I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[19800]
Open Access
Abstract: Large and flexible ligands gain increasing interest in the development of bioactive agents. They challenge the applicability of computational ligand optimization strategies originally developed for small molecules. Free energy perturbation (FEP) is often used for predicting binding affinities of small molecule ligands, however, its use for more complex ligands remains limited. Herein, we report the structure-based design of peptide macrocycles targeting the protein binding site of human adaptor protein 14-3-3. We observe a surprisingly strong dependency of binding affinities on relatively small variations in substituent size. FEP was performed to rationalize observed trends. To account for insufficient convergence of FEP, restrained calculations were performed and complemented with extensive REST MD simulations of the free ligands. These calculations revealed that changes in affinity originate both from altered direct interactions and conformational changes of the free ligand. In addition, MD simulations provided the basis to rationalize unexpected trends in ligand lipophilicity. We also verified the anticipated interaction site and binding mode for one of the high affinity ligands by X-ray crystallography. The introduced fully-atomistic simulation protocol can be used to rationalize the development of structurally complex ligands which will support future ligand maturation efforts.
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Feb 2020
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I19-Small Molecule Single Crystal Diffraction
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Diamond Proposal Number(s):
[18953]
Open Access
Abstract: Eight alkene-functionalized molybdenum-based spherical Keplerate-type (inorganic fullerene) structures have been obtained via both direct and multistep synthetic approaches. Driven by the opportunity to design unique host-guest interactions within hydrophobic, π-electron rich confined environments, we have synthesized {(NH4)42[Mo132O372(L)30(H2O)72]}, where L = (1) acrylic acid, (2) crotonic acid, (3) methacrylic acid, (4) tiglic acid, (5) 3-butenoic acid, (6) 4-pentenoic acid, (7) 5-hexenoic acid, and (8) sorbic acid. The compounds, which are obtained in good yield (10‑40%), contain 30 carboxylate-coordinated alkene ligands which create a central cavity with hydrophobic character. Extensive Nuclear Magnetic Resonance (NMR) spectroscopy studies contribute significantly to the complete characterization of the structures obtained, including both 1D and 2D measurements. In addition, single-crystal X-ray crystallography and subsequently-generated electron density maps are employed to highlight the distribution in ligand tail positions. These alkene-containing structures are shown to effectively encapsulate small alkyl thiols (1-propanethiol (A), 2-propanethiol (B), 1-butanethiol (C), 2-butanethiol (D) and 2-methyl-1-propanethiol (E)) as guests within the central cavity in aqueous solution. The hydrophobically driven clustering of up to 6 equivalents of volatile thiol guests within the central cavity of the Keplerate-type structure results in effective thermal protection, preventing evaporation at elevated temperatures (ΔT ≈ 25 K).
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Jan 2020
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I19-Small Molecule Single Crystal Diffraction
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Diamond Proposal Number(s):
[15768]
Open Access
Abstract: FeII4L6 tetrahedral cage 1 was prepared from a redox-active dicationic naphthalenediimide (NDI) ligand. The +20 charge of the cage makes it a good host for anionic guests, with no binding observed for neutral aromatic molecules. Following reduction by Cp2Co, the cage released anionic guests; subsequent oxidation by AgNTf2 led to re-uptake of anions. In its reduced form, however, 1 was observed to bind neutral C60. The fullerene guest was subsequently ejected following cage re-oxidation. The guest release process was found to be facilitated by anion-mediated transport from organic to aqueous solution. Cage 1 thus employs electron transfer as a stimulus to control the uptake and release of both neutral and charged guests, through distinct pathways.
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Dec 2019
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I03-Macromolecular Crystallography
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Patrick F.
Conlon
,
Olga
Eguaogie
,
Jordan J.
Wilson
,
Jamie S. T.
Sweet
,
Julian
Steinhoegl
,
Klaudia
Englert
,
Oliver G. A.
Hancox
,
Christopher J.
Law
,
Sarah A.
Allman
,
James H. R.
Tucker
,
James P.
Hall
,
Joseph S.
Vyle
Diamond Proposal Number(s):
[20077, 20214]
Open Access
Abstract: Oligodeoxynucleotides incorporating internucleotide phosphoroselenolate linkages have been prepared under solid-phase synthesis conditions using dimer phosphoramidites. These dimers were constructed following the high yielding Michaelis–Arbuzov (M–A) reaction of nucleoside H-phosphonate derivatives with 5′-deoxythymidine-5′-selenocyanate and subsequent phosphitylation. Efficient coupling of the dimer phosphoramidites to solid-supported substrates was observed under both manual and automated conditions and required only minor modifications to the standard DNA synthesis cycle. In a further demonstration of the utility of M–A chemistry, the support-bound selenonucleoside was reacted with an H-phosphonate and then chain extended using phosphoramidite chemistry. Following initial unmasking of methyl-protected phosphoroselenolate diesters, pure oligodeoxynucleotides were isolated using standard deprotection and purification procedures and subsequently characterised by mass spectrometry and circular dichroism. The CD spectra of both modified and native duplexes derived from self-complementary sequences with A-form, B-form or mixed conformational preferences were essentially superimposable. These sequences were also used to study the effect of the modification upon duplex stability which showed context-dependent destabilisation (−0.4 to −3.1 °C per phosphoroselenolate) when introduced at the 5′-termini of A-form or mixed duplexes or at juxtaposed central loci within a B-form duplex (−1.0 °C per modification). As found with other nucleic acids incorporating selenium, expeditious crystallisation of a modified decanucleotide A-form duplex was observed and the structure solved to a resolution of 1.45 Å. The DNA structure adjacent to the modification was not significantly perturbed. The phosphoroselenolate linkage was found to impart resistance to nuclease activity.
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Oct 2019
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I11-High Resolution Powder Diffraction
I19-Small Molecule Single Crystal Diffraction
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Diamond Proposal Number(s):
[15777, 17193]
Open Access
Abstract: Organic molecules tend to close pack to form dense structures when they are crystallised from organic solvents. Porous molecular crystals defy this rule: they contain open space, which is typically stabilised by inclusion of solvent in the interconnected pores during crystallisation. The design and discovery of such structures is often challenging and time consuming, in part because it is difficult to predict solvent effects on crystal form stability. Here, we combine crystal structure prediction (CSP) with a robotic crystallisation screen to accelerate the discovery of stable hydrogen-bonded frameworks. We exemplify this strategy by finding new phases of two well-studied molecules in a computationally targeted way. Specifically, we find a new ‘hidden’ porous polymorph of trimesic acid, δ-TMA, that has a guest-free hexagonal pore structure, as well as three new solvent-stabilized diamondoid frameworks of adamantane-1,3,5,7-tetracarboxylic acid (ADTA). Beyond porous solids, this hybrid computational–experimental approach could be applied to a wide range of materials problems, such as organic electronics and drug formulation.
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Sep 2019
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I02-Macromolecular Crystallography
I04-Macromolecular Crystallography
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Marta
Artola
,
Christinne
Hedberg
,
Rhianna J.
Rowland
,
Lluís
Raich
,
Kassiani
Kytidou
,
Liang
Wu
,
Amanda
Schaaf
,
Maria Joao
Ferraz
,
Gijsbert A.
Van Der Marel
,
Jeroen D. C.
Codée
,
Carme
Rovira
,
Johannes M. F. G.
Aerts
,
Gideon J.
Davies
,
Herman S.
Overkleeft
Diamond Proposal Number(s):
[13587]
Open Access
Abstract: Fabry disease is an inherited lysosomal storage disorder that is characterized by a deficiency in lysosomal α-D-galactosidase activity. One current therapeutic strategy involves enzyme replacement therapy, in which patients are treated with a recombinant enzyme. Co-treatment with enzyme active-site stabilizers is advocated to increase treatment efficacy, a strategy that requires effective and selective enzyme stabilizers. Here, we describe the design and development of an α-D-gal-cyclophellitol cyclosulfamidate as a new class of neutral, conformationally constrained competitive glycosidase inhibitors that act by mimicry of the Michaelis complex conformation. We found that D-galactose-configured α-cyclosulfamidate 4 effectively stabilizes recombinant human α-D-galactosidase (agalsidase beta, Fabrazyme®) both in vitro and in cellulo.
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Aug 2019
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B21-High Throughput SAXS
B23-Circular Dichroism
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Wenjin
Xiao
,
Thomas I. P.
Green
,
Xiaowen
Liang
,
Rosalia Cuahtecontzi
Delint
,
Guillaume
Perry
,
Michael S.
Roberts
,
Kristian
Le Vay
,
Catherine R.
Back
,
Raimomdo
Ascione
,
Haolu
Wang
,
Paul R.
Race
,
Adam W.
Perriman
Open Access
Abstract: We present a new cell membrane modification methodology where the inherent heart tissue homing properties of the infectious bacteria Streptococcus gordonii are transferred to human stem cells. This is achieved via the rational design of a chimeric protein–polymer surfactant cell membrane binding construct, comprising the cardiac fibronectin (Fn) binding domain of the bacterial adhesin protein CshA fused to a supercharged protein. Significantly, the protein–polymer surfactant hybrid spontaneously inserts into the plasma membrane of stem cells without cytotoxicity, instilling the cells with a high affinity for immobilized fibronectin. Moreover, we show that this cell membrane reengineering approach significantly improves retention and homing of stem cells delivered either intracardially or intravenously to the myocardium in a mouse model.
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Jul 2019
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I19-Small Molecule Single Crystal Diffraction
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Diamond Proposal Number(s):
[15768]
Open Access
Abstract: Small titanium-oxo-alkoxide clusters, [TiO(OR)(O2PR′2)]4, synthesised by the stoichiometric reaction of Ti(OiPr)4, phosphinic acid and water, undergo a photo-redox transformation under long-wave UV light. The photo-reaction generates blue coloured, mixed-valence Ti(III)/Ti(IV)-oxo clusters alongside acetone and isopropanol by-products. This reactivity indicates the ability for photoactivated charge separation to occur in even the smallest of Ti-oxo clusters. EPR and NMR spectroscopic studies support a photo-redox mechanism that occurs via an intramolecular, two-electron pathway, directly relating to current doubling effects observed at TiO2 photoanodes in the presence of alcohols. The rate of photo-reaction is solvent dependent, with donor solvents supporting the formation of low coordinate Ti(III) sites. The nature of the electronic transition is identified by DFT and TDDFT calculations as an oxygen to titanium charge transfer and it is possible to finetune the UV absorption onset observed by changing the phosphinate ligand. A two-electron photo-reduced cluster, [Ti4O4(O2PPh2)6], forms spontaneously from the photo-reaction and its structure is identified by X-ray crystallography with supporting DFT calculations. These indicate that [Ti4O4(O2PPh2)6] is high-spin and contains two ferromagnetically coupled electrons delocalised over the Ti4 core. [Ti4O4(O2PPh2)6] undergoes rapid oxidation in air in the solid-state and performs a remarkable single-crystal to single-crystal transformation, to form a stable cluster-superoxide salt.
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Jul 2019
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I22-Small angle scattering & Diffraction
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Open Access
Abstract: A polymerizable amphiphile having two zwitterionic head-groups has been designed. This compound co-organizes with an acid, bis(trifluoromethanesulfonyl)imide (HTf2N), into a gyroid bicontinuous cubic liquid-crystalline phase. In situ polymerization of this phase has been successfully achieved by UV irradiation in the presence of a photoinitiator, yielding a self-standing gyroid-nanostructured polymer film. When the polymer film is placed under different relative humidity conditions or in water, it absorbs water owing to the strong hydration ability of the zwitterionic parts. It has been found that the polymer film preserves the gyroid nanostructure after the water absorption. Based on reconstructed electron density maps, it is assumed that the absorbed water molecules form a 3D continuous network along the gyroid minimal surface, which satisfies several key conditions for inducing fast proton conduction. As expected, such hydrated films show high ionic conductivities in the order of 10−1 S cm−1 when the water content of the film reaches 15.6 wt% at RH = 90%. The high conductivity is attributed to the induction of the Grotthuss mechanism, that is, proton conduction via the hydrogen-bonding network of the incorporated water molecules.
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Jun 2019
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I22-Small angle scattering & Diffraction
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Open Access
Abstract: It is well-known that the Dengue fever virus undergoes a distinct morphological transition from topologically smooth particles to ‘bumpy’ particle on increasing the temperature from that of the mosquito carrier (28 °C) to that of the human host (37 °C). This virus also possesses pH-sensitive surface domains that undergo conformational changes during infection which facilitates exit from the endosomes. Herein we take a bio-inspired approach to design synthetic Dengue virus-mimicking nanoparticles to target triple-negative (TN) breast cancer cells that overexpress SR-B1 scavenger receptors. Thus, sterile pH-responsive methacrylic ABC triblock copolymer vesicles were prepared in aqueous solution via polymerization-induced self-assembly. Microphase separation between two enthalpically-incompatible hydrophobic membrane-forming blocks produced a well-defined framboidal morphology, with surface globules of ∼28 nm diameter protruding from the membrane. The hydrophilic stabilizer block comprises 97% hydroxyl-functionalized chains and 3% phosphorylcholine-functionalized chains, with the latter being critical for selective intracellular uptake. These framboidal vesicles remain intact at neutral pH but become swollen and cationic at pH 5–6 because the tertiary amine residues in the hydrophobic C block become protonated. We demonstrate that such nanoparticles enable selective targeting of TN breast cancer cells. This is because such malignant cells overexpress SR-B1 receptors for naturally-occurring phospholipids and hence take up the phosphorylcholine-decorated framboidal vesicles preferentially. In contrast, negligible cell uptake is observed over the same time period for both human dermal fibroblasts and normal breast cancer cells that minimally express the SR-B1 receptor. Moreover, we show that genetic material within such pH-responsive framboidal vesicles can be efficiently delivered to the cell nuclei while maintaining high cell viability.
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May 2019
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