I24-Microfocus Macromolecular Crystallography
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Suzanne
O'Connor
,
Yann-Vai
Le Bihan
,
Isaac M.
Westwood
,
Manjuan
Liu
,
Oi Wei
Mak
,
Gabriel
Zazeri
,
Ana P. R.
Povinelli
,
Alan M.
Jones
,
Rob
Van Montfort
,
Jóhannes
Reynisson
,
Ian
Collins
Diamond Proposal Number(s):
[6385]
Open Access
Abstract: Heat Shock Protein 70s (HSP70s) are key molecular chaperones that are overexpressed in many cancers and often associated with metastasis and poor prognosis. It has proven difficult to develop ATP-competitive, drug-like small molecule inhibitors of HSP70s due to the flexible and hydrophilic nature of the HSP70 ATP-binding site and its high affinity for endogenous nucleotides. The aim of this study was to explore the potential for the inhibition of HSP70 through alternative binding sites using fragment-based approaches. A surface plasmon resonance (SPR) fragment screen designed to detect secondary binding sites in HSP70 led to the identification by X-ray crystallography of a cryptic binding site in the nucleotide-binding domain (NBD) of HSP70 adjacent to the ATP-binding site. Fragment binding was confirmed and characterized as ATP-competitive using SPR and ligand-observed NMR methods. Molecular dynamics simulations were applied to understand the interactions with the protein upon ligand binding, and local secondary structure changes consistent with interconversion between the observed crystal structures with and without the cryptic pocket were detected. A virtual high-throughput screen (vHTS) against the cryptic pocket was conducted, and five compounds with diverse chemical scaffolds were confirmed to bind to HSP70 with micromolar affinity by SPR. These results identified and characterized a new targetable site on HSP70. While targeting HSP70 remains challenging, the new site may provide opportunities to develop allosteric ATP-competitive inhibitors with differentiated physicochemical properties from current series.
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Jan 2022
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I11-High Resolution Powder Diffraction
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Diamond Proposal Number(s):
[17415]
Open Access
Abstract: Ferritin, a spherically shaped protein complex, is responsible for iron storage in bacteria, plants, animals, and humans. Various ferritin iron core compositions in organisms are associated with specific living requirements, health state, and different biochemical roles of ferritin isomers. Magnetoferritin, a synthetic ferritin derivative, serves as an artificial model system of unusual iron phase structures found in humans. We present the results of a complex structural study of magnetoferritins prepared by controlled in vitro synthesis. Using various complementary methods, it was observed that manipulation of the synthesis technology can improve the physicochemical parameters of the system, which is useful in applications. Thus, a higher synthesis temperature leads to an increase in magnetization due to the formation of the magnetite phase. An increase in the iron loading factor has a more pronounced impact on the protein shell structure in comparison with the pH of the aqueous medium. On the other hand, a higher loading factor at physiological temperature enhances the formation of an amorphous phase instead of magnetite crystallization. It was confirmed that the iron-overloading effect alone (observed during pathological events) cannot contribute to the formation of magnetite.
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Nov 2021
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I02-Macromolecular Crystallography
I03-Macromolecular Crystallography
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Olivier E.
Nonga
,
Darja
Lavogina
,
Erki
Enkvist
,
Katrin
Kestav
,
Apirat
Chaikuad
,
Sarah E.
Dixon-Clarke
,
Alex N.
Bullock
,
Sergei
Kopanchuk
,
Taavi
Ivan
,
Ramesh
Ekambaram
,
Kaido
Viht
,
Stefan
Knapp
,
Asko
Uri
Diamond Proposal Number(s):
[8421]
Open Access
Abstract: We performed an X-ray crystallographic study of complexes of protein kinase PIM-1 with three inhibitors comprising an adenosine mimetic moiety, a linker, and a peptide-mimetic (d-Arg)6 fragment. Guided by the structural models, simplified chemical structures with a reduced number of polar groups and chiral centers were designed. The developed inhibitors retained low-nanomolar potency and possessed remarkable selectivity toward the PIM kinases. The new inhibitors were derivatized with biotin or fluorescent dye Cy5 and then applied for the detection of PIM kinases in biochemical solutions and in complex biological samples. The sandwich assay utilizing a PIM-2-selective detection antibody featured a low limit of quantification (44 pg of active recombinant PIM-2). Fluorescent probes were efficiently taken up by U2OS cells and showed a high extent of co-localization with PIM-1 fused with a fluorescent protein. Overall, the developed inhibitors and derivatives represent versatile chemical tools for studying PIM function in cellular systems in normal and disease physiology.
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Jul 2021
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I19-Small Molecule Single Crystal Diffraction
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Helen M.
O’connor
,
Sergio
Sanz
,
Aaron J.
Scott
,
Mateusz B.
Pitak
,
Wim T.
Klooster
,
Simon J.
Coles
,
Nicholas F.
Chilton
,
Eric J. L.
Mcinnes
,
Paul J.
Lusby
,
Høgni
Weihe
,
Stergios
Piligkos
,
Euan K.
Brechin
Diamond Proposal Number(s):
[11238]
Open Access
Abstract: Three new heterometallic [CrIII8NiII6] coordination cubes of formulae [CrIII8NiII6L24(H2O)12](NO3)12 (1), [CrIII8NiII6L24(MeCN)7(H2O)5](ClO4)12 (2), and [CrIII8NiII6L24Cl12] (3) (where HL = 1-(4-pyridyl)butane-1,3-dione), were synthesised using the paramagnetic metalloligand [CrIIIL3] and the corresponding NiII salt. The magnetic skeleton of each capsule describes a face-centred cube in which the eight CrIII and six NiII ions occupy the eight vertices and six faces of the structure, respectively. Direct current magnetic susceptibility measurements on (1) reveal weak ferromagnetic interactions between the CrIII and NiII ions, with JCr-Ni = + 0.045 cm−1. EPR spectra are consistent with weak exchange, being dominated by the zero-field splitting of the CrIII ions. Excluding wheel-like structures, examples of large heterometallic clusters containing both CrIII and NiII ions are rather rare, and we demonstrate that the use of metalloligands with predictable bonding modes allows for a modular approach to building families of related polymetallic complexes. Compounds (1)–(3) join the previously published, structurally related family of [MIII8MII6] cubes, where MIII = Cr, Fe and MII = Cu, Co, Mn, Pd.
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Feb 2021
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I04-1-Macromolecular Crystallography (fixed wavelength)
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Open Access
Abstract: The β-carboline alkaloid harmine is a potent DYRK1A inhibitor, but suffers from undesired potent inhibition of MAO-A, which strongly limits its application. We synthesized more than 60 analogues of harmine, either by direct modification of the alkaloid or by de novo synthesis of β-carboline and related scaffolds aimed at learning about structure–activity relationships for inhibition of both DYRK1A and MAO-A, with the ultimate goal of separating desired DYRK1A inhibition from undesired MAO-A inhibition. Based on evidence from published crystal structures of harmine bound to each of these enzymes, we performed systematic structure modifications of harmine yielding DYRK1A-selective inhibitors characterized by small polar substituents at N-9 (which preserve DYRK1A inhibition and eliminate MAO-A inhibition) and beneficial residues at C-1 (methyl or chlorine). The top compound AnnH75 remains a potent DYRK1A inhibitor, and it is devoid of MAO-A inhibition. Its binding mode to DYRK1A was elucidated by crystal structure analysis, and docking experiments provided additional insights for this attractive series of DYRK1A and MAO-A inhibitors.
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Dec 2020
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B23-Circular Dichroism
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Diamond Proposal Number(s):
[23955, 20441, 26447]
Open Access
Abstract: The first example of uniformly chiral thin films of silicon phthalocyanines (SiPcs) are reported. The local domains of the films are mapped using circular dichroism (CD) imaging (CDi) technique available at the Diamond B23 beamline. The CDi allowed us to increase the spatial resolution up to 525× when compared with benchtop spectrometers. The results indicate formation on-surface of chiral and stable supramolecular assemblies with homogenous distribution. Chemical functionalization and solvent choice for deposition allow controllable chiroptical properties to be obtained. The method and technique reported in this work could be applied to prepare and characterize a wide variety of chiral thin films.
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Dec 2020
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B18-Core EXAFS
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Miren
Agote-Aran
,
Anna B.
Kroner
,
David S.
Wragg
,
Wojciech A.
Sławiński
,
Martha
Briceno
,
Husn U.
Islam
,
Igor V.
Sazanovich
,
María E.
Rivas
,
Andrew W. J.
Smith
,
Paul
Collier
,
Ines
Lezcano-Gonzalez
,
Andrew M.
Beale
Diamond Proposal Number(s):
[11623]
Open Access
Abstract: Small pore zeolites have shown great potential in a number of catalytic reactions. While Mo-containing medium pore zeolites have been widely studied for methane dehydroaromatisation (MDA), the use of small pore supports has drawn limited attention due to the fast deactivation of the catalyst. This work investigates the structure of the small pore Mo/H-SSZ-13 during catalyst preparation and reaction by operando X-ray absorption spectroscopy (XAS), in situ synchrotron powder diffraction (SPD), and electron microscopy; then, the results are compared with the medium pore Mo/H-ZSM-5. While SPD suggests that during catalyst preparation, part of the MoOx anchors inside the pores, Mo dispersion and subsequent ion exchange was less effective in the small pore catalyst, resulting in the formation of mesopores and Al2(MOO4)3 particles. Unlike Mo/H-ZSM-5, part of the Mo species in Mo/H-SSZ-13 undergoes full reduction to Mo0 during MDA, whereas characterisation of the spent catalyst indicates that differences also exist in the nature of the formed carbon deposits. Hence, the different Mo speciation and the low performance on small pore zeolites can be attributed to mesopores formation during calcination and the ineffective ion exchange into well dispersed Mo-oxo sites. The results open the scope for the optimisation of synthetic routes to explore the potential of small pore topologies.
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Nov 2020
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B21-High Throughput SAXS
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Diamond Proposal Number(s):
[21035]
Open Access
Abstract: Biofilm production is regulated by the Quorum Sensing system. Nowadays, Quorum Sensing represents an appealing target to design new compounds to increase antibiotics effects and avoid development of antibiotics multiresistance. In this research the use of liposomes to target two novel synthetic biofilm inhibitors is presented, focusing on a preformulation study to select a liposome composition for in vitro test. Five different liposome (LP) formulations, composed of phosphatidyl choline, cholesterol and charged surfactant (2:1:1, molar ratio) have been prepared by direct hydration and extrusion. As charged surfactants dicetyl phosphate didecyldimethylammonium chloride, di isobutyl phenoxy ethyl dimethyl benzyl ammonium chloride and stearylamine (SA) and have been used. Liposome charge, size and morphology were investigated by zeta potential, photon correlation spectroscopy, small angle x-ray spectroscopy and electron microscopy. LP-SA was selected for the loading of biofilm inhibitors and subjected to high performance liquid chromatography for entrapment capacity evaluation. LP-SA loaded inhibitors showed a higher diameter (223.6 nm) as compared to unloaded ones (205.7 nm) and a dose-dependent anti-biofilm effect mainly after 48 h of treatment, while free biofilm inhibitors loose activity. In conclusion, our data supported the use of liposomes as a strategy to enhance biofilm inhibitors effect.
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Nov 2020
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I02-Macromolecular Crystallography
I04-Macromolecular Crystallography
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Patrick
Weber
,
Martin
Thonhofer
,
Summer
Averill
,
Gideon J.
Davies
,
Andres Gonzalez
Santana
,
Philipp
Müller
,
Seyed A.
Nasseri
,
Wendy A.
Offen
,
Bettina M.
Pabst
,
Eduard
Paschke
,
Michael
Schalli
,
Ana
Torvisco
,
Marion
Tschernutter
,
Christina
Tysoe
,
Werner
Windischhofer
,
Stephen G.
Withers
,
Andreas
Wolfsgruber
,
Tanja M.
Wrodnigg
,
Arnold E.
Stütz
Open Access
Abstract: Glycosidase inhibitors have shown great potential as pharmacological chaperones for lysosomal storage diseases. In light of this, a series of new cyclopentanoid β-galactosidase inhibitors were prepared and their inhibitory and pharmacological chaperoning activities determined and compared with those of lipophilic analogs of the potent β-d-galactosidase inhibitor 4-epi-isofagomine. Structure-activity relationships were investigated by X-ray crystallography as well as by alterations in the cyclopentane moiety such as deoxygenation and replacement by fluorine of a “strategic” hydroxyl group. New compounds have revealed highly promising activities with a range of β-galactosidase-compromised human cell lines and may serve as leads towards new pharmacological chaperones for GM1-gangliosidosis and Morquio B disease.
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Sep 2020
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B22-Multimode InfraRed imaging And Microspectroscopy
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Diamond Proposal Number(s):
[15393]
Open Access
Abstract: Glycosaminoglycans (GAGs)/proteoglycans (PGs) play a pivotal role in the metastasis of inflammatory breast cancer (IBC). They represent biomarkers and targets in diagnosis and treatment of different cancers including breast cancer. Thus, GAGs/PGs could represent potential prognostic/diagnostic biomarkers for IBC. In the present study, non-IBC MDA-MB-231, MCF7, SKBR3 cells and IBC SUM149 cells, as well as their GAG secretome were analyzed. The latter was measured in toto as dried drops with high-throughput (HT) Fourier Transform InfraRed (FTIR) spectroscopy and imaging. FTIR imaging was also employed to investigate single whole breast cancer cells while synchrotron-FTIR microspectroscopy was used to specifically target their cytoplasms. Data were analyzed by hierarchical cluster analysis and principal components analysis. Results obtained from HT-FTIR analysis of GAG drops showed that the inter-group variability enabled us to delineate between cell types in the GAG absorption range 1350–800 cm−1. Similar results were obtained for FTIR imaging of GAG extracts and fixed single whole cells. Synchrotron-FTIR data from cytoplasms allowed discrimination between non-IBC and IBC. Thus, by using GAG specific region, not only different breast cancer cell lines could be differentiated, but also non-IBC from IBC cells. This could be a potential diagnostic spectral marker for IBC detection useful for patient management.
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Sep 2020
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