental validation using the Caliper technology with either the active or inactive kinase conditions demonstrated the leads, 1a and 2a, to preferentially bind the kinase inactive state. X-ray structural analysis of the kinase domain of hTrkA…1a/2a complexes confirmed the kinase, bind the inhibitor leads in the inactive state and to exhibit a type 2 binding mode with the DFG-out and αC-helix out conformation. The leads also demonstrated sub-micromolar activity in the full length hTrkA cell-based assay and selectivity against the closely related hTrkB isoform. However, the poor microsomal stability and permeability of the leads is suggestive of a multiparametric lead optimization effort requirement for further progression.
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Aug 2019
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I03-Macromolecular Crystallography
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Jon
Read
,
Iain T.
Collie
,
Michelle
Nguyen-mccarty
,
Christopher
Lucaj
,
James
Robinson
,
Leslie
Conway
,
Jayanta
Mukherjee
,
Eileen
Mccall
,
Gerard
Donohoe
,
Elizabeth
Flavell
,
Karolina
Peciak
,
Juli
Warwicker
,
Carly
Dix
,
Bernard G.
Van Den Hoven
,
Andrew
Madin
,
Dean G.
Brown
,
Stephen
Moss
,
Stephen J.
Haggarty
,
Nicholas J.
Brandon
,
Roland W.
Bürli
Abstract: The TRAF2 and NCK interacting kinase (TNIK) has been proposed to play a role in cytoskeletal organization and synaptic plasticity and has been linked, among others, to neurological disorders. However, target validation efforts for TNIK have been hampered by the limited kinase selectivity of small molecule probes and possible functional compensation in mouse models. Both issues are at least in part due to its close homology to the kinases MINK1 (or MAP4K6) and MAP4K4 (or HGK). As part of our interest in validating TNIK as a therapeutic target for neurological diseases, we set up a panel of biochemical and cellular assays, which are described herein. We then examined the activity of known amino-pyridine-based TNIK inhibitors (1, 3) and prepared structurally very close analogs that lack the ability to inhibit the target. We also developed a structurally orthogonal, naphthyridine-based TNIK inhibitor (9) and an inactive control molecule of the same chemical series. These validated small-molecule probes will enable dissection of the function of TNIK family in the context of human disease biology.
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Aug 2019
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I02-Macromolecular Crystallography
I04-1-Macromolecular Crystallography (fixed wavelength)
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Mark
Zak
,
Emily J.
Hanan
,
Patrick
Lupardus
,
David G.
Brown
,
Colin
Robinson
,
Michael
Siu
,
Joseph P.
Lyssikatos
,
F. Anthony
Romero
,
Guiling
Zhao
,
Terry
Kellar
,
Rohan
Mendonca
,
Nicholas C.
Ray
,
Simon C.
Goodacre
,
Peter H.
Crackett
,
Neville
Mclean
,
Christopher A.
Hurley
,
Po-wai
Yuen
,
Yun-xing
Cheng
,
Xiongcai
Liu
,
Marya
Liimatta
,
Pawan Bir
Kohli
,
Jim
Nonomiya
,
Gary
Salmon
,
Gerry
Buckley
,
Julia
Lloyd
,
Paul
Gibbons
,
Nico
Ghilardi
,
Jane R.
Kenny
,
Adam
Johnson
Diamond Proposal Number(s):
[5069, 14629]
Abstract: Disruption of interleukin-13 (IL-13) signaling with large molecule antibody therapies has shown promise in diseases of allergic inflammation. Given that IL-13 recruits several members of the Janus Kinase family (JAK1, JAK2, and TYK2) to its receptor complex, JAK inhibition may offer an alternate small molecule approach to disrupting IL-13 signaling. Herein we demonstrate that JAK1 is likely the isoform most important to IL-13 signaling. Structure-based design was then used to improve the JAK1 potency of a series of previously reported JAK2 inhibitors. The ability to impede IL-13 signaling was thereby significantly improved, with the best compounds exhibiting single digit nM IC50’s in cell-based assays dependent upon IL-13 signaling. Appropriate substitution was further found to influence inhibition of a key off-target, LRRK2. Finally, the most potent compounds were found to be metabolically labile, which makes them ideal scaffolds for further development as topical agents for IL-13 mediated diseases of the lungs and skin (for example asthma and atopic dermatitis, respectively).
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Apr 2019
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I03-Macromolecular Crystallography
I23-Long wavelength MX
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Reema K.
Thalji
,
Kaushik
Raha
,
Daniele
Andreotti
,
Anna
Checchia
,
Haifeng
Cui
,
Giovanni
Meneghelli
,
Roberto
Profeta
,
Federica
Tonelli
,
Simona
Tommasi
,
Tania
Bakshi
,
Brian T.
Donovan
,
Alison
Howells
,
Shruti
Jain
,
Christopher
Nixon
,
Geoffrey
Quinque
,
Lynn
Mccloskey
,
Benjamin D.
Bax
,
Margarete
Neu
,
Pan F.
Chan
,
Robert A.
Stavenger
Diamond Proposal Number(s):
[1195]
Abstract: A series of DNA gyrase inhibitors were designed based on the X-ray structure of a parent thiophene scaffold with the objective to improve biochemical and whole-cell antibacterial activity, while reducing cardiac ion channel activity. The binding mode and overall design hypothesis of one series was confirmed with a co-crystal structure with DNA gyrase. Although some analogs retained both biochemical activity and whole-cell antibacterial activity, we were unable to significantly improve the activity of the series and analogs retained activity against the cardiac ion channels, therefore we stopped optimization efforts.
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Mar 2019
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I02-Macromolecular Crystallography
I04-1-Macromolecular Crystallography (fixed wavelength)
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Gemma V.
White
,
Emma V.
Edgar
,
Duncan S.
Holmes
,
Xiao Qing
Lewell
,
John
Liddle
,
Oxana
Polyakova
,
Kathrine J.
Smith
,
James H.
Thorpe
,
Ann L.
Walker
,
Yichen
Wang
,
Robert J.
Young
,
Alain
Hovnanian
Diamond Proposal Number(s):
[5799]
Abstract: Netherton syndrome (NS) is a rare and debilitating severe autosomal recessive genetic skin disease with high mortality rates particularly in neonates. NS is caused by loss-of-function SPINK5 mutations leading to unregulated kallikrein 5 (KLK5) and kallikrein 7 (KLK7) activity. Furthermore, KLK5 inhibition has been proposed as a potential therapeutic treatment for NS. Identification of potent and selective KLK5 inhibitors would enable further exploration of the disease biology and could ultimately lead to a treatment for NS. This publication describes how fragmentation of known trypsin-like serine protease (TLSP) inhibitors resulted in the identification of a series of phenolic amidine-based KLK5 inhibitors 1. X-ray crystallography was used to find alternatives to the phenol interaction leading to identification of carbonyl analogues such as lactam 13 and benzimidazole 15. These reversible inhibitors, with selectivity over KLK1 (10–100 fold), provided novel starting points for the guided growth towards suitable tool molecules for the exploration of KLK5 biology.
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Jan 2019
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I02-Macromolecular Crystallography
I03-Macromolecular Crystallography
I04-Macromolecular Crystallography
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Stuart
Francis
,
Daniel
Croft
,
Alexander W.
Schuettelkopf
,
Charles
Parry
,
Angelo
Pugliese
,
Ken
Cameron
,
Sophie
Claydon
,
Martin
Drysdale
,
Claire
Gardner
,
Andrea
Gohlke
,
Gillian
Goodwin
,
Christopher H.
Gray
,
Jennifer
Konczal
,
Laura
Mcdonald
,
Mokdad
Mezna
,
Andrew
Pannifer
,
Nikki
Paul
,
Laura
Machesky
,
Heather
Mckinnon
,
Justin
Bower
Diamond Proposal Number(s):
[6683, 8659, 11651]
Open Access
Abstract: Fascin is an actin binding and bundling protein that is not expressed in normal epithelial tissues but overexpressed in a variety of invasive epithelial tumors. It has a critical role in cancer cell metastasis by promoting cell migration and invasion. Here we report the crystal structures of fascin in complex with a series of novel and potent inhibitors. Subsequent structure-based elaboration of this and related compounds enabled the development of a series with nanomolar affinities for fascin, good physicochemical properties and the ability to inhibit fascin-mediated bundling of filamentous actin. These compounds provide promising starting points for fascin-targeted anti-metastatic therapies.
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Jan 2019
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