Polysaccharides of algae 68. Sulfated polysaccharides from the Kamchatka brown alga Laminaria bongardiana

Several fucoidan fractions were isolated from the biomass of the Kamchatka brown alga Laminaria bongardiana by hot water extraction followed by anion-exchange chromatography. Fucoidans were found to be composed of l-fucose, d-galactose, and sulfate as the major components, whereas d-xylose, d-mannose, d-glucuronic acid, and acetate were detected as the minor constituents. Highly sulfated fucoidan fractions F-2 and F-3 were solvolytically desulfated by heating in dimethyl sulfoxide in the presence of pyridine. The structures of native and desulfated polysaccharides were investigated by the methylation analysis and NMR spectroscopy. It was shown that F-2 contains fucan sulfate, the backbone of which is made of 1→3-linked α-l-fucopyranose residues with single α-l-Fucp branches at positions 2 and sulfate groups predominantly at positions 4. Sulfated fucoglucuronomannan, fucoglucuronan, and fucogalactan were detected in F-2 as concomitant polysaccharides. Fucan sulfate and sulfated fucogalactan were the major components of the fraction F-3. The anticoagulant properties of fucoidan fractions were assessed. It was demonstrated that the activity of the fraction F-3 is comparable with that of low-molecular-weight heparin (enoxaparin), whereas the activity of total fucoidan F and the fraction F-2 is ~2/3 and ~1/2, respectively, of the activity of F-3, which is in accordance with the lower sulfate content in these samples. Desulfated preparations F-2deS and F-3deS were completely devoid of anticoagulant activity.

     

Polysaccharides of Algae 58. The polysaccharide composition of the Pacific brown alga <Emphasis Type="Italic">Alaria fistulosa</Emphasis> P. <Emphasis Type="Italic">et</Emphasis> R. (Alariaceae,Laminariales)

Quantitative determination of mannitol, fucoidan and alginate in different parts of the thallus (the blade, the midrip, the sporophylls, and the stipe with rhizoids) of the brown alga Alaria fistulosa, collected from the coastal waters of Paramushir Island, was carried out. Sporophylls were shown to differ considerably in carbohydrate composition from all other parts of the plant. In particular, the fucoidan content in sporophylls is several times as high as that in the blade. Alginate preparations isolated from sporophylls and from blade have different proportions of monomers (mannuronic acid and guluronic acid residues) and different molecular masses. Fucoidan preparations isolated from these parts of the plant differ slightly in the sulfate content. Their specific feature is a rather high galactose content comparable with the content of fucose. The sporophylls of A. fistulosa may be regarded as a rich source for practical isolation of fucoidan. Dedicated to Academician N. K. Kochetkov on the occasion of his 90th birthday. __________ Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 5, pp. 1245–1249, May, 2005.     

Development and validation of an ion‐exchange chromatography method for heparin and its impurities in heparin products

An anion‐exchange liquid chromatography method for the determination of heparin and its impurities (dermatan sulfate and oversulfated chondroitin sulfate) was developed using chemometric‐assisted optimization, including multivariate experimental design and response surface methodology. The separation of heparin, dermatan sulfate, and oversulfated chondroitin sulfate (R_s above 2.0) was achieved on a Dionex RF IC IonPac AS22 column with a gradient elution of 10–70% of 2.5 M sodium chloride and 20 mM Tris phosphate buffer (pH 2.1) at a flow rate of 0.6 mL/min and UV detection at 215 nm. Method validation shows good linearity (r > 0.99), acceptable precision (%relative standard deviations <11.4%) and trueness (%recovery of 92.3–103.9%) for all analytes. The limits of detection for dermatan sulfate and oversulfated chondroitin sulfate are equivalent to 0.11% w/w (10.5 μg/mL) and 0.07% w/w (7.2 μg/mL), while the limits of quantification are 0.32% w/w (31.5 μg/mL) and 0.22% w/w (22.0 μg/mL) relative to heparin, respectively. The method is specific for heparin, dermatan sulfate, and oversulfated chondroitin sulfate without interference from mobile phase and sample matrices and could be used for accurate quantitation the drug and its impurities in a single run. Applications of the method reveal contents of heparin between 90.3 and 97.8%. Dermatan sulfate and oversulfated chondroitin sulfate were not detected in any of the real‐life samples.     

Identification of heparin samples that contain impurities or contaminants by chemometric pattern recognition analysis of proton NMR spectral data

Chemometric analysis of a set of one-dimensional (1D) (1)H nuclear magnetic resonance (NMR) spectral data for heparin sodium active pharmaceutical ingredient (API) samples was employed to distinguish USP-grade heparin samples from those containing oversulfated chondroitin sulfate (OSCS) contaminant and/or unacceptable levels of dermatan sulfate (DS) impurity. Three chemometric pattern recognition approaches were implemented: classification and regression tree (CART), artificial neural network (ANN), and support vector machine (SVM). Heparin sodium samples from various manufacturers were analyzed in 2008 and 2009 by 1D (1)H NMR, strong anion-exchange high-performance liquid chromatography, and percent galactosamine in total hexosamine tests. Based on these data, the samples were divided into three groups: Heparin, DS ≤ 1.0% and OSCS = 0%; DS, DS > 1.0% and OSCS = 0%; and OSCS, OSCS > 0% with any content of DS. Three data sets corresponding to different chemical shift regions (1.95-2.20, 3.10-5.70, and 1.95-5.70 ppm) were evaluated. While all three chemometric approaches were able to effectively model the data in the 1.95-2.20 ppm region, SVM was found to substantially outperform CART and ANN for data in the 3.10-5.70 ppm region in terms of classification success rate. A 100% prediction rate was frequently achieved for discrimination between heparin and OSCS samples. The majority of classification errors between heparin and DS involved cases where the DS content was close to the 1.0% DS borderline between the two classes. When these borderline samples were removed, nearly perfect classification results were attained. Satisfactory results were achieved when the resulting models were challenged by test samples containing blends of heparin APIs spiked with non-, partially, or fully oversulfated chondroitin sulfate A, heparan sulfate, or DS at the 1.0%, 5.0%, and 10.0% (w/w) levels. This study demonstrated that the combination of 1D (1)H NMR spectroscopy with multivariate chemometric methods is a nonsubjective, statistics-based approach for heparin quality control and purity assessment that, once standardized, minimizes the need for expert analysts.     

Polysaccharides of algae 65. Unusual polysaccharide composition of the pacific brown alga Punctaria plantaginea

Quantitative determination revealed the presence of storage glucan (6.0%), fucoidan (19.2%) and alginate (12.7%) in the biomass of the brown alga Punctaria plantaginea collected from the Sea of Japan. The polysaccharides were isolated from the alga by fractional extraction followed by additional purification procedures. Unlike the well-known laminarans the storage polysaccharide from P. plantaginea was shown to be a linear (1→6)-β-d-glucopyranan, which is new for brown alga. The content of guluronic acid (G) residues in the alginate molecules exceeded the content of mannuronic acid residues (M), M/G = 0.5. Poly-G and poly-MG blocks were isolated from the products of partial hydrolysis of alginic acid; however, a heterogeneous mixture of polysaccharide fragments was obtained instead of the expected poly-M fraction. Preliminary data suggests that fucoidan from this alga is a new for brown algae type of sulfated polysaccharide (xylofucan) with a main backbone built of α-l-fucopyranose residues. This chain contains multiple sulfate groups and single non-sulfated β-d-xylopyranose residues as substituents.     

温控分子动力学研究微管蛋白活性肽链的折叠机制

运用温控和常温分子动力学方法, 研究了微管蛋白活性部位Pep1-28肽链的折叠机制, 总模拟时间为380.0 ns. 对于温控分子动力学, 逐渐降温可以清晰显示Pep1-28肽链的折叠途径, 发生明显折叠的温度约为550 K, 其折叠和去折叠可逆机制为U(>1200 K)←→I1(1200-1000 K)←→I2(800 K)←→I3(600 K)←→I4(450 K)←→F1(400 K)←→F2(300 K), 其中U为去折叠态构象, I1、I2、I3和I4是折叠过程中的四个重要的中间态构象, F1和F2是两个结构相近的折叠态构象. 对于常温(300 K)分子动力学, 其构象转变和折叠过程相当迅速, 很难观察到有效、稳定的中间态构象. 尤其引人注意的是, 其折叠态结构陷入了能量局域极小点, 与温控(300 K)的有较大差异, 两者能量差高达297.53 kJ·mol-1. 可见, 温控分子动力学方法不仅清晰地显示多肽和蛋白质折叠过程的重要中间态构象, 为折叠和去折叠机制提供直接、可靠的依据, 而且还有助于跨越较高的构象能垒, 促使多肽和蛋白质折叠以形成全局能量最低的稳定结构.     

Thiacalix[4]arene based reconfigurable molecular switches: set-reset memorized sequential device

The fluorescent chemosensors 3, 5 and 7 based on thiacalix[4]arene bearing naphthyl groups have been designed and synthesized. The optical chemosensor 3 based on a thiacalix[4]arene of cone conformation behaves as "turn-on" optical chemosensor for Fe(3+) and F(-) ions. However, chemosensors 5 and 7 based on a thiacalix[4]arene of 1,3-alternate conformation demonstrate "turn-on" optical behaviour for Hg(2+), F(-) ions (with receptor 5 as turn-on for K(+) ions also) and "turn-off" behaviour for Fe(3+) ions. The simultaneous presence of Fe(3+) and Hg(2+) or K(+) or F(-) ions results in formulation of reversible "on-off" switches. Various molecular logic gates developed in response to molecular switching between these chemical inputs have been integrated into sequential logic circuits with memory function in a feedback loop which mimics "set-reset" molecular level information processing device.     

On-line sheathless capillary electrophoresis/nanoelectrospray ionization-tandem mass spectrometry for the analysis of glycosaminoglycan oligosaccharides

A novel approach in glycosaminoglycomics, based on sheathless on-line capillary electrophoresis/nanoelectrospray ionization-quadrupole time of flight-mass spectrometry (CE/nanoESI-QTOF-MS) and tandem MS of extended chondroitin sulfate/dermatan (CS/DS) oligosaccharide chains is described. The methodology required the construction of a new sheathless CE/nanoESI-QTOF-MS configuration, its implementation and optimization for the high sensitivity analysis of CS/DS oligosaccharide mixtures from conditioned culture medium of decorin transfected human embryonic kidney (HEK) 293 cells. Under newly established sheathless on-line CE/(-)nanoESI conditions for glycosaminoglycan (GAG) ionization and MS detection, single CS/DS oligosaccharide components of extended chain length and increased sulfation degree were identified. Molecular ions corresponding to species carrying 5 and 6 negative charges could be generated for large GAG oligosaccharide species in the negative ion nanoESI-MS. The optimized on-line conditions enabled the detection of molecular ions assigned to oversulfated tetradeca-, octadeca-, and eicosasaccharide CS/DS molecules, which represent the category of largest sulfated GAG-derived oligosaccharides evidenced by CE/ESI-MS. By on-line CE/ESI tandem MS in data-dependent acquisition mode the oversulfated eicosasaccharide species could be sequenced and the localization of the additional sulfate group along the chain could be determined.     

Enthalpy (DeltaH) and entropy (DeltaS) for pi-stacking interactions in near-sandwich configurations: relative importance of electrostatic, dispersive, and charge-transfer effects

Interactions between two aromatic rings with various substituents in a near-sandwich configuration have been quantitatively studied by using the triptycene derived molecular models. This model system allows a stacking arrangement of two arenes to assume a near-perfect face-to-face configuration in its ground state conformation. Comparing to our previous study of the parallel displaced configuration, repulsive interactions are predominant for most arenes currently studied. However, if one arene is strongly electron deficient (Ar2=pentafluorobenzoate), attractive interactions were observed regardless of the character of the other arene (Ar1). For stacking interactions between Me2NC6H4 and C6F5CO groups, a DeltaH of -1.84+/-0.2 kcal/mol and a DeltaS of -2.9+/-0.8 cal/(mol.K) were determined. The general trend in the attractive stacking interaction toward a pentafluorobenzoate is Me2NC6H4>Me3C6H2>Me2C6H3>MeC6H4>MeOC6H4>C6H5>O2NC6H4. The observed trend is consistent with a donor-acceptor relationship and the acceptor is a C6F5CO group.     

Spectroscopic and chemical characterizations of molecular size fractionated humic acid

A sample of humic acid was divided by ultrafiltration into five fractions of different molecular size (F1; 300 000: F2; 100 000-300 000: F3; 50 000-100 000: F4; 10 000-50 000: F5; 1000-10 000 daltons). Characterization by IR, and CPMAS C-13 NMR spectroscopy indicated that the molecules of the fraction of >/=100 000 daltons were primarily aliphatic, while the smaller molecules of the >/=10 000 dalton fraction were predominantly aromatic. Titration (pH) data were consistent with an increase in the number of carboxylate groups per unit mass as molecular size became smaller. A comparative study with unpurified and purified (by treatment with ion exchange elution, acid precipitation and alkaline dissolution) humic acid samples showed chemical alteration with some loss of carboxyl groups in the humic acid.     

How dihydrofolate reductase facilitates protonation of dihydrofolate

Dihydrofolate Reductase (DHFR) catalyzes the reduction of dihydrofolate (H2F) to tetrahydrofolate. On the basis of 10-12.5 ns molecular dynamics simulations of two conformations (closed and occluded) of the ternary DHFR/NADPH/H2F complex from Escherichia coli and a free energy perturbation approach, we have calculated the pKa value for the N5 atom in H2F. Our results suggest that the N5 atom in H2F is responsible for the pH dependency of the catalyzed reaction, meaning that DHFR facilitates protonation of H2F by approximately 4 pKa units. The mechanism behind this increase is due to favorable electrostatic interactions between the Asp27 residue and a proton at the N5 atom. The electrostatic interactions are enhanced by a hydrophobic active site, which to a large extent is made hydrophobic by the M20 loop in DHFR. Moreover, we find that the conformation imposed on H2F by DHFR to some extent also favors protonation of the N5 atom. Our results add support to previous findings and suggestions by Callender and co-workers [e.g., Deng, J.; Callender, R. J. Am. Chem. Soc. 1998, 120, 7730-7737] and explain why mutation of Asp27 may lead to severely reduced activity at neutral pH.     

Identification of lectin activity in the hemolymph ofCastnia licus Drury,a sugar-cane giant borer (Lepidoptera-Castniidae)

Castnia licus Drury, in the larvae stage, is a major pest in the sugarcane industry of Northeastern Brazil (giant borer). A natural hemagglutination activity was detected in the larvae hemolymph of this insect and the activity have not been inhibited by tested carbohydrates. Fractionation with ammonium sulfate showed that the supernatant of the 15–30% fraction (S15-30%) had the lectin’s highest specific activity. Acidic and basic lectin activities were separated by chromatography on CM-cellulose; the fractionated molecular forms showed distinct electrophoresis mobilities.     

Novel antiviral fucoidan from sporophyll of Undaria pinnatifida (Mekabu)

Structural characterization and antiviral activities of fucoidan from sporophyll of Undaria pinnatifida (Mekabu) was examined. The fucoidan was composed of fucose and galactose with an approximately ratio of 1.0:1.1. Degree of substitution of sulfate was 0.72 and its apparent molecular weight was 9,000. Methylation analyses showed that fucoidan had various sugar linkages, and revealed that the fucoidan might have complicated structure. This fucoidan showed potent antiviral activities against herpes simplex virus type 1 (HSV-1), HSV-2, and human cytomegalovirus.     

Combining size-exclusion chromatography and fully automated chip-based nanoelectrospray quadrupole time-of-flight tandem mass spectrometry for structural analysis of chondroitin/dermatan sulfate in human decorin

Chondroitin/dermatan sulfate (CS/DS) chain of decorin (DCN) from human skin fibroblasts (HSk) was released by reductive β-elimination reaction and digested with chondroitin AC I lyase. Enzymatic hydrolysis mixture of CS/DS chains was separated by size-exclusion chromatography (SEC). Collected octasaccharide fraction was subjected to fully automated chip-based nanoelectrospray (nanoESI) quadrupole time-of-flight (QTOF) MS and tandem MS (MS/MS). MS of human skin fibroblasts DCN CS/DS displayed a high complexity due to the large variety of glycoforms, which under chip-nanoESI MS readily ionized to form multiply charged ions. Except for the regularly tetrasulfated octasaccharide, the investigated fraction contained four additional octasaccharides of atypical sulfation status. Two new oversulfated glycoforms and two undersulfated species were identified. Remarkably, the series of decasaccharides discovered in the same SEC pool was found to encompass a trisulfated and a novel hexasulfated [4,5-Δ-GlcAGalNAc(IdoAGalNAc)?] species. MS/MS by collision-induced dissociation (CID) on the [M-4H]? ion corresponding to the previously not reported [4,5-Δ-GlcAGalNAc(IdoAGalNAc)?](5S) corroborated for a novel motif in which three N-acetylgalactosamine (GalNAc) moieties are monosulfated, 4,5-Δ-GlcA and the first IdoA from the non-reducing end bear one sulfate group each, while the second N-acetylgalactosamine from the reducing end is unsulfated.     

Polysaccharides of Algae 71*. Polysaccharides of the Pacific brown alga <Emphasis Type="Italic">Alaria marginata</Emphasis>

The polysaccharide composition in sporophylls of the brown alga Alaria marginata enriched with laminaran and sulfated polysaccharides was studied. It was shown that laminaran molecules had an average degree of polymerization about 30 and consisted mainly of 3-linked β-D-glucopyranose residues, having no more than 10% of 1→6 linkages. The majority of chains (about 60%) were terminated at "reducing" end by mannitol residue. Alginic acid of sporophylls contained mannuronic (M) and guluronic (G) acids residues distributed along the linear polymer molecules as MM, MG, and GG blocks at a ratio of 4: 1: 1. Fucoidan was found to be composed of fucose, galactose, and sulfate as the major constituents, while xylose, mannose, glucuronic acid, and acetate were the minor components. It was shown that fucoidan contained two major components: fucan sulfate, molecules of which are built up of 3-linked fucopyranose residues with branches and sulfate groups at different positions, and fucogalactan, also containing chains of 3-linked fucopyranose residues with branches at positions 4 together with highly branched galactan chains terminated by fucose residues. The fucoidan contained also sulfated glucuronomannan and sulfated glucuronan as minor components.     

Effect of frozen storage on molecular weight, size distribution and conformation of gluten by SAXS and SEC-MALLS

In this study, the effects of frozen (-18 °C) storage time on molecular weight, size distribution, conformation, free amino groups and free sulfhydryl groups of gluten were studied by small-angle X-ray scattering (SAXS), multi-angle laser light scattering (MALLS) in conjunction with a size exclusion chromatography (SEC) and spectrophotometrically. The results showed that the gluten dissolved in 50 mM acetic acid appeared to be similar to quasi-spherical of the chain conformation and the slope of the conformation plot decreased during the storage. Both the molecular weight and radius of gyration of the frozen gluten decreased with the storage time showing a depolymerization in the high molecular weight fraction of gluten (10(5) Da ~ 10(9) Da). Therefore, at constant molecular weight the change of the chain conformation did not show a clear correlation with the storage time. The free amino groups content changed little and the free sulfhydryl groups content of the gluten increased from 9.8 μmol/g for the control to 12.87 μmol/g for 120-day-stored gluten, indicating that the water redistribution and ice recrystallization lead to the breakage of the disulphide bonds and may be one of the reasons for the depolymerization of gluten polymer.     

Fucoidan‐Mimetic Glycopolymers as Tools for Studying Molecular and Cellular Responses in Human Blood Platelets

The marine sulfated polysaccharide fucoidan displays superior ability to induce platelet aggregation compared to other sulfated polysaccharides. As such, it is an attractive tool for studying molecular and cellular responses in activated platelets. The heterogeneous structure, however, poses a problem in such applications. This study describes the synthesis of sulfated α‐l ‐fucoside‐pendant poly(methacryl amides) with homogeneous structures. By using both thiol‐mediated chain transfer and reversible addition‐fragmentation chain transfer polymerization techniques, glycopolymers with different chain lengths are obtained. These glycopolymers show platelet aggregation response and surface changes similar to those of fucoidan, and cause platelet activation through intracellular signaling as shown by extensive protein tyrosine phosphorylation. As the platelet activating properties of the glycopolymers strongly mimic those of fucoidan, this study concludes these fucoidan‐mimetic glycopolymers are unique tools for studying molecular and cellular responses in human blood platelets.

     

Fe(II)(TRIM)(2)]F(2), the First Example of Spin Conversion Monitored by Molecular Vibrations

The new [Fe(II)(TRIM)(2)]F(2) spin-crossover complex (TRIM = 4-(4-imidazolylmethyl)-2-(2-imidazolylmethyl)imidazole) has been synthesized, crystallizing in the monoclinic system, space group P2/n, with Z = 2, a = 9.798(2) ?, b = 8.433(2) ?, c = 14.597(3) ?, and beta = 90.46(1) degrees. The structure was solved by direct methods and refined to conventional agreement indices R = 0.032 and R(w) = 0.034 with 1378 unique reflections for which I > 3sigma(I). The molecular structure consists of [Fe(TRIM)(2)](2+) complex cations hydrogen-bonded to six fluoride anions. The crystal packing results from this highly symmetrical and dense 3D network of hydrogen bonds. The coordination geometry of the iron(II) center can be described as a weakly distorted octahedron, including six nitrogen atoms originating from the two TRIM ligands coordinated to Fe(II) through their imine nitrogen atoms. Investigation of [Fe(II)(TRIM)(2)]F(2) by magnetic susceptibility measurements and M?ssbauer spectroscopy as a function of temperature indicates a 5% thermal variation of the spin fraction between 50 and 150 K, at variance with all previous litterature data. The spin conversion is gradual with 6% LS fraction below 50 K and less than 1% above 150 K. A theoretical approach based on the Ising-like model, completed with harmonic oscillators associated with the 15 vibration modes of the FeN(6) coordination octahedron, successfully fits the data with an energy gap of approximately 40 K between the lowest LS and HS electrovibrational states, an average vibration frequency omega(LS) of 232 K in the LS state, and an average omega(LS)/omega(HS) ratio of 1.3. Taking these results into account, the computed molar entropy change DeltaS associated with a complete conversion between the HS and LS states of Fe(II)(TRIM)(2)F(2) ( approximately 40 J.K(-)(1).mol(-)(1)) is in fair agreement with the expected value.     

Contrasting chemistry of cis- and trans-platinum(II) diamine anticancer compounds: hydrolysis studies of picoline complexes

cis-[PtCl2(NH3)(2-picoline)] (AMD473) is currently on clinical trials as an anticancer drug. The trans isomer, AMD443 (1), is also cytotoxic in a variety of cancer cell lines. The X-ray crystal structure of the trans isomer (1) shows that the pyridine ring is tilted by 69 degrees with respect to the platinum square-plane in contrast to the cis isomer in which it is almost perpendicular (103 degrees ). In the 3-picoline (2) and 4-picoline (3) trans isomers, the ring is tilted by 58 degrees /60 degrees (2 molecules/unit cell) and by 56 degrees , respectively. Hydrolysis may be an important step in the intracellular activation and anticancer mechanism of action of these complexes. The first hydrolysis step is relatively fast even at 277 K, with rate constants (determined by 1H,15N NMR) of k1 = 2.6 x 10(-5) s(-1), 12.7 x 10(-5) s(-1), and 5.2 x 10(-5) s(-1) (I = 0.1 M) for formation of the monoaqua complexes of 1-3, respectively. Although the hydrolysis of 3 is slower than 2, it is hydrolyzed to a greater extent. No formation of the diaqua complex was observed for any of the three complexes at 277 K, and it accounts for <3% of the platinum species at 310 K. In general the extent of hydrolysis of the trans complexes is much less than for their cis analogues. The pK(a) values for the monoaqua adducts of 1-3 were determined to be 5.55, 5.35, and 5.39, respectively, suggesting that they would exist largely as the monohydroxo complex at physiological pH. The pKa values for the diaqua adducts were determined to be 4.03 and 7.01 for 1, 3.97 and 6.78 for 2, and 3.94 and 6.88 for 3, the first pK(a) being >1 unit lower than for related cis complexes.