I03-Macromolecular Crystallography
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Sandra
Röhm
,
Martin
Schroeder
,
Jessica E.
Dwyer
,
Caroline S.
Widdowson
,
Apirat
Chaikuad
,
Benedict-tilman
Berger
,
Andreas C.
Joerger
,
Andreas
Krämer
,
Jule
Harbig
,
Daniel
Dauch
,
Mark
Kudolo
,
Stefan
Laufer
,
Mark C.
Bagley
,
Stefan
Knapp
Diamond Proposal Number(s):
[10619]
Abstract: The p38 MAPK cascade is a key signaling pathway linked to a multitude of physiological functions and of central importance in inflammatory and autoimmune diseases. Although studied extensively, little is known about how conformation-specific inhibitors alter signaling outcomes. Here, we have explored the highly dynamic back pocket of p38 MAPK with allosteric urea fragments. However, screening against known off-targets showed that these fragments maintained the selectivity issues of their parent compound BIRB-796, while combination with the hinge-binding motif of VPC-00628 greatly enhanced inhibitor selectivity. Further efforts focused therefore on the exploration of the αC-out pocket of p38 MAPK, yielding compound 137 as a highly selective type-II inhibitor. Even though 137 is structurally related to a recent p38 type-II chemical probe, SR-318, the data presented here provide valuable insights into back-pocket interactions that are not addressed in SR-318 and it provides an alternative chemical tool with good cellular activity targeting also the p38 back pocket.
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Dec 2020
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I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[105433]
Open Access
Abstract: Extracellular signal-regulated kinase 3 (ERK3), known also as mitogen-activated protein kinase 6 (MAPK6), is an atypical member of MAPK kinase family, which has been poorly studied. Little is known regarding its function in biological processes, yet this atypical kinase has been suggested to play important roles in the migration and invasiveness of certain cancers. The lack of tools, such as a selective inhibitor, hampers the study of ERK3 biology. Here, we report the crystal structure of the kinase domain of this atypical MAPK kinase, providing molecular insights into its distinct ATP binding pocket compared to the classical MAPK ERK2, explaining differences in their inhibitor binding properties. Medium-scale small molecule screening identified a number of inhibitors, several of which unexpectedly exhibited remarkably high inhibitory potencies. The crystal structure of CLK1 in complex with CAF052, one of the most potent inhibitors identified for ERK3, revealed typical type-I binding mode of the inhibitor, which by structural comparison could likely be maintained in ERK3. Together with the presented structural insights, these diverse chemical scaffolds displaying both reversible and irreversible modes of action, will serve as a starting point for the development of selective inhibitors for ERK3, which will be beneficial for elucidating the important functions of this understudied kinase.
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Nov 2020
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I11-High Resolution Powder Diffraction
I19-Small Molecule Single Crystal Diffraction
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Stephen P.
Argent
,
Ivan
Da Silva
,
Alex
Greenaway
,
Mathew
Savage
,
Jack
Humby
,
Andrew J.
Davies
,
Harriott
Nowell
,
William
Lewis
,
Pascal
Manuel
,
Chiu C.
Tang
,
Alexander J.
Blake
,
Michael W.
George
,
Alexander V.
Markevich
,
Elena
Besley
,
Sihai
Yang
,
Neil R.
Champness
,
Martin
Schroeder
Diamond Proposal Number(s):
[861, 11622, 15833, 9443]
Open Access
Abstract: Designing porous materials which can selectively adsorb CO2 or CH4 is an important environmental and industrial goal which requires an understanding of the host–guest interactions involved at the atomic scale. Metal–organic polyhedra (MOPs) showing permanent porosity upon desolvation are rarely observed. We report a family of MOPs (Cu-1a, Cu-1b, Cu-2), which derive their permanent porosity from cavities between packed cages rather than from within the polyhedra. Thus, for Cu-1a, the void fraction outside the cages totals 56% with only 2% within. The relative stabilities of these MOP structures are rationalized by considering their weak nondirectional packing interactions using Hirshfeld surface analyses. The exceptional stability of Cu-1a enables a detailed structural investigation into the adsorption of CO2 and CH4 using in situ X-ray and neutron diffraction, coupled with DFT calculations. The primary binding sites for adsorbed CO2 and CH4 in Cu-1a are found to be the open metal sites and pockets defined by the faces of phenyl rings. More importantly, the structural analysis of a hydrated sample of Cu-1a reveals a strong hydrogen bond between the adsorbed CO2 molecule and the Cu(II)-bound water molecule, shedding light on previous empirical and theoretical observations that partial hydration of metal−organic framework (MOF) materials containing open metal sites increases their uptake of CO2. The results of the crystallographic study on MOP–gas binding have been rationalized using DFT calculations, yielding individual binding energies for the various pore environments of Cu-1a.
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Oct 2020
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B22-Multimode InfraRed imaging And Microspectroscopy
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Xinchen
Kang
,
Bin
Wang
,
Kui
Hu
,
Kai
Lyu
,
Xue
Han
,
Ben F.
Spencer
,
Mark D.
Frogley
,
Floriana
Tuna
,
Eric J. L.
Mcinnes
,
Robert A. W.
Dryfe
,
Buxing
Han
,
Sihai
Yang
,
Martin
Schroeder
Diamond Proposal Number(s):
[19171]
Open Access
Abstract: Efficient electro-reduction of CO2 over metal–organic framework (MOF) materials is hindered by the poor contact between thermally synthesized MOF particles and the electrode surface, which leads to low Faradaic efficiency for a given product and poor electrochemical stability of the catalyst. We report a MOF-based electrode prepared via electro-synthesis of MFM-300(In) on an indium foil, and its activity for the electrochemical reduction of CO2 is assessed. The resultant MFM-300(In)-e/In electrode shows a 1 order of magnitude improvement in conductivity compared with that for MFM-300(In)/carbon-paper electrodes. MFM-300(In)-e/In exhibits a current density of 46.1 mA cm–2 at an applied potential of −2.15 V vs Ag/Ag+ for the electro-reduction of CO2 in organic electrolyte, achieving an exceptional Faradaic efficiency of 99.1% for the formation of formic acid. The facile preparation of the MFM-300(In)-e/In electrode, coupled with its excellent electrochemical stability, provides a new pathway to develop efficient electro-catalysts for CO2 reduction.
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Sep 2020
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I11-High Resolution Powder Diffraction
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Diamond Proposal Number(s):
[14555]
Open Access
Abstract: Temperature or pressure-swing sorption in porous metal-organic framework (MOF) materials has been proposed for new gas separation technologies. The high tuneability of MOFs toward particular adsorbates and the relatively low energy penalty for system regeneration means that reversible physisorption in MOFs has the potential to create economic and environmental benefits compared with state-of-the-art chemisorption systems. However, for MOF-based sorbents to be commercialised they have to show long-term stability under the conditions imposed by the application. Here, we demonstrate the structural stability of MFM-300(Al) to the presence of a series of industrially-relevant toxic and corrosive gases, including SO2, NO2 and NH3, over four years using long duration synchrotron X-ray powder diffraction. Full structural analysis of gas-loaded MFM-300(Al) confirms the retention of these toxic gas molecules within the porous framework for up to 200 weeks, and cycling adsorption experiments verified the reusability of MFM-300(Al) for the capture of these toxic air pollutants.
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Aug 2020
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B22-Multimode InfraRed imaging And Microspectroscopy
I11-High Resolution Powder Diffraction
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Xiaolin
Li
,
Juehua
Wang
,
Xinran
Zhang
,
Xue
Han
,
Ivan
Da Silva
,
Christopher G.
Morris
,
Shaojun
Xu
,
Damian M.
Wilary
,
Yinyong
Sun
,
Yongqiang
Cheng
,
Claire A.
Murray
,
Chiu C.
Tang
,
Mark D.
Frogley
,
Gianfelice
Cinque
,
Tristan
Lowe
,
Haifei
Zhang
,
Anibal J.
Ramirez-cuesta
,
K. Mark
Thomas
,
Leslie W.
Bolton
,
Sihai
Yang
,
Martin
Schroeder
,
Nannan
Bai
Diamond Proposal Number(s):
[13247]
Open Access
Abstract: The demand for xylenes is projected to increase over the coming decades. The separation of xylene isomers, particularly p- and m-xylenes, is vital for the production of numerous polymers and materials. However, current state-of-the-art separation is based upon fractional crystallisation at 220 K which is highly energy intensive. Here, we report the discrimination of xylene isomers via refinement of the pore size in a series of porous metal–organic frameworks, MFM-300, at sub-angstrom precision leading to the optimal kinetic separation of all three xylene isomers at room temperature. The exceptional performance of MFM-300 for xylene separation is confirmed by dynamic ternary breakthrough experiments. In-depth structural and vibrational investigations using synchrotron X-ray diffraction and terahertz spectroscopy define the underlying host–guest interactions that give rise to the observed selectivity (p-xylene < o-xylene < m-xylene) and separation factors of 4.6–18 for p- and m-xylenes.
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Aug 2020
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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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B22-Multimode InfraRed imaging And Microspectroscopy
I11-High Resolution Powder Diffraction
I12-JEEP: Joint Engineering, Environmental and Processing
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Harry G. W.
Godfrey
,
Lydia
Briggs
,
Xue
Han
,
William J. F.
Trenholme
,
Christopher
Morris
,
Mathew
Savage
,
Louis
Kimberley
,
Oxana
Magdysyuk
,
Michael
Drakopoulos
,
Claire A.
Murray
,
Chiu C.
Tang
,
Mark D.
Frogley
,
Gianfelice
Cinque
,
Sihai
Yang
,
Martin
Schroeder
Diamond Proposal Number(s):
[11278]
Open Access
Abstract: Understanding the mechanism of assembly and function of metal-organic frameworks (MOFs) is important for the development of practical materials. Herein, we report a time-resolved diffraction analysis of the kinetics of formation of a robust MOF, MFM-300(Fe), which shows high adsorption capacity for CO2 (9.55 mmol g−1 at 293 K and 20 bar). Applying the Avrami-Erofe’ev and the two-step kinetic Finke-Watzky models to in situ high-energy synchrotron X-ray powder diffraction data obtained during the synthesis of MFM-300(Fe) enables determination of the overall activation energy of formation (50.9 kJ mol−1), the average energy of nucleation (56.7 kJ mol−1), and the average energy of autocatalytic growth (50.7 kJ mol−1). The synthesis of MFM-300(Fe) has been scaled up 1000-fold, enabling the successful breakthrough separations of the CO2/N2 mixture in a packed-bed with a selectivity for CO2/N2 of 21.6. This study gives an overall understanding for the intrinsic behaviors of this MOF system, and we have determined directly the binding domains and dynamics for adsorbed CO2 molecules within the pores of MFM-300(Fe).
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Nov 2019
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B22-Multimode InfraRed imaging And Microspectroscopy
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Gemma L.
Smith
,
Jennifer E.
Eyley
,
Xue
Han
,
Xinran
Zhang
,
Jiangnan
Li
,
Nicholas M.
Jacques
,
Harry G. W.
Godfrey
,
Stephen P.
Argent
,
Laura J.
Mccormick Mcpherson
,
Simon J.
Teat
,
Yongqiang
Cheng
,
Mark D.
Frogley
,
Gianfelice
Cinque
,
Sarah
Day
,
Chiu C.
Tang
,
Timothy L.
Easun
,
Svemir
Rudic
,
Anibal J.
Ramirez-cuesta
,
Sihai
Yang
,
Martin
Schroeder
Abstract: Emissions of SO2 from flue gas and marine transport have detrimental impacts on the environment and human health, but SO2 is also an important industrial feedstock if it can be recovered, stored and transported efficiently. Here we report the exceptional adsorption and separation of SO2 in a porous material, [Cu2(L)] (H4L = 4′,4‴-(pyridine-3,5-diyl)bis([1,1′-biphenyl]-3,5-dicarboxylic acid)), MFM-170. MFM-170 exhibits fully reversible SO2 uptake of 17.5 mmol g−1 at 298 K and 1.0 bar, and the SO2 binding domains for trapped molecules within MFM-170 have been determined. We report the reversible coordination of SO2 to open Cu(ii) sites, which contributes to excellent adsorption thermodynamics and selectivities for SO2 binding and facile regeneration of MFM-170 after desorption. MFM-170 is stable to water, acid and base and shows great promise for the dynamic separation of SO2 from simulated flue gas mixtures, as confirmed by breakthrough experiments.
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Oct 2019
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I11-High Resolution Powder Diffraction
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Sergey A.
Sapchenko
,
Marina O.
Barsukova
,
Rodion V.
Belosludov
,
Konstantin A.
Kovalenko
,
Denis G.
Samsonenko
,
Artem S.
Poryvaev
,
Alena M.
Sheveleva
,
Matvey V.
Fedin
,
Artem S.
Bogomyakov
,
Danil N.
Dybtsev
,
Martin
Schroeder
,
Vladimir P.
Fedin
Abstract: Two new isostructural microporous coordination frameworks [Mn3(Hpdc)2(pdc)2] (1) and [Mg3(Hpdc)2(pdc)2] (2) (pdc2– = pyridine-2,4-dicarboxylate) showing primitive cubic (pcu) topology have been prepared and characterized. The pore aperture of the channels is too narrow for the efficient adsorption of N2; however, both compounds demonstrate substantially higher uptake of CO2 (119.9 mL·g–1 for 1 and 102.5 mL·g–1 for 2 at 195 K, 1 bar). Despite of their structural similarities, 2 shows a typical reversible type I isotherm for adsorption/desorption of CO2, while 1 features a two-step adsorption process with a very broad hysteresis between the adsorption and desorption curves. This behavior can be explained by a combination of density functional theory calculations, sorption, and X-ray diffraction analysis and gives insights into the further development of new sorbents showing adsorption/desorption hysteresis.
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May 2019
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