I24-Microfocus Macromolecular Crystallography
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Alex G.
Baldwin
,
David W.
Foley
,
Ross
Collins
,
Hyunah
Lee
,
D. Heulyn
Jones
,
Ben
Wahab
,
Loren
Waters
,
Josephine
Pedder
,
Marie
Paine
,
Gui Jie
Feng
,
Lucia
Privitera
,
Alexander
Ashall-Kelly
,
Carys
Thomas
,
Jason A.
Gillespie
,
Lauramariú
Schino
,
Delia
Belelli
,
Cecilia
Rocha
,
Gilles
Maussion
,
Andrea I.
Krahn
,
Thomas M.
Durcan
,
Jonathan M.
Elkins
,
Jeremy J.
Lambert
,
John R.
Atack
,
Simon E.
Ward
Open Access
Abstract: LIMKs are serine/threonine and tyrosine kinases responsible for controlling cytoskeletal dynamics as key regulators of actin stability, ensuring synaptic health through normal synaptic bouton structure and function. However, LIMK1 overactivation results in abnormal dendritic synaptic development that characterizes the pathogenesis of Fragile X Syndrome (FXS). As a result, the development of LIMK inhibitors represents an emerging disease-modifying therapeutic approach for FXS. We report the discovery of MDI-114215 (85), a novel, potent allosteric dual-LIMK1/2 inhibitor that demonstrates exquisite kinome selectivity. 85 reduces phospho-cofilin in mouse brain slices and rescues impaired hippocampal long-term potentiation in brain slices from FXS mice. We also show that LIMK inhibitors are effective in reducing phospho-cofilin levels in iPSC neurons derived from FXS patients, demonstrating 85 to be a potential therapeutic candidate for FXS that could have broad application to neurological disorders or cancers caused by LIMK1/2 overactivation and actin instability.
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Dec 2024
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Claudia
Tredup
,
Suzanne
Ackloo
,
Hartmut
Beck
,
Peter J.
Brown
,
Alex N.
Bullock
,
Alessio
Ciulli
,
Ivan
Dikic
,
Kristina
Edfeldt
,
Aled M.
Edwards
,
Jonathan M.
Elkins
,
Henner F.
Farin
,
Edward A.
Fon
,
Matthias
Gstaiger
,
Judith
Günther
,
Anna-Lena
Gustavsson
,
Sandra
Häberle
,
Laura
Isigkeit
,
Kilian V. M.
Huber
,
Andras
Kotschy
,
Oliver
Krämer
,
Andrew R.
Leach
,
Brian D.
Marsden
,
Hisanori
Matsui
,
Daniel
Merk
,
Florian
Montel
,
Monique P. C.
Mulder
,
Susanne
Müller
,
Dafydd R.
Owen
,
Ewgenij
Proschak
,
Sandra
Röhm
,
Alexandra
Stolz
,
Michael
Sundström
,
Frank
Von Delft
,
Timothy M.
Willson
,
Cheryl H.
Arrowsmith
,
Stefan
Knapp
Open Access
Abstract: Target 2035 is a global initiative that seeks to identify a pharmacological modulator of most human proteins by the year 2035. As part of an ongoing series of annual updates of this initiative, we summarise here the efforts of the EUbOPEN project whose objectives and results are making a strong contribution to the goals of Target 2035. EUbOPEN is a public–private partnership with four pillars of activity: (1) chemogenomic library collections, (2) chemical probe discovery and technology development for hit-to-lead chemistry, (3) profiling of bioactive compounds in patient-derived disease assays, and (4) collection, storage and dissemination of project-wide data and reagents. The substantial outputs of this programme include a chemogenomic compound library covering one third of the druggable proteome, as well as 100 chemical probes, both profiled in patient derived assays, as well as hundreds of data sets deposited in existing public data repositories and a project-specific data resource for exploring EUbOPEN outputs.
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Nov 2024
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I24-Microfocus Macromolecular Crystallography
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Fernando H.
De Souza Gama
,
Luiz A.
Dutra
,
Michael
Hawgood
,
Caio Vinícius
Dos Reis
,
Ricardo A. M.
Serafim
,
Marcos A.
Ferreira
,
Bruno V. M.
Teodoro
,
Jéssica Emi
Takarada
,
André S.
Santiago
,
Dimitrios-Ilias
Balourdas
,
Ann-Sofie
Nilsson
,
Bruno
Urien
,
Vitor M.
Almeida
,
Carina
Gileadi
,
Priscila Z.
Ramos
,
Anita
Salmazo
,
Stanley N. S.
Vasconcelos
,
Micael R.
Cunha
,
Susanne
Mueller
,
Stefan
Knapp
,
Katlin B.
Massirer
,
Jonathan M.
Elkins
,
Opher
Gileadi
,
Alessandra
Mascarello
,
Bennie B. L. G.
Lemmens
,
Cristiano R. W.
Guimarães
,
Hatylas
Azevedo
,
Rafael M.
Counago
Abstract: Vaccinia-related kinase 1 (VRK1) and the δ and ε isoforms of casein kinase 1 (CK1) are linked to various disease-relevant pathways. However, the lack of tool compounds for these kinases has significantly hampered our understanding of their cellular functions and therapeutic potential. Here, we describe the structure-based development of potent inhibitors of VRK1, a kinase highly expressed in various tumor types and crucial for cell proliferation and genome integrity. Kinome-wide profiling revealed that our compounds also inhibit CK1δ and CK1ε. We demonstrate that dihydropteridinones 35 and 36 mimic the cellular outcomes of VRK1 depletion. Complementary studies with existing CK1δ and CK1ε inhibitors suggest that these kinases may play overlapping roles in cell proliferation and genome instability. Together, our findings highlight the potential of VRK1 inhibition in treating p53-deficient tumors and possibly enhancing the efficacy of existing cancer therapies that target DNA stability or cell division.
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May 2024
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I04-Macromolecular Crystallography
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Scott H.
Henderson
,
Fiona J.
Sorrell
,
James M.
Bennett
,
Oleg
Fedorov
,
Marcus T.
Hanley
,
Paulo H.
Godoi
,
Roberta
Ruela De Sousa
,
Sean
Robinson
,
Iva
Hopkins Navratilova
,
Jonathan M.
Elkins
,
Simon E.
Ward
Open Access
Abstract: elective inhibitors of DYRK1A are of interest for the treatment of cancer, Type 2 diabetes and neurological disorders. Optimization of imidazo [1,2-b]pyridazine fragment 1 through structure−activity relationship exploration and in silico drug design efforts led to the discovery of compound 17 as a potent cellular inhibitor of DYRK1A with selectivity over much of the kinome. The binding mode of compound 17 was elucidated with X-ray crystallography, facilitating the rational design of compound 29, an imidazo [1,2-b]pyridazine with improved kinase selectivity with respect to closely related CLK kinases.
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Apr 2024
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I03-Macromolecular Crystallography
I04-1-Macromolecular Crystallography (fixed wavelength)
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Esra
Balikci
,
Anne-Sophie M. C.
Marques
,
Ludwig G.
Bauer
,
Raina
Seupel
,
James
Bennett
,
Brigitt
Raux
,
Karly
Buchan
,
Klemensas
Simelis
,
Usha
Singh
,
Catherine
Rogers
,
Jennifer
Ward
,
Carol
Cheng
,
Tamas
Szommer
,
Kira
Schützenhofer
,
Jonathan M.
Elkins
,
David L.
Sloman
,
Ivan
Ahel
,
Oleg
Fedorov
,
Paul E.
Brennan
,
Kilian V. M.
Huber
Diamond Proposal Number(s):
[19301, 28172]
Open Access
Abstract: Cofactor mimicry represents an attractive strategy for the development of enzyme inhibitors but can lead to off-target effects due to the evolutionary conservation of binding sites across the proteome. Here, we uncover the ADP-ribose (ADPr) hydrolase NUDT5 as an unexpected, noncovalent, off-target of clinical BTK inhibitors. Using a combination of biochemical, biophysical, and intact cell NanoBRET assays as well as X-ray crystallography, we confirm catalytic inhibition and cellular target engagement of NUDT5 and reveal an unusual binding mode that is independent of the reactive acrylamide warhead. Further investigation of the prototypical BTK inhibitor ibrutinib also revealed potent inhibition of the largely unstudied NUDIX hydrolase family member NUDT14. By exploring structure–activity relationships (SARs) around the core scaffold, we identify a potent, noncovalent, and cell-active dual NUDT5/14 inhibitor. Cocrystallization experiments yielded new insights into the NUDT14 hydrolase active site architecture and inhibitor binding, thus providing a basis for future chemical probe design.
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Apr 2024
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I04-1-Macromolecular Crystallography (fixed wavelength)
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Ricardo A. M.
Serafim
,
Fiona J.
Sorrell
,
Benedict-Tilman
Berger
,
Ross J.
Collins
,
Stanley N. S.
Vasconcelos
,
Katlin B.
Massirer
,
Stefan
Knapp
,
James
Bennett
,
Oleg
Fedorov
,
Hitesh
Patel
,
William J.
Zuercher
,
Jonathan M.
Elkins
Diamond Proposal Number(s):
[15433]
Abstract: SLK (STE20-like kinase) and STK10 (serine/threonine kinase 10) are closely related kinases whose enzymatic activity is linked to the regulation of ezrin, radixin, and moesin function and to the regulation of lymphocyte migration and the cell cycle. We identified a series of 3-anilino-4-arylmaleimides as dual inhibitors of SLK and STK10 with good kinome-wide selectivity. Optimization of this series led to multiple SLK/STK10 inhibitors with nanomolar potency. Crystal structures of exemplar inhibitors bound to SLK and STK10 demonstrated the binding mode of the inhibitors and rationalized their selectivity. Cellular target engagement assays demonstrated the binding of the inhibitors to SLK and STK10 in cells. Further selectivity analyses, including analysis of activity of the reported inhibitors against off-targets in cells, identified compound 31 as the most potent and selective inhibitor of SLK and STK10 yet reported.
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Aug 2021
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I03-Macromolecular Crystallography
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Diamond Proposal Number(s):
[15433]
Open Access
Abstract: Kinases represent one of the most intensively pursued groups of targets in modern-day drug discovery. Often it is desirable to achieve selective inhibition of the kinase of interest over the remaining ∼500 kinases in the human kinome. This is especially true when inhibitors are intended to be used to study the biology of the target of interest. We present a pipeline of open-source software that analyzes public domain data to repurpose compounds that have been used in previous kinase inhibitor development projects. We define the dual-specificity tyrosine-regulated kinase 1A (DYRK1A) as the kinase of interest, and by addition of a single methyl group to the chosen starting point we remove glycogen synthase kinase β (GSK3β) and cyclin-dependent kinase (CDK) inhibition. Thus, in an efficient manner we repurpose a GSK3β/CDK chemotype to deliver 8b, a highly selective DYRK1A inhibitor.
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Aug 2020
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I24-Microfocus Macromolecular Crystallography
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Gerson S.
Profeta
,
Caio V.
Dos Reis
,
André Da S.
Santiago
,
Paulo H. C.
Godoi
,
Angela M.
Fala
,
Carrow I.
Wells
,
Roger
Sartori
,
Anita P. T.
Salmazo
,
Priscila Z.
Ramos
,
Katlin B.
Massirer
,
Jonathan M.
Elkins
,
David H.
Drewry
,
Opher
Gileadi
,
Rafael M.
Counago
Diamond Proposal Number(s):
[16171]
Open Access
Abstract: Calcium/Calmodulin-dependent Protein Kinase Kinase 2 (CAMKK2) acts as a signaling hub, receiving signals from various regulatory pathways and decoding them via phosphorylation of downstream protein kinases - such as AMPK (AMP-activated protein kinase) and CAMK types I and IV. CAMKK2 relevance is highlighted by its constitutive activity being implicated in several human pathologies. However, at present, there are no selective small-molecule inhibitors available for this protein kinase. Moreover, CAMKK2 and its closest human homolog, CAMKK1, are thought to have overlapping biological roles. Here we present six new co-structures of potent ligands bound to CAMKK2 identified from a library of commercially-available kinase inhibitors. Enzyme assays confirmed that most of these compounds are equipotent inhibitors of both human CAMKKs and isothermal titration calorimetry (ITC) revealed that binding to some of these molecules to CAMKK2 is enthalpy driven. We expect our results to advance current efforts to discover small molecule kinase inhibitors selective to each human CAMKK.
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Nov 2019
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I03-Macromolecular Crystallography
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Carrow
Wells
,
Rafael M.
Counago
,
Juanita C.
Limas
,
Tuanny L.
Almeida
,
Jeanette Gowen
Cook
,
David H
Drewry
,
Jonathan M.
Elkins
,
Opher
Gileadi
,
Nirav R.
Kapadia
,
Alvaro
Lorente-Macias
,
Julie E.
Pickett
,
Alexander
Riemen
,
Roberta R.
Ruela-De-Sousa
,
Timothy M.
Willson
,
Cunyu
Zhang
,
William J
Zuercher
,
Reena
Zutshi
,
Alison D.
Axtman
Diamond Proposal Number(s):
[14664]
Abstract: Inhibitors based on a 3-acylaminoindazole scaffold were synthesized to yield potent dual AAK1/BMP2K inhibitors. Optimization furnished a small molecule chemical probe (SGC-AAK1-1, 25) that is potent and selective for AAK1/BMP2K over other NAK family members, demonstrates narrow activity in a kinome-wide screen, and is functionally active in cells. This inhibitor represents one of the best available small molecule tools to study the functions of AAK1 and BMP2K.
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Oct 2019
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I03-Macromolecular Crystallography
I04-Macromolecular Crystallography
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Open Access
Abstract: Aurora kinases B and C (AURKB/AURKC) are activated by binding to the C-terminal domain of INCENP. Full activation requires phosphorylation of two serine residues of INCENP that are conserved through evolution, although the mechanism of this activation has not been explained. Here we present crystal structures of the fully active complex of AURKC bound to INCENP, consisting of phosphorylated, activated, AURKC and INCENP phosphorylated on its TSS motif, revealing the structural and biochemical mechanism of synergistic activation of AURKC:INCENP. The structures show that TSS motif phosphorylation stabilises the kinase activation loop of AURKC. The TSS motif phosphorylations alter the substrate-binding surface consistent with a mechanism of altered kinase substrate selectivity and stabilisation of the protein complex against unfolding. We also analyse the binding of the most specific available AURKB inhibitor, BRD-7880, and demonstrate that the well-known Aurora kinase inhibitor VX-680 disrupts binding of the phosphorylated INCENP TSS motif.
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Jul 2019
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