Resolving the Chemical Formula of Nesquehonite via NMR Crystallography, DFT Computation, and Complementary Neutron Diffraction.

Nesquehonite is a magnesium carbonate mineral relevant to carbon sequestration envisioned for carbon capture and storage of CO2 . Its chemical formula remains controversial today, assigned as either a hydrated magnesium carbonate [MgCO3 ⋅ 3H2 O], or a hydroxy- hydrated- magnesium bicarbonate [Mg(HCO3 )OH ⋅ 2H2 O]. The resolution of this controversy is central to understanding this material's thermodynamic, phase, and chemical behavior. In an NMR crystallography study, using rotational-echo double-resonance 13 C{1 H} (REDOR), 13 C-1 H distances are determined with precision, and the combination of 13 C static NMR lineshapes and density functional theory (DFT) calculations are used to model different H atomic coordinates. [MgCO3 ⋅ 3H2 O] is found to be accurate, and evidence from neutron powder diffraction bolsters these assignments. Refined H positions can help understand how H-bonding stabilizes this structure against dehydration to MgCO3 . More broadly, these results illustrate the power of NMR crystallography as a technique for resolving questions where X-ray diffraction is inconclusive.

Step-by-step from amorphous phosphate to nano-structured calcium hydroxyapatite: monitoring by solid-state 1H and 31P NMR and spin dynamics.

The solid-state 1H, 31P NMR spectra and cross-polarization (CP MAS) kinetics in the series of samples containing amorphous phosphate phase (AMP), composite of AMP + nano-structured calcium hydroxyapatite (nano-CaHA) and high-crystalline nano-CaHA were studied under moderate spinning rates (5-30 kHz). The combined analysis of the solid-state 1H and 31P NMR spectra provides the possibility to determine the hydration numbers of the components and the phase composition index. A broad set of spin dynamics models (isotropic/anisotropic, relaxing/non-relaxing, secular/semi-non-secular) was applied and fitted to the experimental CP MAS data. The anisotropic model with the angular averaging of dipolar coupling was applied for AMP and nano-CaHA for the first time. It was deduced that the spin diffusion in AMP is close to isotropic, whereas it is highly anisotropic in nano-CaHA being close to the Ising-type. This can be caused by the different number of internuclear interactions that must be explicitly considered in the spin system for AMP (I-S spin pair) and nano-CaHA (IN-S spin system with N ≥ 2). The P-H distance in nano-CaHA was found to be significantly shorter than its crystallographic value. An underestimation can be caused by several factors, among those - proton conductivity via a large-amplitude motion of protons (O-H tumbling and the short-range diffusion) that occurs along OH- chains. The P-H distance deduced for AMP, i.e. the compound with HPO42- as the dominant structure, is fairly well matched to the crystallographic data. This means that the CP MAS kinetics is a capable technique to obtain complementary information on the proton localization in H-bonds and the proton transfer in the cases where traditional structure determination methods fail.

Modulation of the powder properties of lamotrigine by crystal forms.

The mechanical properties of powders determine the ease of manufacture and ultimately the quality of the oral solid dosage forms. Although poor mechanical properties of an active pharmaceutical ingredient (API) can be mitigated by using suitable excipients in a formulation, the effectiveness of that approach is limited for high dose drugs or multidrug tablets. In this context, improving the mechanical properties of the APIs through solid form optimisation is a good strategy to address such a challenge. This work explores the powder and tableting properties of various lamotrigine (LAM) solid forms with the aim to facilitate direct compression by overcoming the poor tabletability of LAM. The two drug-drug crystals of LAM with nicotinamide and valproic acid demonstrate superior flowability and tabletability over LAM. The improved powder properties are rationalised by structure analysis using energy framework, scanning electron microscopy, and Heckel analysis.

Mechanism of self/nonself-discrimination in Brassica self-incompatibility.

Self-incompatibility (SI) is a breeding system that promotes cross-fertilization. In Brassica, pollen rejection is induced by a haplotype-specific interaction between pistil determinant SRK (S receptor kinase) and pollen determinant SP11 (S-locus Protein 11, also named SCR) from the S-locus. Although the structure of the B. rapa S9-SRK ectodomain (eSRK) and S9-SP11 complex has been determined, it remains unclear how SRK discriminates self- and nonself-SP11. Here, we uncover the detailed mechanism of self/nonself-discrimination in Brassica SI by determining the S8-eSRK-S8-SP11 crystal structure and performing molecular dynamics (MD) simulations. Comprehensive binding analysis of eSRK and SP11 structures reveals that the binding free energies are most stable for cognate eSRK-SP11 combinations. Residue-based contribution analysis suggests that the modes of eSRK-SP11 interactions differ between intra- and inter-subgroup (a group of phylogenetically neighboring haplotypes) combinations. Our data establish a model of self/nonself-discrimination in Brassica SI.

A new modulated crystal structure of the ANS complex of the St John's wort Hyp-1 protein with 36 protein molecules in the asymmetric unit of the supercell.

Superstructure modulation, with violation of the strict short-range periodic order of consecutive crystal unit cells, is well known in small-molecule crystallography but is rarely reported for macromolecular crystals. To date, one modulated macromolecular crystal structure has been successfully determined and refined for a pathogenesis-related class 10 protein from Hypericum perforatum (Hyp-1) crystallized as a complex with 8-anilinonaphthalene-1-sulfonate (ANS) [Sliwiak et al. (2015), Acta Cryst. D71, 829-843]. The commensurate modulation in that case was interpreted in a supercell with sevenfold expansion along c. When crystallized in the additional presence of melatonin, the Hyp-1-ANS complex formed crystals with a different pattern of structure modulation, in which the supercell shows a ninefold expansion of c, manifested in the diffraction pattern by a wave of reflection-intensity modulation with crests at l = 9n and l = 9n ± 4. Despite complicated tetartohedral twinning, the structure has been successfully determined and refined to 2.3 Šresolution using a description in a ninefold-expanded supercell, with 36 independent Hyp-1 chains and 156 ANS ligands populating the three internal (95 ligands) and five interstitial (61 ligands) binding sites. The commensurate superstructures and ligand-binding sites of the two crystal structures are compared, with a discussion of the effect of melatonin on the co-crystallization process.

[Research progress in structure and function of pectin methylesterase].

Pectin methylesterase (PME) is an important pectinase that hydrolyzes methyl esters in pectin to release methanol and reduce the degree of methylation of pectin. At present, it has broad application prospects in food processing, tea beverage, paper making and other production processes. With the in-depth study of PME, the crystal structures with different sources have been reported. Analysis of these resolved crystal structures reveals that PME belongs to the right-hand parallel ß-helix structure, and its catalytic residues are two aspartic acids and a glutamine, which play the role of general acid-base, nucleophile and stable intermediate, in the catalytic process. At the same time, the substrate specificity is analyzed to understand the recognition mechanism of the substrate and active sites. This paper systematically reviews these related aspects.

Research progress in structure and function of pectin methylesterase / 生物工程学报

Pectin methylesterase (PME) is an important pectinase that hydrolyzes methyl esters in pectin to release methanol and reduce the degree of methylation of pectin. At present, it has broad application prospects in food processing, tea beverage, paper making and other production processes. With the in-depth study of PME, the crystal structures with different sources have been reported. Analysis of these resolved crystal structures reveals that PME belongs to the right-hand parallel β-helix structure, and its catalytic residues are two aspartic acids and a glutamine, which play the role of general acid-base, nucleophile and stable intermediate, in the catalytic process. At the same time, the substrate specificity is analyzed to understand the recognition mechanism of the substrate and active sites. This paper systematically reviews these related aspects.

A pair of new tirucallane triterpenoid epimers from the stems of Picrasma quassioides.

A pair of new tirucallane triterpenoid epimers, picraquassins M and N (1> and 2), were isolated from the stems of Picrasma quassioides (D. Don) Benn. Their structures were determined based on comprehensive spectroscopic and X-ray crystallographic analyses. In addition, their AChE inhibitory activity, cytotoxicity against five human tumour cell lines (SW480, MCF-7, HepG2, Hela, and PANC-1), and antimicrobial activity against two bacteria (Staphylococcus. aureus 209P and Escherichia coli ATCC0111) and two fungi (Candida albicans FIM709 and Aspergillus niger R330) were evaluated.

Titanocene Selenide Sulfides Revisited: Formation, Stabilities, and NMR Spectroscopic Properties.

[TiCp2S5] (phase A), [TiCp2Se5] (phase F), and five solid solutions of mixed titanocene selenide sulfides [TiCp2SexS5-x] (Cp = C5H5-) with the initial Se:S ranging from 1:4 to 4:1 (phases B⁻E) were prepared by reduction of elemental sulfur or selenium or their mixtures by lithium triethylhydridoborate in thf followed by the treatment with titanocene dichloride [TiCp2Cl2]. Their 77Se and 13C NMR spectra were recorded from the CS2 solution. The definite assignment of the 77Se NMR spectra was based on the PBE0/def2-TZVPP calculations of the 77Se chemical shifts and is supported by 13C NMR spectra of the samples. The following complexes in varying ratios were identified in the CS2 solutions of the phases B⁻E: [TiCp2Se5] (51), [TiCp2Se4S] (41), [TiCp2Se3S2] (31), [TiCp2SSe3S] (36), [TiCp2SSe2S2] (25), [TiCp2SSeS3] (12), and [TiCp2S5] (01). The disorder scheme in the chalcogen atom positions of the phases B⁻E observed upon crystal structure determinations is consistent with the spectral assignment. The enthalpies of formation calculated for all twenty [TiCp2SexS5-x] (x = 0⁻5) at DLPNO-CCSD(T)/CBS level including corrections for core-valence correlation and scalar relativistic, as well as spin-orbit coupling contributions indicated that within a given chemical composition, the isomers of most favourable enthalpy of formation were those, which were observed by 77Se and 13C NMR spectroscopy.

Efficient Manipulation of Continuous AFI-Type Aluminophosphate Membranes with Distinctive Microstructures on Macroporous α-Al2O3 Substrates.

The availability of continuous and well-defined AFI-type aluminophosphate membranes (AFI membranes) would trigger their applications in innovative materials. A well-designed manipulation strategy is proposed to produce continuous AFI membranes with four different microstructures over porous α-Al2O3 substrates. A double-layer and highly c-oriented AFI membrane of hexagonal prisms is obtained when a thin layer of medium molecular weight (MMW) chitosan is employed as the structure-directing matrix together with aluminum isopropoxide (AIP) as the Al source. It can be transformed to a single-layer and highly c-oriented AFI membrane of hexagonal prisms if the structure-directing matrix is replaced by a thin layer of low molecular weight (LMW) chitosan. When the Al source is changed to pseudo-boehmite, the single-layer AFI membrane is composed of highly ordered spherical agglomerates of small crystals. Furthermore, the membrane will turn to the double-layer AFI membrane of highly-ordered crystal agglomerates if a thin layer of MMW chitosan is used once again, keeping pseudo-boehmite as the Al source. The manipulation methodology established here is rather reliable with a pretty high reproducibility.

Bio-inspired nano-traps for uranium extraction from seawater and recovery from nuclear waste.

Nature can efficiently recognize specific ions by exerting second-sphere interactions onto well-folded protein scaffolds. However, a considerable challenge remains to artificially manipulate such affinity, while being cost-effective in managing immense amounts of water samples. Here, we propose an effective approach to regulate uranyl capture performance by creating bio-inspired nano-traps, illustrated by constructing chelating moieties into porous frameworks, where the binding motif's coordinative interaction towards uranyl is enhanced by introducing an assistant group, reminiscent of biological systems. Representatively, the porous framework bearing 2-aminobenzamidoxime is exceptional in sequestering high uranium concentrations with sufficient capacities (530 mg g-1) and trace quantities, including uranium in real seawater (4.36 mg g-1, triple the benchmark). Using a combination of spectroscopic, crystallographic, and theory calculation studies, it is revealed that the amino substituent assists in lowering the charge on uranyl in the complex and serves as a hydrogen bond acceptor, boosting the overall uranyl affinity of amidoxime.

Crystallographic and morphological analysis of sandblasted highly translucent dental zirconia.

OBJECTIVE: To assess the influence of alumina sandblasting on four highly translucent dental zirconia grades. METHODS: Fully sintered zirconia disk-shaped specimens (15-mm diameter; 0.5-mm thickness) of four highly translucent yttria partially stabilized zirconia (Y-PSZ) grades (KATANA HT, KATANA STML, KATANA UTML, Kuraray Noritake; Zpex Smile, Tosoh) were sandblasted with 50-µm alumina (Al2O3) sand (Kulzer) or left 'as-sintered' (control) (n=5). For each zirconia grade, the translucency was measured using a colorimeter. Surface roughness was assessed using 3D confocal laser microscopy, upon which the zirconia grades were statistically compared for surface roughness using a Kruskal-Wallis test (n=10). X-ray diffraction (XRD) with Rietveld analysis was used to assess the zirconia-phase composition. Micro-Raman spectroscopy was used to assess the potentially induced residual stress. RESULTS: The translucency of KATANA UTML was the highest (36.7±1.8), whereas that of KATANA HT was the lowest (29.5±0.9). The 'Al2O3-sandblasted' and 'as-sintered' zirconia revealed comparable surface-roughness Sa values. Regarding zirconia-phase composition, XRD with Rietveld analysis revealed that the 'as-sintered' KATANA UTML contained the highest amount of cubic zirconia (c-ZrO2) phase (71wt%), while KATANA HT had the lowest amount of c-ZrO2 phase (41wt%). KATANA STML and Zpex Smile had a comparable zirconia-phase composition (60wt% c-ZrO2 phase). After Al2O3-sandblasting, a significant amount (over 25wt%) of rhombohedral zirconia (r-ZrO2) phase was detected for all highly translucent zirconia grades. SIGNIFICANCE: Al2O3-sandblasting did not affect the surface roughness of the three highly translucent Y-PSZ zirconia grades, but it changed its phase composition.

Structural Searching of Biosynthetic Enzymes to Predict Protein Targets of Natural Products.

Recently, we have demonstrated that site comparison methodology using flavonoid biosynthetic enzymes as the query could automatically identify structural features common to different flavonoid-binding proteins, allowing for the identification of flavonoid targets such as protein kinases. With the aim of further validating the hypothesis that biosynthetic enzymes and therapeutic targets can contain a similar natural product imprint, we collected a set of 159 crystallographic structures representing 38 natural product biosynthetic enzymes by searching the Protein Databank. Each enzyme structure was used as a query to screen a repository of approximately 10 000 ligandable sites by active site similarity. We report a full analysis of the screening results and highlight three retrospective examples where the natural product validates the method, thereby revealing novel structural relationships between natural product biosynthetic enzymes and putative protein targets of the natural product. From a prospective perspective, our work provides a list of up to 64 potential novel targets for 25 well-characterized natural products.

Affinity Crystallography Reveals the Bioactive Compounds of Industrial Juicing Byproducts of Punica granatum for Glycogen Phosphorylase.

BACKGROUND: Glycogen phosphorylase (GP) is a pharmaceutical target for the discovery of new antihyperglycaemic agents. Punica granatum is a well-known plant for its potent antioxidant and antimicrobial activities but so far has not been examined for antihyperglycaemic activity. OBJECTIVE: The aim was to examine the inhibitory potency of eighteen polyphenolic extracts obtained from Punica granatum fruits and industrial juicing byproducts against GP and discover their most bioactive ingredients. METHOD: Kinetic experiments were conducted to measure the IC50 values of the extracts while affinity crystallography was used to identify the most bioactive ingredient. The inhibitory effect of one of the polyphenolic extracts was also verified ex vivo, in HepG2 cells. RESULTS: All extracts exhibited significant in vitro inhibitory potency (IC50 values in the range of low µg/mL). Affinity crystallography revealed that the most bioactive ingredients of the extracts were chlorogenic and ellagic acids, found bound in the active and the inhibitor site of GP, respectively.While ellagic acid is an established GP inhibitor, the inhibition of chlorogenic acid is reported for the first time. Kinetic analysis indicated that chlorogenic acid is an inhibitor with Ki=2.5 x 10-3Mthat acts synergistically with ellagic acid. CONCLUSION: Our study provides the first evidence for a potential antidiabetic usage of Punica granatum extracts as antidiabetic food supplements. Although, more in vivo studies have to be performed before these extracts reach the stage of antidiabetic food supplements, our study provides a first positive step towards this process.

Inhibition activity of a traditional Chinese herbal formula Huang-Lian-Jie-Du-Tang and its major components found in its plasma profile on neuraminidase-1.

Huang-Lian-Jie-Du-Tang (HLJDT), a traditional formula with four TCM herbs, has been used for hundred years for different diseases. The current study aimed to assess the inhibitory activity of HLJDT against H1N1 neuraminidase (NA-1), and identify potent NA-1 inhibitors from its plasma profile. The in vitro NA-1 study has shown that the water extract of HLJDT potently inhibited NA-1 (IC50 = 112.6 µg/ml; Ki = 55.6 µg/ml) in a competitive mode. The IC50 values of the water extracts of its four herbs were as follows: Coptidis Rhizoma, 96.1 µg/ml; Phellodendri Chinensis Cortex, 108.6 µg/ml; Scutellariae Radix, 303.5 µg/ml; Gardeniae Fructus, 285.0 µg/ml. Thirteen compounds found in the plasma profile of HLJDT were also identified as potent NA-1 inhibitors, which included jatrorrhizine, palmatine, epiberberine, geniposide, oroxylin A, berberine, coptisine, baicalein, wogonoside, phellodendrine, wogonin, oroxylin A-7-O-glucuronide and baicalin (sorted in ascending order by their IC50 values). Their inhibitory activities were consistent with molecular docking analysis when considering crystallographic water molecules in the ligand-binding pocket of NA-1. Our current findings suggested that HLJDT can be used as a complementary medicine for H1N1 infection and its potent active compounds can be developed as NA-1 inhibitors.

Low Energy Surface Activation of Zirconia Based Restorations.

PURPOSE: To evaluate the influence of low energy surface activation technique on the biaxial flexure strength of zirconia frameworks. MATERIALS AND METHODS: Zirconia discs were prepared by cutting CAD/CAM zirconia blocks. Sintered discs were airborne particle abraded using one of the following particles: 30 µm alumina particles, 50 µm alumina particles, or modified round edges 30 µm alumina particles at low pressure. Scanning electron microscopy, x-ray diffraction analysis, surface roughness, and biaxial flexure strength tests were performed (n = 20). Fractured specimens were fractographically analyzed (α = 0.05). RESULTS: Low energy surface activation resulted in 7% monoclinic crystallographic transformation, increasing surface roughness from 0.05 to 0.3 µm and in significant increase in biaxial flexure strength (1718 MPa) compared 30 µm (1064 MPa), 50 µm (1210 MPa), and as-sintered specimens (1150 MPa). CONCLUSIONS: Low energy surface activation of zirconia specimens improved the biaxial flexure strength of zirconia frameworks without creation of surface damage. Clinical implications: by controlling particle size and shape of alumina, the flexure strength of zirconia restorations could be increased usinglow pressure particle abrasion.

Evaluation of crystallographic orientation of biological apatite in vertebral cortical bone in ovariectomized cynomolgus monkeys treated with minodronic acid and alendronate.

Quantitative analysis of the orientational distribution of biological apatite (BAp) crystals is proposed as a new index of bone quality. This study aimed to analyze BAp c-axis orientation in ovariectomized (OVX) monkeys treated with amino-bisphosphonates minodronic acid and alendronate as reference. Sixty female monkeys aged 9-17 years were divided into five groups: one sham group and four OVX groups. The sham group and one OVX group were treated daily with vehicle for 17 months. The other three groups were treated daily with minodronic acid at doses of 0.015 and 0.15 mg/kg, and alendronate at 0.5 mg/kg orally, respectively. The seventh lumbar vertebrae were subjected to analysis of the preferential BAp c-axis orientation in the ventral cortical bone. The BAp c-axis orientation along the craniocaudal axis was significantly increased in the OVX monkeys. The high dose of minodronic acid suppressed the OVX-induced increase in the BAp c-axis orientation, whereas alendronate showed a non-significant tendency to suppress the increase in the orientation. In analysis with other parameters, the BAp c-axis orientation was positively correlated with bone formation indices in biochemical markers and bone histomorphometry and negatively correlated with the increase in lumbar bone mineral density. On the other hand, the BAp c-axis orientation was not correlated with bone resorption indices, except for the eroded surface. These results indicate that the increase in BAp c-axis orientation was ameliorated by minodronic acid treatment in OVX monkeys, mainly by suppression of bone formation increase.

Three new sesquiterpene lactones from Inula britannica.

One new 1,10-secoeudesmanolide (1), two eudesmanolides (2 and 3), together with nine known compounds (4-12) were isolated from the aerial parts of Inula britannica. The structures of the new compounds were elucidated by detailed spectroscopic analysis, including HRESIMS and 2D-NMR spectroscopic method. In addition, compounds 1-4 were tested for their inhibitory effects against LPS-induced NO production in RAW264.7 macrophages.

In-silico analysis of heat shock protein 47 for identifying the novel therapeutic agents in the management of oral submucous fibrosis.

BACKGROUND: Heat shock proteins-47 (HSP47) is a collagen specific molecular chaperone, involved in the processing and/or secretion of procollagen. It seems to be regularly upregulated in various fibrotic or collagen disorders. Hence, this protein can be a potential target for the treatment of various fibrotic diseases including oral submucous fibrosis (OSF), which is a collagen metabolic disorder of oral cavity and whose etiopathogeneic mechanism and therapeutic protocols are still not well documented. AIM: The aim of this study is to identify the novel therapeutic agents using in-silico methods for the management of OSF. OBJECTIVES: The objectives of this study are to identify the binding sites of HSP47 on the collagen molecule and to identify the lead compound with anti-HSP47 activity from the library of natural compounds, using in-silico methodology. MATERIALS AND METHODS: The web-based and tool based in-silico analysis of the HSP47 and collagen molecules are used in this study. The crystal structure of collagen and HSP47 were retrieved from Protein Data Bank website. The binding site identification and the docking studies are done using Molegro Virtual Docker offline tool. RESULTS: Out of the 104 Natural compounds, six ligands are found to possess best binding affinity to the binding amino acid residues. Silymarin binds with the 4AU2A receptor and the energy value are found to be -178.193 with four Hbonds. The other best five natural compounds are hesperidin, ginkgolides, withanolides, resveratrol, and gingerol. Our findings provide the basis for the in-vitro validation of the above specified compounds, which can possibly act as "lead" molecules in designing the drugs for OSF. CONCLUSION: HSP47 can be a potential candidate to target, in order to control the production of abundance collagen in OSF. Hence, the binding sites of HSP47 with collagen are identified and some natural compounds with a potential to bind with these binding receptors are also recognized. These natural compounds might act as anti-HSP47 lead molecules in designing novel therapeutic agents for OSF, which are so far unavailable.

A zebrafish in vivo phenotypic assay to identify 3-aminothiophene-2-carboxylic acid-based angiogenesis inhibitors.

Abstract Small molecules that inhibit angiogenesis are attractive drug candidates for cancer, retinopathies, and age-related macular degeneration. In vivo, phenotypic screening in zebrafish (Danio rerio) emerges as a powerful methodology to identify and optimize novel compounds with pharmacological activity. Zebrafish provides several advantages for in vivo phenotypic screens especially for angiogenesis, since it develops rapidly, externally, and does not rely on a functional cardiovascular system to survive for several days during development. In this study, we utilize a transgenic line that allows the noninvasive monitoring of angiogenesis at a cellular level. The inhibition of angiogenesis can be observed under a fluorescent stereoscope and quantified. To exemplify the versatility and robustness of the zebrafish screen, we have employed a series of 60 novel compounds that were designed based on a potent VEGFR2 inhibitor. Herein, we report their structure-based design, synthesis, and in vivo zebrafish screening for optimal activity, toxicity, and off-target effects, which revealed six reversible inhibitors of angiogenesis.