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PubMed2002

First total syntheses of the phytotoxins solanapyrones D and E via the domino Michael protocol.

The phytotoxins solanapyrones D (1) and E (2) have been synthesized from the decalone prepared by the domino Michael reaction of the kinetic enolate of optically pure acetylcyclohexene with methyl crotonate. The decalone was transformed into a solanapyrone core by equilibration into thermodynamically stable trans-decalone (11), dehydroxylation, and dehydration. Condensation of a methyl acetoacetate equivalent followed by cyclization installed a pyrone moiety. Introduction of a formyl or hydroxymethyl unit into the pyrone ring via Pummerer related reactions furnished solanapyrones D (1) and E (2).

Alternaria↗

PubMed2003

Paeonianins A-E, new dimeric and monomeric ellagitannins from the fruits of Paeonia lactiflora.

Four new dimeric ellagitannins, paeonianins A-D (2-5), were isolated from the fruits of Paeonia lactiflora, together with a new ellagitannin monomer, paeonianin E (1). Their structures were determined by spectroscopic methods. Paeonianins A-D (2-5) are positional isomers formed by condensation of pentagalloyl-beta-D-glucose (8) with 5-desgalloylstachyurin (6) or casuariin (7). Paeonianin E is a C-glycosidic ellagitannin having a gallic acid methyl ester moiety at the glucose C-1 position. This is the first report of the isolation of dimeric ellagitannins from a plant in the family Paeoniaceae.

Fruit↗

PubMed1997

Studies on the synthesis of two tetrasaccharides and the reactivity difference between them.

Studies on the reactivity of two synthetic tetrasaccharides as glycosyl acceptors showed that condensation of the methyl alpha-glycoside with a disaccharide donor afforded a hexasaccharide, but condensation of the methyl beta-glycoside with the disaccharide did not yield the corresponding hexasaccharide under the same conditions. A combination of theoretical results and 2D NMR indicated that the reactivity difference between the methyl alpha-glycoside and the methyl beta-glycoside was determined mainly by steric effects.

Carbohydrate Conformation↗

PubMed2005

Mapping long-range interactions in alpha-synuclein using spin-label NMR and ensemble molecular dynamics simulations.

The intrinsically disordered protein alpha-synuclein plays a key role in the pathogenesis of Parkinson's disease (PD). We show here that the native state of alpha-synuclein consists of a broad distribution of conformers with an ensemble-averaged hydrodynamic radius significantly smaller than that expected for a random coil structure. This partial condensation is driven by interactions between the highly charged C-terminus and a large hydrophobic central region of the protein sequence. We suggest that this structure could inhibit the formation of alpha-synuclein aggregates, which are thought to be the cytotoxic species responsible for neurodegeneration in PD.

Computer Simulation↗

PubMed2002

Synthesis of the ABC ring system of manzamine A.

A synthesis of the core ABC ring system of the manzamine alkaloids is described, starting from arecoline. The key steps involve a Claisen rearrangement to set up a 4-substituted-3-methylenepiperidine and a stereoselective azomethine ylide dipolar cycloaddition reaction. Condensation of the aldehyde 6 and sarcosine ethyl ester hydrochloride salt gives an intermediate azomethine ylide, which undergoes an intramolecular cycloaddition reaction to set up two new rings and three new chiral centers stereoselectively. The aldehyde 6 was not a suitable substrate for related azomethine ylide cycloaddition reactions with other amines. However, the related dimethyl acetal 26 could be condensed with a variety of amines to give the desired tricyclic products. The cycloaddition reaction with N-methyl or N-allyl glycine ethyl ester gave almost exclusively the exo adduct, whereas cycloaddition with glycine ethyl ester gave the endo adduct.

Arecoline↗

PubMed2006

Synthesis and conformational analysis of new cyclobutane-fused nucleosides.

[structure: see text]. A stereselective synthesis of 3-oxabicyclo[3.2.0]heptane nucleoside analogues, which were designed as conformational mimics of the anti-HIV agents 2',3'-didehydro-2',3'-dideoxythimidine (stavudine, d4T) and 2',3'-didehydro-2',3'-dideoxyadenosine (d4A), is described. The target compounds were prepared by condensation of a common intermediate bicyclic acetate, derived from a homochiral 2(5H)-furanone, with pyrimidine and purine bases under modified Vorbrüggen conditions. The conformational behavior of the synthesized nucleoside analogues was studied by NMR spectroscopy and X-ray crystallography.

Anti-HIV Agents↗

PubMed2005

The carboligation reaction of acetohydroxyacid synthase II: steady-state intermediate distributions in wild type and mutants by NMR.

The thiamin diphosphate (ThDP)-dependent enzyme acetohydroxyacid synthase (AHAS) catalyzes the first common step in branched-chain amino acid biosynthesis. By specific ligation of pyruvate with the alternative acceptor substrates 2-ketobutyrate and pyruvate, AHAS controls the flux through this branch point and determines the relative rates of synthesis of isoleucine, valine, and leucine, respectively. We used detailed NMR analysis to determine microscopic rate constants for elementary steps in the reactions of AHAS II and mutants altered at conserved residues Arg-276, Trp-464, and Met-250. In Arg276Lys, both the condensation of the enzyme-bound hydroxyethyl-ThDP carbanion/enamine (HEThDP) with the acceptor substrates and acetohydroxyacid release are slowed several orders of magnitude relative to the wild-type enzyme. We propose that the interaction of the guanidinium moiety of Arg-264 with the carboxylate of the acceptor ketoacid provides an optimal alignment of substrate and HEThDP orbitals in the reaction trajectory for acceptor ligation, whereas its interaction with the carboxylate of the covalent HEThDP-acceptor adduct plays a similar role in product release. Both Trp-464 and Met-250 affect the acceptor specificity. The high preference for ketobutyrate in the wild-type enzyme is lost in Trp464Leu as a consequence of similar forward rate constants of carboligation and product release for the alternative acceptors. In Met250Ala, the turnover rate is determined by the condensation of HEThDP with pyruvate and release of the acetolactate product, whereas the parallel steps with 2-ketobutyrate are considerably faster. We speculate that the specificity of carboligation and product liberation may be cumulative if the former is not completely committed.

Acetolactate Synthase↗

PubMed2002

A concise synthesis of the fully functional lactide core of cycloviracin B with implications for the structural assignment of related glycolipids.

The absolute stereochemistry at the site of attachment of the fatty acid residues to the lactide core of the glycolipids cycloviracin B1 (1) and glucolipsin A (13) has been elucidated as (3R,3'R) by comparison of their 13C NMR data with those of the three possible, differently configured core structures 9, 12, and 14. Moreover, a careful analysis of this set of NMR data allows us to conclude that the structures previously proposed for a seemingly closely related class of antivirally active compounds, i.e., the fattiviracin family, need revision. The key step en route to the symmetrical dilactones 9 and 12 consists of a highly efficient cyclodimerization process which exploits the template effect exerted by potassium cations on the hydroxy acid cyclization precursor. The latter is obtained in excellent overall yield by a sequence involving ring-opening Claisen condensation of pentadecanolide to form the functionalized beta-ketoester 4, asymmetric hydrogenation catalyzed by [(BINAP)RuCl2]2.NEt3, and a beta-selective glycosylation reaction using trichloroacetimidate 6. The unsymmetrical dilactone 14, in contrast, is prepared by a stepwise approach based on a Yamaguchi lactonization as the means to close the macrocyclic ring.

Anti-Bacterial Agents↗

PubMed2005

Hygrocins a and B, naphthoquinone macrolides from Streptomyces hygroscopicus.

Two new naphthoquinone macrolides, hygrocins A (1) and B (2), were isolated from the fermentation broth of Streptomyces hygroscopicus. Hygrocin A is not stable due to the presence of an active methylene group (C-22), which undergoes intramolecular aldol condensation with the quinone ring to yield a gamma-lactam derivative, 6. Its structural elucidation was achieved by chemical conversion to 3, an unusual diazomethane derivative, and confirmed by its alkaline hydrolysis product 4, hydrogenation derivative 5, and "degradation" product 6. The structure of hygrocin B was determined by combined chemical and spectroscopic methods.

Lactams, Macrocyclic↗

PubMed2001

The formation of 2-hydroxy-4-hydroxymethyl-3-(indol-3-yl)-cyclopent-2-enone derivatives from ascorbigens.

A facile preparation is described of 3-(indol-3-yl)-2-hydroxy-4-hydroxymethylcyclopent-2-enone and its N-derivatives in 15-40% yields by the degradation of ascorbigen or its N-derivatives in a warm solution of L-ascorbic acid through a sequential domino reaction. The same cyclopentenone derivatives were obtained in 30-40% yields by the condensation of (N-alkylindol-3-yl)glycolic acids with ascorbic acid. 2,6-Dihydroxy-1-(indol-3-yl)hexa-1,4-diene-3-one and 2-hydroxy-4-hydroxymethyl-5-(indol-3-yl)cyclopent-2-enone were identified as intermediates in this reaction.

Ascorbic Acid↗

PubMed2004

A novel and conserved pocket of human kappa-Fab fragments: design, synthesis, and verification of directed affinity ligands.

Antibodies of type IgG may be divided into two classes, called lambda or kappa, depending on the type of light chain. We have identified a conserved pocket between the two domains CH1 and CL of human IgG kappa-Fab, which is not present in the lambda type. This pocket was used as a target docking site with the purpose of exploring the possibilities of designing affinity ligands that could function as such even after immobilization to gel. The idea of the design arose mainly from the results of the saturated transfer difference (STD-NMR) screening of 46 compounds identified by means of virtual docking of 60 K diverse compounds from the Available Chemicals Directory (ACD). Surface plasmon resonance (SPR) was used as an alternative method to monitor binding in solution. A total of 24 compounds belonging to a directed library were designed, synthesized, and screened in solution. They consist essentially of an amino acid condensed to a N,N'-methylated phenyl urea. STD-NMR results suggest that a small hydrophobic side chain in the condensed amino acid promotes binding, whereas a hydroxyl-group-containing side chain implies absence of STD-NMR signals. Three compounds of the directed library were immobilized and evaluated as chromatographic probes. In one case, using D-Pro as the condensed amino acid, columns packed with ligand-coupled Sepharose (Amersham Biosciences) retained two different monoclonal samples of kappa-Fab fragments with different variable regions, whereas a sample of monoclonal lambda-Fab fragments was not retained under similar chromatographic conditions.

Antibodies, Monoclonal↗

PubMed2002

Sebastianines A and B, novel biologically active pyridoacridine alkaloids from the Brazilian ascidian Cystodytes dellechiajei.

Fractionation of the crude methanol extract of the ascidian Cystodytes dellechiajei collected in Brazil yielded two novel alkaloids, sebastianine A (1) and sebastianine B (2). The structures of both 1 and 2 were established by analysis of spectroscopic data, indicating an unprecedented ring system for both compounds, comprising a pyridoacridine system fused with a pyrrole unit in sebastianine A (1) and a pyridoacridine system fused with a pyrrolidine system condensed with alpha-hydroxyisovaleric acid in sebastianine B (2). Both alkaloids displayed a cytotoxic profile against a panel of HCT-116 colon carcinoma cells indicative of a p53 dependent mechanism.

Acridines↗

PubMed2005

Synthesis of arieianal, a prenylated benzoic acid from Piper arieianum.

Arieianal (1) is a complex prenylated benzoic acid that was isolated from Piper arieianum. It has been synthesized through a convergent sequence that joins a functionalized diterpenoid chain to a protected aromatic core. Key steps include use of a copper enolate for selective displacement of an allylic bromide in the presence of an allylic acetate and a stereoselective Horner-Wadsworth-Emmons condensation to afford the desired E olefin of the isoprenoid side chain. After the diterpenoid chain was joined to the aromatic ring, use of sodium metal in hot sBuOH allowed selective cleavage of two benzyl ether protecting groups, and a sequence of oxidations gave the target compound. This synthesis confirms the structure assigned to the natural product and establishes a route that may be used to prepare more active analogues.

Benzoates↗

PubMed2001

Determination of arylglycerol-beta-aryl ethers and other linkages in lignins using DFRC/(31)P NMR.

An analytical method for lignins has been developed that involves derivatization followed by reductive cleavage (DFRC), depolymerization, and quantitative (31)P NMR spectroscopy. This technique detects and quantifies the various ether linkages present in softwood residual kraft lignins (RKL) and milled wood lignins (MWL). In addition, the technique supplies new quantitative information about beta-aryl ethers linked to condensed and noncondensed aromatic moieties, including dibenzodioxocins. Within RKL, beta-aryl ether bonds connected to condensed phenolic moieties predominated over those connected to noncondensed phenolic moieties. In addition, the amount of DFRC monomers determined by gas chromatography was minute in the RKL but large in the MWL. This indicates that almost all noncondensed beta-aryl ether linkages were cleaved during kraft pulping. The method offers new avenues for the detailed investigation of the bonding patterns of native and technical lignins.

Chromatography, Gas↗

PubMed2001

Total synthesis of 2',3',4',5',5' '-(2)h(5)-ribonucleosides: the key building blocks for NMR structure elucidation of large RNA.

The diastereospecific chemical syntheses of uridine-2',3',4',5',5' '-(2)H(5) (21a), adenosine-2',3',4',5',5' '-(2)H(5) (21b), cytidine-2',3',4',5',5' '-(2)H(5)(2)H(5) (21c), and guanosine-2',3',4',5',5' '-(2)H(5) (21d) (>97 atom % (2)H at C2', C3', C4', and C5'/C5' ') have been achieved for their use in the solution NMR structure determination of oligo-RNA by the Uppsala "NMR-window" concept (refs 4a-c, 5a, 6), in which a small (1)H segment is NMR-visible, while the rest is made NMR-invisible by incorporation of the deuterated blocks 21a-d. The deuterated ribonucleosides 21a-d have been prepared by the condensation of appropriately protected aglycone with 1-O-acetyl-2,3,5-tri-O-(4-toluoyl)-alpha/beta-D-ribofuranose-2,3,4,5,5'-(2)H(5) (19), which has been obtained via diastereospecific deuterium incorporation at the C2 center of appropriate D-ribose-(2)H(4) derivatives either through an oxidation-reduction-inversion sequence or a one-step deuterium-proton exchange in high overall yield (44% and 24%, respectively).

Deuterium↗

PubMed2004

Structure of the Mg2+-loaded C-lobe of cardiac troponin C bound to the N-domain of cardiac troponin I: comparison with the Ca2+-loaded structure.

Cardiac troponin C (cTnC) is the Ca(2+)-binding component of the troponin complex and, as such, is the Ca(2+)-dependent switch in muscle contraction. This protein consists of two globular lobes, each containing a pair of EF-hand metal-binding sites, connected by a linker. In the N lobe, Ca(2+)-binding site I is inactive and Ca(2+)-binding site II is primarily responsible for initiation of muscle contraction. The C lobe contains Ca(2+)/Mg(2+)-binding sites III and IV, which bind Mg(2+) with lower affinity and play a structural as well as a secondary role in modulating the Ca(2+) signal. To understand the structural consequences of Ca(2+)/Mg(2+) exchange in the C lobe, we have determined the NMR solution structure of the Mg(2+)-loaded C lobe, cTnC(81-161), in a complex with the N domain of cardiac troponin I, cTnI(33-80), and compared it with a refined Ca(2+)-loaded structure. The overall tertiary structure of the Mg(2+)-loaded C lobe is very similar to that of the refined Ca(2+)-loaded structure as evidenced by the root-mean-square deviation of 0.94 A for all backbone atoms. While metal-dependent conformational changes are minimal, substitution of Mg(2+) for Ca(2+) is characterized by condensation of the C-terminal portion of the metal-binding loops with monodentate Mg(2+) ligation by the conserved Glu at position 12 and partial closure of the cTnI hydrophobic binding cleft around site IV. Thus, conformational plasticity in the Ca(2+)/Mg(2+)-dependent binding loops may represent a mechanism to modulate C-lobe cTnC interactions with the N domain of cTnI.

Animals↗

PubMed2005

Is biomedical nuclear magnetic resonance limited by a revisitable paradigm in physics?

The history of nuclear magnetic resonance (NMR) can be divided generally into two phases: before the Second World War, molecular beam methods made it possible to detect the whole set of spins. However, these methods were destructive for the sample and had a very low precision. The publications of F. Bloch and E. Purcell in 1946 opened up a second phase for NMR with the study of condensed matter, but at the expense of an enormous loss in theoretical sensitivity. During more than half a century, the method of Bloch and Purcell, based on inductive detection of the NMR signal, has allowed many developments in biomedicine. But, curiously, this severely constraining limitation on sensitivity has not been called into question during this half-century, as if the pioneers of the pre-war period had been forgotten.

Animals↗

PubMed2000

Identification of DNA adducts of acetaldehyde.

Acetaldehyde is a mutagen and carcinogen which occurs widely in the human environment, sometimes in considerable amounts, but little is known about its reactions with DNA. In this study, we identified three new types of stable acetaldehyde DNA adducts, including an interstrand cross-link. These were formed in addition to the previously characterized N(2)-ethylidenedeoxyguanosine. Acetaldehyde was allowed to react with calf thymus DNA or deoxyguanosine. The DNA was isolated and hydrolyzed enzymatically; in some cases, the DNA was first treated with NaBH(3)CN. Reaction mixtures were analyzed by HPLC, and adducts were isolated and characterized by UV, (1)H NMR, and MS. The major adduct was N(2)-ethylidenedeoxyguanosine (1), which was identified as N(2)-ethyldeoxyguanosine (7) after treatment of the DNA with NaBH(3)CN. The new acetaldehyde adducts were 3-(2-deoxyribos-1-yl)-5,6,7, 8-tetrahydro-8-hydroxy-6-methylpyrimido[1,2-a]purine-10(3H)one (9), 3-(2-deoxyribos-1-yl)-5,6,7,8-tetrahydro-8-(N(2)-deoxyguanosyl+ ++)- 6-methylpyrimido[1,2-a]purine-10(3H)one (12), and N(2)-(2, 6-dimethyl-1,3-dioxan-4-yl)deoxyguanosine (11). Adduct 9 has been previously identified in reactions of crotonaldehyde with DNA. However, the distribution of diastereomers was different in the acetaldehyde and crotonaldehyde reactions, indicating that the formation of 9 from acetaldehyde does not proceed through crotonaldehyde. Adduct 12 is an interstrand cross-link. Although previous evidence indicates the formation of cross-links in DNA reacted with acetaldehyde, this is the first reported structural characterization of such an adduct. This adduct is also found in crotonaldehyde-deoxyguanosine reactions, but in a diastereomeric ratio different than that observed here. A common intermediate, N(2)-(4-oxobut-2-yl)deoxyguanosine (6), is proposed to be involved in formation of adducts 9 and 12. Adduct 11 is produced ultimately from 3-hydroxybutanal, the major aldol condensation product of acetaldehyde. Levels of adducts 9, 11, and 12 were less than 10% of those of N(2)-ethylidenedeoxyguanosine (1) in reactions of acetaldehyde with DNA. As nucleosides, adducts 9, 11, and 12 were stable, whereas N(2)-ethylidenedeoxyguanosine (1) had a half-life of 5 min. These new stable adducts of acetaldehyde may be involved in determination of its mutagenic and carcinogenic properties.

Acetaldehyde↗