Synthesis and High‐Resolution NMR Structure of a β3‐Octapeptide with and without a Tether Introduced by Olefin Metathesis

Bridging between (i)‐ and (i+3)‐positions in a β³‐peptide with a tether of appropriate length is expected to prevent the corresponding 3₁₄‐helix from unfolding (Fig. 1). The β³‐peptide H‐β³hVal‐β³hLys‐β³hSer(All)‐β³hPhe‐β³hGlu‐β³hSer(All)‐β³hTyr‐β³hIle‐OH ( 1 ; with allylated βhSer residues in 3‐ and 6‐position), and three tethered β‐peptides 2 – 4 (related to 1 through ring‐closing metathesis) have been synthesized (solid‐phase coupling, Fmoc strategy, on chlorotrityl resin; Scheme). A comparative CD analysis of the tethered β‐peptide 4 and its non‐tethered analogue 1 suggests that helical propensity is significantly enhanced (threefold CD intensity) by a (CH₂)₄ linker between the β³hSer side chains (Fig. 2). This conclusion is based on the premise that the intensity of the negative Cotton effect near 215 nm in the CD spectra of β³‐peptides represents a measure of ‘helical content’. An NMR analysis in CD₃OH of the two β³‐octapeptide derivatives without (i.e., 1 ) and with tether (i.e., 4 ; Tables 1–6, and Figs. 4 and 5) provided structures of a degree of precision (by including the complete set of side chain–side chain and side chain–backbone NOEs) which is unrivaled in β‐peptide NMR‐solution‐structure determination. Comparison of the two structures (Fig. 5) reveals small differences in side‐chain arrangements (separate bundles of the ten lowest‐energy structures of 1 and 4 , Fig. 5, A and B ) with little deviation between the two backbones (superposition of all structures of 1 and 4 , Fig. 5, C ). Thus, the incorporation of a CH₂? O? (CH₂)₄? O? CH₂ linker between the backbone of the β³‐amino acids in 3‐ and 6‐position (as in 4 ) does accurately constrain the peptide into a 3₁₄‐helix. The NMR analysis, however, does not suggest an increase in the population of a 3₁₄‐helical backbone conformation by this linkage. Possible reasons for the discrepancy between the conclusion from the CD spectra and from the NMR analysis are discussed.     

Structural Insight into IAPP‐Derived Amyloid Inhibitors and Their Mechanism of Action

Designed peptides derived from the islet amyloid polypeptide (IAPP) cross‐amyloid interaction surface with Aβ (termed interaction surface mimics or ISMs) have been shown to be highly potent inhibitors of Aβ amyloid self‐assembly. However, the molecular mechanism of their function is not well understood. Using solution‐state and solid‐state NMR spectroscopy in combination with ensemble‐averaged dynamics simulations and other biophysical methods including TEM, fluorescence spectroscopy and microscopy, and DLS, we characterize ISM structural preferences and interactions. We find that the ISM peptide R3‐GI is highly dynamic, can adopt a β‐like structure, and oligomerizes into colloid‐like assemblies in a process that is reminiscent of liquid–liquid phase separation (LLPS). Our results suggest that such assemblies yield multivalent surfaces for interactions with Aβ40. Sequestration of substrates into these colloid‐like structures provides a mechanistic basis for ISM function and the design of novel potent anti‐amyloid molecules.     

Synthesis,and Helix or Hairpin‐Turn Secondary Structures of ‘Mixed’ α/β‐Peptides Consisting of Residues with Proteinogenic Side Chains and of 2‐Amino‐2‐methylpropanoic Acid (Aib)

Twelve peptides, 1 – 12 , have been synthesized, which consist of alternating sequences of α‐ and β‐amino acid residues carrying either proteinogenic side chains or geminal dimethyl groups (Aib). Two peptides, 13 and 14 , containing 2‐methyl‐3‐aminobutanoic acid residues or a ‘random mix’ of α‐, β²‐, and β³‐amino acid moieties were also prepared. The new compounds were fully characterized by CD (Figs. 1 and 2), and ¹H‐ and ¹³C‐NMR spectroscopy, and high‐resolution mass spectrometry (HR‐MS). In two cases, 3 and 14 , we discovered novel types of turn structures with nine‐ and ten‐membered H‐bonded rings forming the actual turns. In two other cases, 8 and 11 , we found 14/15‐helices, which had been previously disclosed in mixed α/β‐peptides containing unusual β‐amino acids with non‐proteinogenic side chains. The helices are formed by peptides containing the amino acid moiety Aib in every other position, and their backbones are primarily not held together by H‐bonds, but by the intrinsic conformations of the containing amino acid building blocks. The structures offer new possibilities of mimicking peptide–protein and protein–protein interactions (PPI).     

A Self‐Assembled Spherical Complex Displaying a Gangliosidic Glycan Cluster Capable of Interacting with Amyloidogenic Proteins

Physiological and pathological functions of glycans are promoted through their clustering effects as exemplified by a series of gangliosides, sialylated glycosphingolipids, which serve as acceptors for bacterial toxins and viruses. Furthermore, ganglioside GM1 clusters on neuronal cell membranes specifically interact with amyloidogenic proteins, triggering their conformational transitions and leading to neurodegeneration. Here we develop a self‐assembled spherical complex that displays a cluster of the GM1 pentasaccharide, and successfully demonstrate its ability to interact with amyloid β and α‐synuclein. Due to the lack of hydrophobic lipid moieties, which would stably trap these cohesive proteins or give rise to toxic aggregates, this artificial cluster enabled NMR spectroscopic characterization of the early encounter stage of protein interactions with its outer carbohydrate moieties, which were not observable with previous glycan clusters.     

The effect of antagonists on the conformational exchange of the retinoid X receptor alpha ligand‐binding domain

The effect of retinoid X receptor (RXR) antagonists on the conformational exchange of the RXR ligand‐binding domain (LBD) remains poorly characterized. To address this question, we used nuclear magnetic resonance spectroscopy to compare the chemical shift perturbations induced by RXR antagonists and agonists on the RXRα LBD when partnered with itself as a homodimer and as the heterodimeric partner with the peroxisome proliferator‐activated receptor γ (PPARγ) LBD. Chemical shift mapping on the crystal structure showed that agonist binding abolished a line‐broadening effect caused by a conformational exchange on backbone amide signals for residues in helix H3 and other regions of either the homo‐ or hetero‐dimer, whereas binding of antagonists with similar binding affinities failed to do so. A lineshape analysis of a glucocorticoid receptor‐interacting protein 1 NR box 2 coactivator peptide showed that the antagonists enhanced peptide binding to the RXRα LBD homodimer, but to a lesser extent than that enhanced by the agonists. This was further supported by a lineshape analysis of the RXR C‐terminal residue, threonine 462 (T462) in the homodimer but not in the heterodimer. Contrary to the agonists, the antagonists failed to abolish a line‐broadening effect caused by a conformational exchange on the T462 signal corresponding to the RXRα LBD–antagonist–peptide ternary complex. These results suggest that the antagonists lack the ability of the agonists to shift the equilibrium of multiple RXRα LBD conformations in favor of a compact state, and that a PPARγ LBD‐agonist complex can prevent the antagonist from enhancing the RXRα LBD‐coactivator binding interaction. Copyright © 2009 John Wiley & Sons, Ltd.     

Diffusion Measurements vs. Chemical Shift Titration for Determination of Association Constants on the Example of Camphor–Cyclodextrin Complexes

Measurements on camphor–cyclodextrin complexes reveal that precise association constants are more easily determined by chemical shift titration. Diffusion measurements using HR-DOSY allow easy following of the complex composition at different concentration ratios and estimation of the binding energy. Linear dependence of the diffusion coefficients on the molecular mass of free and associated cyclodextrins has been observed in D₂O. The solution structures of α- and β-cyclodextrin complexes of camphor in D₂O were deduced from intermolecular cross-relaxation data. Different preferential orientation in the 2:1 α-CD and 1:1 β-CD species have been derived in contrast to the loose 1:1 complex with γ-CD. Proton NMR chemical shift values proved to be much more sensitive to diastereomeric complex formation than diffusion coefficients.     

Lateral thermal expansion of cellulose Iβ and IIII polymorphs

Measurements of the thermal expansion coefficients (TECs) of cellulose crystals in the lateral direction are reported. Oriented films of highly crystalline cellulose I_β and III_I were prepared and then investigated with X‐ray diffraction at specific temperatures from room temperature to 250 °C during the heating process. Cellulose I_β underwent a transition into the high‐temperature phase with the temperature increasing above 220–230 °C; cellulose III_I was transformed into cellulose I_β when the sample was heated above 200 °C. Therefore, the TECs of I_β and III_I below 200 °C were measured. For cellulose I_β, the TEC of the a axis increased linearly from room temperature at α_a = 4.3 × 10^?5 °C^?1 to 200 °C at α_a = 17.0 × 10^?5 °C^?1, but the TEC of the b axis was constant at α_b = 0.5 × 10^?5 °C^?1. Like cellulose I_β, cellulose III_I also showed an anisotropic thermal expansion in the lateral direction. The TECs of the a and b axes were α_a = 7.6 × 10^?5 °C^?1 and α_b = 0.8 × 10^?5 °C^?1. The anisotropic thermal expansion behaviors in the lateral direction for I_β and III_I were closely related to the intermolecular hydrogen‐bonding systems. © 2002 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 40: 1095–1102, 2002     

Stereoisomeric flavor compounds. Part LXV: Preparative resolution of the enantiomers of chiral dihydrofuranones by recycling chromatography

Preparative resolution of the enantiomers of several chiral dihydrofuranones, known to be important flavor compounds, has been achieved by combining the use of bonded β-cyclo-dextrin as chiral stationary phase with closed-loop recycling chromatography. The purity of the separated enantiomers has been determined by chirospecific capillary GC analysis, using heptakis(2,3-di-O-methyl-6-TBDMS)-β-cyclodextrin as the chiral stationary phase.     

Preparative HPLC. Part 2. Purification of β-lactam derivatives using laboratory-assembled equipment

The capabilities of a preparative chromatograph assembled at moderate cost from commercially available components are examined in relation to the purification of β-lactam derivatives. It is shown that high efficiency separations can be achieved rapidly, economically, and on a scale sufficient to provide adequate quantities of material for spectroscopic identification and biological testing. In the synthesis of a large batch of aminopropyl silica for preparative HPLC purification of an impure sample of cephacetrile, three different grades of silica were investigated. The material giving the best performance was prepared on a 100 g scale and baseline separations for 0.5 g loadings of the impure cephacetrile were obtained on a 30 cm × 2.2 cm i.d. column. The pure cephalosporin was recovered in high yield by freeze drying of the eluate.     

Billion‐Fold Enhancement in Sensitivity of Nuclear Magnetic Resonance Spectroscopy for Magnesium Ions in Solution

β‐nuclear magnetic resonance (NMR) spectroscopy is highly sensitive compared to conventional NMR spectroscopy, and may be applied for several elements across the periodic table. β‐NMR has previously been successfully applied in the fields of nuclear and solid‐state physics. In this work, β‐NMR is applied, for the first time, to record an NMR spectrum for a species in solution. ³¹Mg β‐NMR spectra are measured for as few as 10⁷ magnesium ions in ionic liquid (EMIM‐Ac) within minutes, as a prototypical test case. Resonances are observed at 3882.9 and 3887.2 kHz in an external field of 0.3 T. The key achievement of the current work is to demonstrate that β‐NMR is applicable for the analysis of species in solution, and thus represents a novel spectroscopic technique for use in general chemistry and potentially in biochemistry.     

The epitaxial growth of gaas using alkylarsine: Part 2. molecular orbital calculation

Semi-empirical molecular orbital calculations were carried out for the compounds (C₂H₅)₃As, (C₂H₅)₃Ga and RAsH₂ (R = C₂H₅, i-C₃H₇, i-C₄H₉, and t-C₄H₉) by using the CNDO/2-U program, and their capability of β-elimination reaction is compared on the basis of the torsion energy to the transition state, electrostatic interactions and orbital overlapping between the central atom and the β-hydrogen, and bond order of the metal-carbon, and carbon-hydrogen bond. In the comparison of (C₂H₅)₃As with (C₂H₅)₃Ga, we found that the β-elimination of (C₂H₅)₃As could hardly be expected to take place in the thermal decomposition. The capability of β-elimination would be smaller in C₂H₅AsH₂ than that in (C₂H₅)₃As. Moreover when the ethyl group is replaced by a t-butyl group in RAsH₂, the β-elimination reaction appears to become more difficult and a large possibility for a radical process is suggested.     

由(E)-β-碘代烯基砜和末端炔合成多取代的1,3-烯炔

通过(E)-b-碘代烯基砜与末端炔的Sonogashira偶联反应,以中等到良好的产率合成了磺酰基取代的1,3-烯炔。在NiCl2(PPh3)2催化下,产物与格氏试剂发生脱磺酰基偶联反应,磺酰基被进一步转化为不同的取代基。     

Synthesis of Racemic Δ3‐2‐Hydroxybakuchiol and Its Analogues

The first synthetic approach to (±)‐Δ³‐2‐hydroxybakuchiol (=4‐[(1E,5E)‐3‐ethenyl‐7‐hydroxy‐3,7‐dimethylocta‐1,5‐dien‐1‐yl]phenol; 14 ) and its analogues 13a – 13f was developed by 12 steps (Schemes 2 and 3). The key features of the approach are the construction of the quaternary C‐center bearing the ethenyl group by a Johnson–Claisen rearrangement (→ 6 ); and of an (E)‐alkenyl iodide via a Takai–Utimoto reaction (→ 11 ); and an arylation via a Negishi cross‐coupling reaction (→ 12e – 12f ).     

Non‐empirical calculations of NMR indirect carbon‐carbon coupling constants. Part 5: Bridged bicycloalkanes

All possible J(C,C) of the bicarbocyclic frameworks together with J(C,H) and J(H,H) at bridgeheads in the series of six bridged bicycloalkanes, bicyclo[1.1.0]butane, bicyclo[2.1.0]pentane, bicyclo[3.1.0]hexane, bicyclo[2.2.0]hexane, bicyclo[3.2.0]heptane and bicyclo[3.3.0]octane, were calculated at the SOPPA level with correlation consistent Dunning sets cc‐pVTZ‐Cs augmented with inner core s‐functions and locally dense Sauer sets aug‐cc‐pVTZ‐J augmented with tight s‐functions and rationalized in terms of the multipath coupling mechanism and hybridization effects explaining many interesting structural trends. Copyright © 2003 John Wiley & Sons, Ltd.     

Xanthones from <Emphasis Type="Italic">Halenia corniculata</Emphasis>. 2. Quantitative Determination of Total γ-Pyrone Content in the Aerial Part

A method for quantitative determination of total γ-pyrone content in the aerial part of Halenia corniculata was developed. Their total content in various samples of the aerial part was investigated.__________Translated from Khimiya Prirodnykh Soedinenii, No. 3, pp. 245–247, May–June, 2005.     

Antiparallel Self‐Association of a γ,α‐Hybrid Peptide: More Relevance of Weak Interactions

To learn how a preorganized peptide‐based molecular template, together with diverse weak non‐covalent interactions, leads to an effective self‐association, we investigated the conformational characteristics of a simple γ,α‐hybrid model peptide, Boc‐γ‐Abz‐Gly‐OMe. The single‐crystal X‐ray diffraction analysis revealed the existence of a fully extended β‐strand‐like structure stabilized by two non‐conventional C?H???O=C intramolecular H‐bonds. The 2D ¹H NMR ROESY experiment led us to propose that the flat topology of the urethane‐γ‐Abz‐amide moiety is predominantly preserved in a non‐polar environment. The self‐association of the energetically more favorable antiparallel β‐strand‐mimic in solid‐state engenders an unusual ‘flight of stairs’ fabricated through face‐to‐face and edge‐to‐edge Ar???Ar interactions. In conjunction with FT‐IR spectroscopic analysis in chloroform, we highlight that conformationally semi‐rigid γ‐Abz foldamer in appositely designed peptides may encourage unusual β‐strand or β‐sheet‐like self‐association and supramolecular organization stabilized via weak attractive forces.     

Chemical Constltuents from the Roots of Zizyphus jujuba Mill. var. spinosa (I)

The chemical constituents of the roots of Zizyphus jujuba Mill. var. spinosa were investigated with a combination of Sephadex LH-20 column, centrifugal partition chromatography and RP-18 low pressure liquid chromatography. We isolated seven flavonoids-quercetin ( 1 ), (+)-dihydroquercetin ( 2 ), (+)-dihydrokaempferol ( 7 ), quercetin-3-0-β-glucoside ( 8 ), 2-hydroxynaringenin ( 11 ), rutin ( 12 ), and quercetin 3-0-(2^G-β-D-xylopyranosylrutinoside) ( 13 ); four catechins-(-)-gallocatechin ( 3 ), (-)-epigallocatechin ( 4 ), (-)-catechin ( 5 ), and (-)-epicatechin ( 6 ); and two phenolic carboxylic acids-p-hydroxybenzoic acid ( 9 ) and protocatechuic acid ( 10 ) from the water soluble fraction of the ethanolic extract NMR date of 13 were assigned by 2D NMR techniques.