I02-Macromolecular Crystallography
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Diamond Proposal Number(s):
[442]
Abstract: Selectivity remains a challenge for ATP-mimetic kinase inhibitors, an issue that may be overcome by targeting unique residues or binding pockets. However, to date only few strategies have been developed. Here we identify that bulky residues located N-terminal to the DFG motif (DFG-1) represent an opportunity for designing highly selective inhibitors with unexpected binding modes. We demonstrate that several diverse inhibitors exerted selective, non-canonical binding modes that exclusively target large hydrophobic DFG-1 residues present in many kinases including PIM, CK1, DAPK and CLK. Using the CLK family as a model, structural and biochemical data revealed that the DFG-1 valine controlled a non-canonical binding mode in CLK1, providing a rational for selectivity over the closely-related CLK3 which harbors a smaller DFG-1 alanine. Our data suggests that targeting the restricted back pocket in the small fraction of kinases that harbor bulky DFG-1 residues offers a versatile selectivity filter for inhibitor design.
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Aug 2020
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I03-Macromolecular Crystallography
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David
Smil
,
Jong Fu
Wong
,
Eleanor
Williams
,
Roslin J.
Adamson
,
Alison
Howarth
,
David
Mcleod
,
Ahmed
Mamai
,
Soyoung
Kim
,
Brian
Wilson
,
Taira
Kiyota
,
Ahmed
Aman
,
Julie
Owen
,
Gennady
Poda
,
Kurumi
Horiuchi
,
Ekaterina
Kuznetsova
,
Haiching
Ma
,
J. Nicole
Hamblin
,
Sue
Cramp
,
Owen
Roberts
,
Aled M.
Edwards
,
David
Uehling
,
Rima
Al-awar
,
Alex N.
Bullock
,
Jeff
O'meara
,
Methvin
Isaac
Abstract: There are currently no effective chemotherapeutic drugs approved for the treatment of diffuse intrinsic pontine glioma (DIPG), an aggressive pediatric cancer resident in the pons region of the brainstem. Radiation therapy is beneficial but not curative, with the condition being uniformly fatal. Analysis of the genomic landscape surrounding DIPG has revealed that activin receptor-like kinase-2 (ALK2) constitutes a potential target for therapeutic intervention given its dysregulation in the disease. We adopted an open science approach to develop a series of potent, selective, orally bioavailable, and brain penetrant ALK2 inhibitors based on lead compound LDN-214117. Modest structural changes to the C-3, C-4, and C-5 position substituents of the core pyridine ring afforded compounds M4K2009, M4K2117, and M4K2163, each with a superior potency, selectivity, and/or blood-brain barrier (BBB) penetration profile. Robust in vivo pharmacokinetic (PK) properties and tolerability mark these inhibitors as advanced pre-clinical compounds suitable for further development and evaluation in orthotopic models of DIPG.
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Aug 2020
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I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[19880]
Open Access
Abstract: Rising numbers of cases of multidrug- and extensively drug-resistant Pseudomonas aeruginosa over recent years have created an urgent need for novel therapeutic approaches to cure potentially fatal infections. One such approach is virulence attenuation where anti-virulence compounds, designed to reduce pathogenicity without affording bactericidal effects, are employed to treat infections. P. aeruginosa uses the pqs quorum sensing (QS) system, to coordinate the expression of a large number of virulence determinants as well as bacterial-host interactions and hence represents an excellent anti-virulence target.
We report the synthesis and identification of a new series of thiazole-containing quinazolinones capable of inhibiting PqsR, the transcriptional regulator of the pqs QS system. The compounds demonstrated high potency (IC50 < 300 nM) in a whole-cell assay, using a mCTX::PpqsA-lux-based bioreporter for the P. aeruginosa PAO1-L and PA14 strains. Structural evaluation defined the binding modes of four analogues in the ligand-binding domain of PqsR through X-ray crystallography. Further work showed the ability of 6-chloro-3((2-pentylthiazol-4-yl)methyl)quinazolin-4(3H)-one (18) and 6-chloro-3((2-hexylthiazol-4-yl)methyl)quinazolin-4(3H)-one (19) to attenuate production of the PqsR-regulated virulence factor pyocyanin. Compounds 18 and 19 showed a low cytotoxic profile in the A549 human epithelial lung cell line making them suitable candidates for further pre-clinical evaluation.
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Aug 2020
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I04-1-Macromolecular Crystallography (fixed wavelength)
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Robert J
Watson
,
Paul
Bamborough
,
Heather A.
Barnett
,
Chun-wa
Chung
,
Rob
Davis
,
Laurie J.
Gordon
,
Paola
Grandi
,
Massimo
Petretich
,
Alex
Phillipou
,
Rab K.
Prinjha
,
Inmaculada
Rioja
,
Peter
Soden
,
Thilo
Werner
,
Emmanuel H
Demont
Abstract: Pan-BET inhibitors interact equipotently with all eight bromodomains of the BET family of proteins. They have shown profound efficacy in-vitro and in-vivo in oncology and immuno-modulatory models and a number are currently in clinical trials where significant safety signals have been reported. It is therefore important to understand the functional contribution of each bromodomain to assess the opportunity to tease apart efficacy and toxicity. This article discloses the in-vitro and cellular activity profile of GSK789, a potent, cell permeable and highly selective inhibitor of the first bromodomains of the BET family.
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Jul 2020
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I24-Microfocus Macromolecular Crystallography
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William
Mahy
,
Mikesh
Patel
,
David
Steadman
,
Hannah L.
Woodward
,
Benjamin N.
Atkinson
,
Fredrik
Svensson
,
Nicky J.
Willis
,
Alister
Flint
,
Dimitra
Papatheodorou
,
Yuguang
Zhao
,
Luca
Vecchia
,
Reinis R.
Ruza
,
James
Hillier
,
Sarah
Frew
,
Amy
Monaghan
,
Artur
Costa
,
Magda
Bictash
,
Magnus
Walter
,
E. Yvonne
Jones
,
Paul V.
Fish
Diamond Proposal Number(s):
[19946, 14744]
Abstract: The Wnt family of proteins are secreted signaling proteins that play key roles in regulating cellular functions. Recently, carboxylesterase Notum was shown to act as a negative regulator of Wnt signaling by mediating the removal of an essential palmitoleate. Here we disclose two new chemical scaffolds that inhibit Notum enzymatic activity. Our approach was to create a fragment library of 250 acids for screening against Notum in a biochemical assay followed by structure determination by X-ray crystallography. Twenty fragments were identified as hits for Notum inhibition and 14 of these fragments were shown to bind in the palmitoleate pocket of Notum. Optimization of 1-phenylpyrrole 20, guided by structure-based drug design, identified 20z as the most potent compound from this series. Similarly, optimization of 1-phenylpyrrolidine 8 gave acid 26. This work demonstrates that inhibition of Notum activity can be achieved by small, drug-like molecules possessing favorable in vitro ADME profiles.
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Jul 2020
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I02-Macromolecular Crystallography
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Bettina
Borreschmidt Hansen
,
Tue
Heesgaard Jepsen
,
Mogens
Larsen
,
Rikke
Sindet
,
Thomas
Vifian
,
Mia
Nørreskov Burhardt
,
Jens
Larsen
,
Jimmi
Gerner Seitzberg
,
Martin A.
Carnerup
,
Anders
Jerre
,
Christina
Mølck
,
Paola
Lovato
,
Sanjay
Rai
,
Venkatarathnam
Reddy Nasipireddy
,
Andreas
Ritzén
Abstract: Herein, we report the discovery of a series of JAK1-selective kinase inhibitors with high potency and excellent JAK family subtype selectivity. A fragment screening hit 1 with a pyrazolopyridone core and a JAK1 bias was selected as the starting point for our fragment-based lead generation efforts. A two-stage strategy was chosen with the dual aims of improving potency and JAK1 selectivity: Optimization of the lipophilic ribose pocket-targeting substituent was followed by the introduction of a variety of P-loop-targeting functional groups. Combining the best moieties from both stages of the optimization afforded compound 40, which showed excellent potency and selectivity. Metabolism studies in vitro and in vivo together with an in vitro safety evaluation suggest that 40 may be a viable lead compound for the development of highly subtype-selective JAK1 inhibitors.
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Jun 2020
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I24-Microfocus Macromolecular Crystallography
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Sarah J.
Bucknell
,
Mark A.
Ator
,
Alastair
Brown
,
Jason
Brown
,
Andrew
Cansfield
,
Julie
Cansfield
,
John
Christopher
,
Miles
Congreve
,
Gabriella
Cseke
,
Francesca
Deflorian
,
Christopher
Jones
,
Jonathan S.
Mason
,
Alistair
O'brien
,
Gregory R.
Ott
,
Mark
Pickworth
,
Stacey
Southall
Diamond Proposal Number(s):
[14637, 23280]
Abstract: Structure-based drug design enabled the discovery of 8, HTL22562, a CGRP receptor antagonist. The structure of 8 complexed with the CGRP receptor was determined at 1.6 Å resolution. Compound 8 is a highly potent, selective, metabolically stable and soluble compound suitable for a range of administration routes that have the potential to provide rapid systemic exposures with resultant high levels of receptor coverage (e.g. subcutaneous). The low lipophilicity coupled with a low anticipated clinically efficacious plasma exposure for migraine also suggests a reduced potential for hepatotoxicity. These properties have led to 8 being taken forward as a clinical candidate for acute treatment of migraine.
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Jun 2020
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I03-Macromolecular Crystallography
I04-1-Macromolecular Crystallography (fixed wavelength)
I04-Macromolecular Crystallography
I24-Microfocus Macromolecular Crystallography
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Diamond Proposal Number(s):
[18781, 14320, 20574]
Abstract: Nowadays it is possible to combine X-ray crystallography and fragment screening in a medium throughput fashion to chemically probe the surfaces used by proteins to interact and use the outcome of the screens to systematically design protein-protein inhibitors. To prove it we first performed a bioinformatics analysis of the Protein Data Bank protein complexes, which revealed over 400 cases where the crystal lattice of the target in the free form is such that large portions of the interacting surfaces are free from lattice contacts and therefore accessible to fragments during soaks. Among the tractable complexes identified, we then performed single fragment crystal screens on two particular interesting cases: the Il1β-ILR and p38α-TAB1 complexes. The result of the screens showed that fragments tend to bind in clusters, highlighting the small-molecule hotspots on the surface of the target protein. In most of the cases the hotspots overlapped with the binding sites of the interacting proteins.
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Jun 2020
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I02-Macromolecular Crystallography
I04-1-Macromolecular Crystallography (fixed wavelength)
I04-Macromolecular Crystallography
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Andrew S.
Bell
,
Zhiyong
Yu
,
Jennie A.
Hutton
,
Megan H.
Wright
,
James A.
Brannigan
,
Daniel
Paape
,
Shirley M.
Roberts
,
Charlotte L.
Sutherell
,
Markus
Ritzefeld
,
Anthony
Wilkinson
,
Deborah F
Smith
,
Robin
Leatherbarrow
,
Edward W.
Tate
Diamond Proposal Number(s):
[1221, 7864]
Abstract: The leishmaniases, caused by Leishmania species of protozoan parasites, are neglected tropical diseases with 12-15 million cases worldwide. Current therapeutic approaches are limited by toxicity, resistance and cost. N-Myristoyltransferase (NMT), an enzyme ubiquitous and essential in all eukaryotes, has been validated via genetic and pharmacological methods as a promising antileishmanial target. Here we describe a comprehensive structure activity relationship study of a thienopyrimidine series previously identified in a high throughput screen against Leishmania NMT, across 68 compounds in enzyme- and cell-based assay formats. Using a chemical tagging target engagement biomarker assay we identify the first inhibitor in this series with on-target NMT activity in leishmania parasites. Furthermore, crystal structure analyses of 12 derivatives in complex with Leishmania major NMT revealed key factors important for future structure-guided optimization delivering IMP-105 (43), a compound with modest activity against L. donovani intracellular amastigotes and excellent selectivity (>660-fold) for Leishmania NMT over human NMTs.
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Jun 2020
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I04-Macromolecular Crystallography
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Jo
Waaler
,
Ruben G. G.
Leenders
,
Sven T.
Sowa
,
Shoshy
Alam Brinch
,
Max
Lycke
,
Piotr
Nieczypor
,
Sjoerd
Aertssen
,
Sudarshan
Murthy
,
Albert
Galera-prat
,
Eddy
Damen
,
Anita
Wegert
,
Marc
Nazaré
,
Lari
Lehtiö
,
Stefan
Krauss
Diamond Proposal Number(s):
[19951]
Abstract: Tankyrases 1 and 2 are central biotargets in the WNT/β-catenin signaling and Hippo signaling pathways. We have previously developed tankyrase inhibitors bearing a 1,2,4-triazole moiety and binding predominantly to the adenosine binding site of the tankyrase catalytic domain. Here we describe a systematic structure-guided lead optimization approach of these tankyrase inhibitors. The central 1,2,4-triazole template and trans-cyclobutyl linker of the lead compound 1 were left unchanged, while side-group East, West, and South moieties were altered by introducing different building blocks defined as point mutations. The systematic study provided a novel series of compounds reaching picomolar IC50 inhibition in WNT/β-catenin signaling cellular reporter assay. The novel optimized lead 13 resolves previous atropisomerism, solubility, and Caco-2 efflux liabilities. 13 shows a favorable ADME profile, including improved Caco-2 permeability and oral bioavailability in mice, and exhibits antiproliferative efficacy in the colon cancer cell line COLO 320DM in vitro.
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Jun 2020
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