I03-Macromolecular Crystallography
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Yue
Wu
,
Zhihong
Li
,
Samanpreet
Kaur
,
Zewei
Zhang
,
Jie
Yue
,
Anthony
Tumber
,
Haoshu
Zhang
,
Zhe
Song
,
Peiyao
Yang
,
Ying
Dong
,
Fulai
Yang
,
Xiang
Li
,
Christopher J.
Schofield
,
Xiaojin
Zhang
Diamond Proposal Number(s):
[23459]
Open Access
Abstract: Factor inhibiting hypoxia-inducible factor (FIH) is a JmjC domain 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase that catalyzes protein hydroxylations, including of specific asparagines in the C-terminal transcriptional activation domains of hypoxia-inducible factor alpha (HIF-α) isoforms. FIH is of medicinal interest due to its ability to alter metabolism and modulate the course of the HIF-mediated hypoxic response. We report the development of a light-induced, lysine (Lys106)-targeting irreversible covalent inhibitor of FIH. The approach is complementary to optogenetic methods for regulation of transcription. The covalently reacting inhibitor NBA-ZG-2291 was the result of structure-guided modification of the reported active site binding FIH inhibitor ZG-2291 with an appropriately positioned o-nitrobenzyl alcohol (o-NBA) group. The results demonstrate that NBA-ZG-2291 forms a stable covalent bond in a light-dependent process with Lys106 of FIH, inactivating its hydroxylation activity and resulting in sustained upregulation of FIH-dependent HIF target genes. The light-controlled inhibitors targeting a lysine residue enable light and spatiotemporal control of FIH activity in a manner useful for dissecting the context-dependent physiological roles of FIH.
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May 2025
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I03-Macromolecular Crystallography
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Yue
Wu
,
Yafen
Chen
,
Thomas
Corner
,
Yu
Nakashima
,
Eidarus
Salah
,
Zhihong
Li
,
Linjian
Zhang
,
Le
Yang
,
Anthony
Tumber
,
Zhuoli
Sun
,
Yukang
Wen
,
Ailin
Zhong
,
Fulai
Yang
,
Xiang
Li
,
Zhihong
Zhang
,
Christopher
Schofield
,
Xiaojin
Zhang
Diamond Proposal Number(s):
[23459]
Abstract: In animals limiting oxygen upregulates hypoxia-inducible factor (HIF) promoting a metabolic shift towards glycolysis. Factor inhibiting HIF (FIH) is an asparaginyl hydroxylase that regulates HIF function by reducing its interaction with histone acetyl transferases. HIF levels are negatively regulated by the HIF prolyl hydroxylases (PHDs), which like FIH, are 2-oxoglutarate(2OG) oxygenases. Genetic loss of FIH promotes both glycolysis and aerobic metabolism. FIH has multiple non-HIF substrates making it challenging to connect its biochemistry with physiology. A structure-mechanism guided approach identified a highly potent in vivo active FIH inhibitor, ZG-2291, binding of which promotes a conformational flip of a catalytically important tyrosine, enabling selective inhibition of FIH over other JmjC subfamily 2OG oxygenases. Consistent with genetic studies, ZG-2291 promotes thermogenesis and ameliorates symptoms of obesity and metabolic dysfunction in ob/ob mice. The results reveal ZG-2291 as a useful probe for the physiological functions of FIH and identify FIH inhibition as a promising strategy for obesity treatment.
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Jun 2024
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I03-Macromolecular Crystallography
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Thomas P.
Corner
,
Ryan Z. R.
Teo
,
Yue
Wu
,
Eidarus
Salah
,
Yu
Nakashima
,
Giorgia
Fiorini
,
Anthony
Tumber
,
Amelia
Brasnett
,
James P.
Holt-Martyn
,
William D.
Figg
,
Xiaojin
Zhang
,
Lennart
Brewitz
,
Christopher J.
Schofield
Diamond Proposal Number(s):
[23459]
Open Access
Abstract: The human 2-oxoglutarate (2OG)- and Fe(II)-dependent oxygenases factor inhibiting hypoxia-inducible factor-α (FIH) and HIF-α prolyl residue hydroxylases 1–3 (PHD1–3) regulate the response to hypoxia in humans via catalysing hydroxylation of the α-subunits of the hypoxia-inducible factors (HIFs). Small-molecule PHD inhibitors are used for anaemia treatment; by contrast, few selective inhibitors of FIH have been reported, despite their potential to regulate the hypoxic response, either alone or in combination with PHD inhibition. We report molecular, biophysical, and cellular evidence that the N-hydroxythiazole scaffold, reported to inhibit PHD2, is a useful broad spectrum 2OG oxygenase inhibitor scaffold, the inhibition potential of which can be tuned to achieve selective FIH inhibition. Structure-guided optimisation resulted in the discovery of N-hydroxythiazole derivatives that manifest substantially improved selectivity for FIH inhibition over PHD2 and other 2OG oxygenases, including Jumonji-C domain-containing protein 5 (∼25-fold), aspartate/asparagine-β-hydroxylase (>100-fold) and histone Nε-lysine demethylase 4A (>300-fold). The optimised N-hydroxythiazole-based FIH inhibitors modulate the expression of FIH-dependent HIF target genes and, consistent with reports that FIH regulates cellular metabolism, suppressed lipid accumulation in adipocytes. Crystallographic studies reveal that the N-hydroxythiazole derivatives compete with both 2OG and the substrate for binding to the FIH active site. Derivatisation of the N-hydroxythiazole scaffold has the potential to afford selective inhibitors for 2OG oxygenases other than FIH.
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Oct 2023
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I07-Surface & interface diffraction
I11-High Resolution Powder Diffraction
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Diamond Proposal Number(s):
[24359, 23666]
Open Access
Abstract: Membranes with high selectivity offer an attractive route to molecular separations, where technologies such as distillation and chromatography are energy intensive. However, it remains challenging to fine tune the structure and porosity in membranes, particularly to separate molecules of similar size. Here, we report a process for producing composite membranes that comprise crystalline porous organic cage films fabricated by interfacial synthesis on a polyacrylonitrile support. These membranes exhibit ultrafast solvent permeance and high rejection of organic dyes with molecular weights over 600 g mol−1. The crystalline cage film is dynamic, and its pore aperture can be switched in methanol to generate larger pores that provide increased methanol permeance and higher molecular weight cut-offs (1,400 g mol−1). By varying the water/methanol ratio, the film can be switched between two phases that have different selectivities, such that a single, ‘smart’ crystalline membrane can perform graded molecular sieving. We exemplify this by separating three organic dyes in a single-stage, single-membrane process.
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Jan 2022
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I15-1-X-ray Pair Distribution Function (XPDF)
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Diamond Proposal Number(s):
[18630]
Open Access
Abstract: The structures of Zr and Hf metal–organic frameworks (MOFs) are very sensitive to small changes in synthetic conditions. One key difference affecting the structure of UiO MOF phases is the shape and nuclearity of Zr or Hf metal clusters acting as nodes in the framework; although these clusters are crucial, their evolution during MOF synthesis is not fully understood. In this paper, we explore the nature of Hf metal clusters that form in different reaction solutions, including in a mixture of DMF, formic acid, and water. We show that the choice of solvent and reaction temperature in UiO MOF syntheses determines the cluster identity and hence the MOF structure. Using in situ X-ray pair distribution function measurements, we demonstrate that the evolution of different Hf cluster species can be tracked during UiO MOF synthesis, from solution stages to the full crystalline framework, and use our understanding to propose a formation mechanism for the hcp UiO-66(Hf) MOF, in which first the metal clusters aggregate from the M6 cluster (as in fcu UiO-66) to the hcp-characteristic M12 double cluster and, following this, the crystalline hcp framework forms. These insights pave the way toward rationally designing syntheses of as-yet unknown MOF structures, via tuning the synthesis conditions to select different cluster species.
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Nov 2021
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B18-Core EXAFS
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Diamond Proposal Number(s):
[25651]
Open Access
Abstract: In this paper, we demonstrate a novel synthetic route to assemble reduced graphene oxide (rGO) uniformly coated on BiSI composite and investigate its potential as the active electrode material for supercapacitors. In this strategy, graphene oxide (GO) was not a simple physical mixture with the BiSI material but bismuth cations were uniformly anchored on the surface of GO by chemical bonding during material growth and the size of GO can determine the final size of rGO coated BiSI composite. The galvanostatic charge–discharge measurement results show that the BiSI–rGO electrode has a maximum specific capacity of 234 C g−1 at the current density of 1 A g−1 and excellent capacity retention of 92.4% after 2000 cycles. In situ XANES and EXAFS were employed to study the electrochemical oxidation and reduction processes of the bismuth-based material with rGO coating and investigate the origins of the structural stabilities. The results show that our novel rGO coating route can not only significantly increase the capacity but also improve cycling stability.
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Jun 2021
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I11-High Resolution Powder Diffraction
I19-Small Molecule Single Crystal Diffraction
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Diamond Proposal Number(s):
[21726, 23666]
Open Access
Abstract: A molecular crystal of a 2-D hydrogen-bonded organic framework (HOF) undergoes an unusual structural transformation after solvent removal from the crystal pores during activation. The conformationally flexible host molecule, ABTPA, adapts its molecular conformation during activation to initiate a framework expansion. The microcrystalline activated phase was characterized by three-dimensional electron diffraction (3D ED), which revealed that ABTPA uses out-of-plane anthracene units as adaptive structural anchors. These units change orientation to generate an expanded, lower density framework material in the activated structure. The porous HOF, ABTPA-2, has robust dynamic porosity (SABET = 1183 m2 g-1) and exhibits negative area thermal expansion. We use crystal structure prediction (CSP) to understand the underlying energetics behind the structural transformation and discuss the challenges facing CSP for such flexible molecules.
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Jun 2020
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I02-Macromolecular Crystallography
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Wei
Wang
,
Jill M.
Marinis
,
Allison M.
Beal
,
Shivraj
Savadkar
,
Yue
Wu
,
Mohammed
Khan
,
Pardeep S.
Taunk
,
Nan
Wu
,
Wenyu
Su
,
Jingjing
Wu
,
Aarif
Ahsan
,
Emma
Kurz
,
Ting
Chen
,
Inedouye
Yaboh
,
Fei
Li
,
Johana
Gutierrez
,
Brian
Diskin
,
Mautin
Hundeyin
,
Michael
Reilly
,
John D.
Lich
,
Philip A.
Harris
,
Mukesh K.
Mahajan
,
James H.
Thorpe
,
Pamela
Nassau
,
Julie E.
Mosley
,
Joshua
Leinwand
,
Juan A.
Kochen Rossi
,
Ankita
Mishra
,
Berk
Aykut
,
Michael
Glacken
,
Atsuo
Ochi
,
Narendra
Verma
,
Jacqueline I.
Kim
,
Varshini
Vasudevaraja
,
Dennis
Adeegbe
,
Christina
Almonte
,
Ece
Bagdatlioglu
,
Deirdre J.
Cohen
,
Kwok-Kin
Wong
,
John
Bertin
,
George
Miller
Abstract: Pancreatic ductal adenocarcinoma (PDA) is characterized by immune tolerance and immunotherapeutic resistance. We discovered upregulation of receptor-interacting serine/threonine protein kinase 1 (RIP1) in tumor-associated macrophages (TAMs) in PDA. To study its role in oncogenic progression, we developed a selective small-molecule RIP1 inhibitor with high in vivo exposure. Targeting RIP1 reprogrammed TAMs toward an MHCIIhiTNFα+IFNγ+ immunogenic phenotype in a STAT1-dependent manner. RIP1 inhibition in TAMs resulted in cytotoxic T cell activation and T helper cell differentiation toward a mixed Th1/Th17 phenotype, leading to tumor immunity in mice and in organotypic models of human PDA. Targeting RIP1 synergized with PD1-and inducible co-stimulator-based immunotherapies. Tumor-promoting effects of RIP1 were independent of its co-association with RIP3. Collectively, our work describes RIP1 as a checkpoint kinase governing tumor immunity.
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Nov 2018
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I12-JEEP: Joint Engineering, Environmental and Processing
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Hamish
Yeung
,
Adam F.
Sapnik
,
Felicity
Massingberd-Mundy
,
Michael W.
Gaultois
,
Yue
Wu
,
Duncan X.
Fraser
,
Sebastian
Henke
,
Roman
Pallach
,
Niclas
Heidenreich
,
Oxana
Magdysyuk
,
Nghia T.
Vo
,
Andrew L.
Goodwin
Diamond Proposal Number(s):
[16354, 16450]
Abstract: There is an increasingly large amount of interest in metal‐organic frameworks (MOFs) for a variety of applications, from gas sensing and separations to electronics and catalysis. Their exciting properties arise from their modular architectures, which self‐assemble from different combinations of metal‐based and organic building units. However, the exact mechanisms by which they crystallize remain poorly understood, thus limiting any realisation of real “structure by design”. We report important new insight into MOF formation, gained using in situ X‐ray diffraction, pH and turbidity measurements to uncover for the first time the evolution of metastable intermediate species in the canonical zeolitic imidazolate framework system, ZIF‐8. We reveal that the intermediate species exist in a dynamic pre‐equilibrium prior to network assembly and, depending on the reactant concentrations and the progress of reaction, the pre‐equilibrium can be made to favour under‐ or over‐coordinated Zn‐imidazolate species, thus accelerating or inhibiting crystallization, respectively. We thereby find that concentration can be effectively used as a synthetic handle to directly control particle size, with great implications for industrial scale‐up and gas sorption applications. These finding enables us to rationalise the apparent contradictions between previous studies of ZIF‐8 and, importantly, opens up new opportunities for the control of crystallization in network solids more generally, from the design of local structure to assembly of particles with precise dimensions.
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Nov 2018
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I15-Extreme Conditions
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Diamond Proposal Number(s):
[13843]
Abstract: Crystallization via metastable phases plays an important role in chemical manufacturing, bio-mineralization, and protein crystallization, but the kinetic pathways leading from metastable phases to the stable crystalline modifications are not well understood. In particular, the fast crys-tallization of amorphous intermediates makes a detailed characterization challenging. To circum-vent this problem, we devised a system that allows trapping and stabilizing the amorphous in-termediates of representative carbonates (calcium, strontium, barium, manganese, and cadmium). The long-term stabilization of these transient species enabled a detailed investigation of their composition, structure, and morphology. Total scattering experiments with high-energy syn-chrotron radiation revealed a short-range order of several Ångström in all amorphous intermedi-ates. From the synchrotron data, a structural model of amorphous calcium carbonate was de-rived that indicates a lower coordination number of calcium compared to the crystalline poly-morphs. Our study shows that a multi-step crystallization pathway via amorphous intermediates is open to many carbonates. We could isolate and characterize these transient species, thereby providing new insights into their crystallization mechanism.
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Oct 2018
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