Effect of sequence on peptide geometry in 5-tert-butylprolyl type VI beta-turn mimics

The influence of sequence on turn geometry was examined by incorporating (2S,5R)-5-tert-butylproline (5-(t)BuPro) into a series of dipeptides and tetrapeptides. (2S,5R)-5-tert-Butylproline and proline were respectively introduced at the C-terminal residue of N-acetyl dipeptide N'-methylamides 1 and 2. The conformational analysis of these analogues was performed using NMR and CD spectroscopy as well as X-ray diffraction to examine the factors that control the prolyl amide (in this text, the term "prolyl amide" refers to the tertiary amide composed of the pyrrolidine nitrogen of the prolyl residue and the carbonyl of the N-terminal residue) equilibrium and stabilize type VI beta-turn conformation. The high cis-isomer population with aromatic residues N-terminal to proline was shown to result from a stacking interaction between the partial positive charged prolyl amide nitrogen and the aromatic pi-system as seen in the crystal structure of 1c. The effect of sequence on the prolyl amide equilibrium of 5-(t)BuPro-tetrapeptides (Ac-Xaa-Yaa-5-(t)BuPro-Zaa-XMe, 13 and 14) was studied by varying the amino acids at the Xaa, Yaa, and Zaa positions. High (>80%) cis-isomer populations were obtained with alkyl groups at the Xaa position, an aromatic residue at the Yaa position, and either an alanine or a lysine residue at the Zaa position of the 5-(t)BuPro-tetrapeptide methyl esters in water. Tetrapeptides Ac-Ala-Phe-5-(t)BuPro-Zaa-OMe (Zaa = Ala, Lys), 14d and 14f, with high cis-isomer content adopted type VIa beta-turn conformations as shown by their NMR and CD spectra. Although a pattern of amide proton temperature coefficient values indicative of a hairpin geometry was observed in peptides 14d and 14f, the value magnitudes did not indicate strong hydrogen bonding in water.     

Rapid, iterative assembly of octyl alpha-1,6-oligomannosides and their 6-deoxy equivalents

Mycobacterium tuberculosis is the cause of the deadly human disease tuberculosis. In studies over the last 40 years it has been revealed that this organism possesses a complex cell wall including glycophospholipids such as the phosphatidylinositiol mannosides (PIMs), lipomannan (LM) and lipoarabinomannan (LAM). These glycolipids all contain a common alpha-1,6-linked mannoside core, and the higher PIMs and LAM possess alpha-1,2-linked mannosyl residues. It has been shown that simple alpha-1,6-linked oligomannosides can act as substrates for alpha-1,6-mannosyltransferases in mycobacteria. Here we report a simple iterative synthesis of a series of hydrophobic octyl alpha-1,6-linked oligomannosides from mono- through to tetrasaccharides. We have utilized a single thioglycoside donor and alcohol acceptor. Further, we have developed conditions for the conversion of each of these compounds to the 6-deoxy congeners. Deoxygenation of the 6-position of the terminal mannosyl residue should prevent these compounds acting as substrates for the abundant alpha-1,6-mannosyltransferases in mycobacteria and should permit detection of the elusive alpha-1,2-mannosyltransferase activity responsible for elaboration of LM to mature LAM and the biosynthesis of the higher PIMs.     

Synthesis, characterization, and supramolecular properties of a hydrophilic porphyrin--beta-cyclodextrin conjugate

Reductive amination of 6-deoxy-6-formyl-beta-cyclodextrin with 5-(p-aminophenyl)-10,15,20-tris(p-sulfonatophenyl)porphyrin in the presence of an excess of sodium cyanoborohydride affords the hydrophilic cyclodextrin-porphyrin conjugate 3 in 23% yield. The structure of 3 was confirmed by NMR spectroscopy and mass spectrometry techniques. Compound 3 showed a marked tendency to dimerize in aqueous conditions via the formation of intermolecular porphyrin-cyclodextrin inclusion complexes and/or through electrostatic interactions. Information on the structure of these aggregates has been obtained by the use of circular dichroism and UV-vis spectroscopy. Aggregation can be avoided by the use of heptakis(2,3,6-tri-O-methyl)-beta-cyclodextrin (TM beta CD) that forms a 1:1 inclusion complex with compound 3.     

Arsenic-containing ribofuranosides and dimethylarsinic acid in green seaweed,Codium fragile

Three water-soluble arsenic compounds were isolated from the green seaweed Codium fragile. These compounds were identified as 1-glycerophosphoryl-2-hydroxy-3-[5′-deoxy-5′-(dimethylarsinoyl)-β-ribofuranosyloxy]propane (1a), 1′ -(1,2-dihydroxypropyl)-5′ -deoxy-5′ -(dimethylarsinoyl)-β-ribofuranoside (1b), and dimethylarsinic acid ((CH₃)₂AsOOH). The structures of these compounds were ascertained by ¹H NMR spectroscopy. Compounds 1a and 1b accounted for 60 % and dimethylarsinic acid for 5% of the water-soluble arsenic.     

5-Amino-5-deoxyribose derivatives. Synthesis and use in the preparation of “Reversed” Nucleosides

Methyl 5-amino-5-deoxy-2,3-O-isopropylidene-β-D-ribofuranoside (III) has been synthesized and used as an intermediate in the preparation of the kinetin analog, methyl 5-deoxy-5-(purin-6-yl)amino-β-D-ribofuranoside (X). The related 1-substituted adenine, methyl 5- (6-aminopurin-1-yl)-5-deoxy-2,3-O-isopropylidene-β-D-ribofuranoside (XIII), was prepared by cyclization of 1-benzyl-5-cyano-4-ethoxymethyleneaminoimidazole (XI) with III and subsequent debenzylation with sodium in liquid ammonia. The structures and stereochemistry of these compounds were established by a combination of ultraviolet and nuclear magnetic resonance spectroscopy.     

Optically active zwitterionic lambda(5)Si,lambda(5)Si'-disilicates: syntheses, crystal structures, and behavior in aqueous solution

The zwitterionic lambda(5)Si,lambda(5)Si'-disilicates 1-8 were synthesized and characterized by solid-state and solution NMR spectroscopy. In addition, compounds 26 H(2)O, 32 CH(3)CN, 45/2 CH(3)CN, 6CH(3)OH, 7, and 8CH(3)OHCH(3)CN were studied by single-crystal X-ray diffraction. The optically active (Delta,Delta,R,R,R,R)-configured compounds 1-8 contain two pentacoordinate (formally negatively charged) silicon atoms and two tetracoordinate (formally positively charged) nitrogen atoms. One (ammonio)alkyl group is bound to each of the two silicon centers, and two tetradentate (R,R)-tartrato(4-) ligands bridge the silicon atoms. Although these lambda(5)Si,lambda(5)Si'-disilicates contain SiO(4)C skeletons, some of them display a remarkable stability in aqueous solution as shown by NMR spectroscopy and ESI mass spectrometry.     

Studies of the biosynthesis of DTX-5a and DTX-5b by the dinoflagellate Prorocentrum maculosum: regiospecificity of the putative Baeyer-Villigerase and insertion of a single amino acid in a polyketide chain

The biosynthetic origins of the diarrhetic shellfish poisoning toxins DTX-5a and DTX-5b have been elucidated by supplementing cultures of the producing organism Prorocentrum maculosum with stable isotope labeled precursors and determining the incorporation patterns by 13C NMR spectroscopy. The amino acid residue in the sulfated side chain is found to originate from glycine, and oxygen insertion in the chain is shown to occur after polyketide formation.     

cis,cis- and trans,trans-ceratospongamide, new bioactive cyclic heptapeptides from the Indonesian red alga Ceratodictyon spongiosum and symbiotic sponge Sigmadocia symbiotica

Chemical investigation of the marine red alga (Rhodophyta) Ceratodictyon spongiosum containing the symbiotic sponge Sigmadocia symbiotica collected from Biaro Island, Indonesia, yielded two isomers of a new and bioactive thiazole-containing cyclic heptapeptide, cis,cis-ceratospongamide (1) and trans, trans-ceratospongamide (2). Isolation of these peptides was assisted by bioassay-guided fractionation using a brine shrimp toxicity assay (Artemia salina). The structures of the ceratospongamides, which each consist of two L-phenylalanine residues, one (L-isoleucine)-L-methyloxazoline residue, one L-proline residue, and one (L-proline)thiazole residue, were established through extensive NMR spectroscopy, including (1)H-(13)C HMQC-TOCSY, and (1)H-(15)N HMBC experiments, as well as chemical degradation and chiral analysis. cis,cis- and trans,trans-ceratospongamide are stable conformational isomers of the two proline amide bonds. Molecular modeling of these two ceratospongamide isomers showed the trans, trans isomer to be quite planar, whereas the cis,cis isomer has a more puckered overall conformation. trans,trans-Ceratospongamide exhibits potent inhibition of sPLA(2) expression in a cell-based model for antiinflammation (ED(50) 32 nM), whereas the cis,cis isomer is inactive. trans,trans-Ceratospongamide was also shown to inhibit the expression of a human-sPLA(2) promoter-based reporter by 90%.     

Molecules with new topologies derived from hydrogen-bonded dimers of tetraurea calix[4]arenes

Tetraurea calix[4]arenes 2 have been synthesized in which two adjacent aryl urea residues are connected to a loop by an aliphatic chain -O-(CH(2))(n)-O-. The remaining urea residues have a bulky 3,5-di-tert-butylphenyl residue and an omega-alkenyloxyphenyl residue. Since this bulky residue cannot pass through the loop, only one homodimer (22) is formed in apolar solvents, for steric reasons, in which the two alkenyl residues penetrate the two macrocyclic loops. Covalent connection of these alkenyl groups by olefin metathesis followed by hydrogenation creates compounds 3, which consist of molecules with hitherto unknown topology. Their molecular structure was confirmed by (1)H NMR spectroscopy and ESIMS, and for one example by single-crystal X-ray analysis.     

Synthesis, characterization and dioxygen reactivity of copper(I) complexes with glycoligands

A new family of copper(I) complexes with "glycoligands" containing a central saccharide scaffold, with 2-picolyl ether groups or 2-picolylamine or N-imidazolylamine groups, has been prepared and characterized. For this purpose, the following tetradentate ligands have been synthesized: methyl 2,3-di-O-(2-picolyl)-alpha-D-lyxofuranoside (L1), 1,5-anhydro-2-deoxy-3,4-di-O-(2-picolyl)-d-galactitol (L2), 5-(amino-N-(2-salicyl))-5-deoxy-1,2-O-isopropylidene-3-O-(2-picolyl)-alpha-D-xylofuranose (L3), and 5-(amino-N-(2-salicyl))-5-deoxy-1,2-O-isopropylidene-3-O-(methylimidazol-2-yl)-alpha-D-xylofuranose (L4). The ligands and the complexes were characterized by elemental analysis, IR, 1H and 13C NMR spectroscopies, ESI mass spectrometry, and cyclic voltammetry. Collaterally with the experimental work, HF-DFT(B3LYP/6-31G*) computations were performed to obtain additional structural information. The Cu(I) complexes are found to be pentacoordinated. The redox properties and the O2-reactivity of the Cu(I)Ln complexes have been studied. Reactions of Cu(I) complexes with dioxygen in ethanol yield stable Cu(II) complexes as confirmed by UV-visible spectrophotometry and EPR spectroscopy.     

An efficient approach for the characterization of mucin-type glycopeptides: the effect of O-glycosylation on the conformation of synthetic mucin peptides

Despite the growing importance of mucin core O-glycosylation in many biological processes including the protection of epithelial cell surfaces, the immune response, cell adhesion, inflammation, and tumorigenesis/metastasis, the regulation mechanism and conformational significance of the multiple introduction of α-GalNAc residues by UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferases (ppGalNAcTs) remains unclear. Here we report an efficient approach by combining MS and NMR spectroscopy that allows for the identification of O-glycosylation site(s) and the effect of O-glycosylation on the peptide backbone structures during enzymatic mucin domain assembly by using an isoform UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase-T2 (ppGalNAcT2) in vitro. An electron-capture dissociation device in a linear radio-frequency quadrupole ion trap (RFQ-ECD) combined with a time-of-flight (TOF) mass spectrometer was employed for the identification of Thr/Ser residues occupied by α-GalNAc branching among multiple and potential O-glycosylation sites in the tandem repeats of human mucin glycoproteins MUC4 (Thr-Ser-Ser-Ala-Ser-Thr-Gly-His-Ala-Thr-Pro-Leu-Pro-Val-Thr-Asp) and MUC5AC (Pro-Thr-Thr-Val-Gly-Ser-Thr-Thr-Val-Gly). In the present study, O-glycosylation was initiated specifically at Thr10 in naked MUC4 peptide and additional introduction of α-GalNAc proceeded preferentially but randomly at three other Thr residues to afford densely glycosylated MUC4 containing six α-GalNAc residues at Thr1, Ser2, Ser5, Thr6, Thr10, and Thr15. On the contrary, O-glycosylation of naked MUC5AC peptide occurred predominantly at consecutive Thr residues and led to MUC5AC with four α-GalNAc residues at Thr2, Thr3, Thr7, and Thr8. The solution structures determined by NMR spectroscopic studies elicited that the preferential introduction of α-GalNAc at Thr10 of MUC4 stabilizes specifically a β-like extended backbone structure at this area, whereas other synthetic models with a single α-GalNAc residue at Thr1, Thr6, or Thr15 did not exhibit any converged three-dimensional structure at the proximal peptide moiety. Such conformational impact on the underlying peptides was proved to be remarkable in the glycosylation at the consecutive Thr residues of MUC5AC.     

Hydrogen-bonding effect on C NMR chemical shifts of amino acid residue carbonyl carbons of some peptides in the crystalline state

¹³C cross polarization-magic angle spinning NMR spectra were measured for a series of peptides containing -valine, -leucine and -aspartic acid residues, for which the crystal structures were already determined by X-ray diffraction, in order to investigate the relationship between hydrogen-bond lengths (R_N…O) and ¹³C chemical shifts of amide carbonyl carbons in the peptides. From these experimental results, it was found that the isotropic ¹³C chemical shifts (δ_iso) of the amino acid residues move linearly downfield with a decrease in R_N…O within the hydrogen-bonded length range considered here and also shown in our previous work on glycine and -alanine residues as expressed by δ_iso(ppm) = a − bR_N…O(Å) where a and b are 215.4 (ppm) and 14.2 (ppm Å⁻¹) for the -valine residue, 202.2 (ppm) and 10.0 (ppm Å⁻¹) for the -leucine residue, and 199.0 (ppm) and 9.6 (ppm Å⁻¹) for the -aspartic acid residue, respectively. Using these relations, the R_N…O values of some polypeptides in the crystalline state were determined through the observation of the amide carbonyl carbon chemical shifts. These values were compared with those determined by the X-ray diffraction method. Furthermore, quantum-chemical calculation of the ¹³C shielding constant for a model compound was carried out by the finite perturbation theory INDO method in order to ascertain the ¹³C shielding behavior in the formation of hydrogen bonds.     

Synthesis and chromatographic study of methyl-2,3-O-isopropylidene-5-dimethyl-arsinoyl-β-d-ribofuranoside and methyl-2,3-O-isopropylidene-5-deoxy-5-dimethyl-thioarsinoyl-β-d-ribofuranoside

The synthesis of two riboside-containing arsenic compounds, methyl-2,3-O-isopropylidene-5-dimethyl-arsinoyl-β-d-ribofuranoside and methyl-2,3-O-isopropylidene-5-deoxy-5-dimethyl-thioarsinoyl-β-d- ribofuranoside is presented in this paper. Intermediates and final products of the synthesis were examined by gas chromatography and thin layer chromatography. The purity of the products was assessed by NMR spectroscopy. Trimethylsilylation was used to volatilise sugar compounds and thus use of the costly HPLC–MS technique was avoided. The results affirmed the presence of tautomers in case of arsenosugars.     

Novel photoswitchable receptors: synthesis and cation-induced self-assembly into dimeric complexes leading to stereospecific [2+2]-photocycloaddition of styryl dyes containing a 15-crown-5 ether unit

Styryl dyes 4a-e containing a 15-crown-5 ether unit and a quinoline residue with a sulfonatoalkyl or sulfonatobenzyl N-substituent were synthesized. The relationship between the photochemical behavior of these dyes and their aggregates derived from complexation with Mg(2+) in MeCN was studied using (1)H NMR and absorption spectroscopy. The E-isomers of 4a-e were shown to form highly stable dimeric (2:2) complexes with Mg(2+). Upon irradiation with visible light, the dimeric complexes undergo two competing photoreactions, viz., geometric E --> Z isomerization, resulting in an anion-capped 1:1 complex of the Z-isomer with Mg(2+) and stereospecific syn-head-to-tail [2+2]-cycloaddition, affording a single isomer of bis-crown-containing cyclobutane. The N-substituent in the dye has a dramatic effect on the photochemical behavior of the dimeric complex. Molecular dynamics and semiempirical quantum-chemical calculations were carried out to interpret the observed photocycloaddition in the dimer. Conformational equilibria for the dimer of (E)-4b were analyzed using (1)H NMR spectroscopy.     

On the effect of covalently appended quinolones on termini of DNA duplexes

Quinolones are gyrase inhibitors that are widely used as antibiotics in the clinic. When covalently attached to oligonucleotides as 5'-acylamido substituents, quinolones were found to stabilize duplexes of oligonucleotides against thermal denaturation. For short duplexes, such as qu-T*GCGCA, where qu is a quinolone residue and T is a 5'-amino-5'-deoxythymidine residue, an increase in the UV melting point of up to 27.8 degrees C was measured. The stabilizing effect was demonstrated for all quinolones tested, namely nalidixic acid, oxolinic acid, pipemidic acid, cinoxacin, norfloxacin, and ofloxacin. The three-dimensional structure of (oa-T*GCGCA)2, where oa is an oxolinic acid residue, was solved by two-dimensional NMR spectroscopy and restrained molecular dynamics. In this complex, the oxolinic acid residues disrupt the terminal T1:A6 base pairs and stack on the G2:C5 base pairs. The displaced adenosine residues bind in the minor groove of the core duplex, while the thymidine residues pack against the oxolinic acid residues. The "molecular cap" thus formed fits tightly on the G:C base pairs, resulting in increased base-pairing fidelity, as demonstrated in UV melting experiments with the sequence oa-T*GGTTGAC and target strands containing a mismatched nucleobase. The structure of the "molecular cap" with its disrupted terminal base pair may also be helpful for modeling how quinolones block re-ligation of DNA strands in the active site of gyrases.     

Simultaneous LC-MS-MS Analysis of Capecitabine and its Metabolites (5′-deoxy-5-fluorocytidine, 5′-deoxy-5-fluorouridine, 5-fluorouracil) After Off-Line SPE from Human Plasma

A new single extraction procedure was developed to isolate capecitabine and its major metabolites (5′-deoxy-5-fluorocytidine, 5′-deoxy-5-fluorouridine, and 5-fluorouracil) from human plasma. The simultaneous extraction of the four analytes was performed on an Atoll XWP solid phase support. Separation and detection were by liquid chromatography (5 µm Atlantis C₁₈, 150 × 2.1 mm) and Turbospray Mass spectrometry in negative mode. To our knowledge, this report is the first to use these conditions for the simultaneous analysis of capecitabine and its metabolites.     

Methyl 5-Deoxy-α and β-D-Xylofuranosides

Abstract

Synthesized from D-xylose, methyl 5-deoxy-α-D-xylofuranoside (1) and methyl 5-deoxy-β-D-xylofuranoside (2) were obtained in overall yields of 24 and 26 %, respectively. The key step in the synthesis was the separation of an anomeric mixture on a strong anion exchanger in OH^? form. NMR data and mass spectra of title compounds 1, 2, methyl 2,3-di-O-acetyl-5-deoxy-α-D-xylofuranoside (3), and methyl 2,3-di-O-acetyl-5-deoxy-β-D-xylofuranoside (4) are discussed. The conformations of 1 and 2 were established from the best fit between calculated and experimental coupling constants using Karplus equation.     

The cyclobutane dimers of 2'-deoxyuridine, 2'-deoxycytidine, 5-methyl-2'-deoxycytidine and 5-bromo-2'-deoxyuridine

Irradiation of DNA and RNA pyrimidine nucleosides with UV light in frozen aqueous solution or in solution with acetone often results in the formation of cyclobutane dimers (CBDs). Many of these photodimers have not been characterized. We present here the results of work designed to achieve the isolation, spectroscopic characterization and determination of the stereochemical nature of a number of little studied or previously unstudied CBDs of four 2'-deoxyribonuclesides. These nucleosides are 2'-deoxyuridine (dUrd), 2'-deoxycytidine (dCyd), 5-methyl-2'-deoxycytidine (5-MedCyd) and 5-bromo-2'-deoxyuridine (5-BrdUrd). In particular, we have isolated and characterized six dUrd CBDs, five dCyd CBDs, five 5-MedCyd CBDs and four 5-BrdUrd CBDs. Photoproducts were studied by UV spectroscopy, mass spectrometry, proton NMR spectroscopy and via chemical approaches. Also presented are results from less definitive studies of a number of (6-4) (or 5-4) photoadducts of these nucleosides. In addition, results from exploratory photochemical studies of other 2'-deoxyribonucleosides in frozen solution, as well as some mixtures of two nucleosides, are given. The latter results indicate that 5-iodo-2'-deoxyuridine (5-IdUrd), 5-bromo-2'-deoxycytidine and 5-iodo-2'-deoxycytidine each form putative CBDs and that 5-BrdUrd is capable of forming putative mixed CBDs and (6-4) and/or (5-4) adducts with thymidine (Thd); 5-IdUrd similarly forms a (6-4) (or (5-4)) adduct with Thd.     

Enzymatic synthesis and the structure elucidation of novel trisaccharides comprised of D-galactose,N-acetyl-D-glucosamine,and D-fructose

Enzymatic synthesis of trisaccharides from N-acetylsucrosamine and lactose utilizing the transgalactosylation activity of Aspergillus oryzae β-galactosidase provided two reaction products. Structure analyses by various 2D NMR spectroscopy and MS indicated that the products were β-D-fructofuranosyl β-D-galactopyranosyl-(1→6)-2-acetamido-2-deoxy-α-D-glucopyranoside and β-D-galactopyranosyl-(1→6)-β-D-fructofuranosyl-(2?1)-2-acetamido-2-deoxy-α-D-glucopyranoside. Moreover, J-resolved-HMBC experiments indicated that the conformations around the glycosidic bonds of these trisaccharides were very similar. Examination about the pH and thermal stabilities of the glycosidic bonds in the GlcNAc–Fru moiety of the two trisaccharides indicated apparent difference.     

An analysis of the interactions between the Sem-5 SH3 domain and its ligands using molecular dynamics, free energy calculations, and sequence analysis.

The Src-homology-3 (SH3) domain of the Caenorhabditis elegans protein Sem-5 binds proline-rich sequences. It is reported that the SH3 domains broadly accept amide N-substituted residues instead of only recognizing prolines on the basis of side chain shape or rigidity. We have studied the interactions between Sem-5 and its ligands using molecular dynamics (MD), free energy calculations, and sequence analysis. Relative binding free energies, estimated by a method called MM/PBSA, between different substitutions at sites -1, 0, and +2 of the peptide are consistent with the experimental data. A new method to calculate atomic partial charges, AM1-BCC method, is also used in the binding free energy calculations for different N-substitutions at site -1. The results are very similar to those obtained from widely used RESP charges in the AMBER force field. AM1-BCC charges can be calculated more rapidly for any organic molecule than can the RESP charges. Therefore, their use can enable a broader and more efficient application of the MM/PBSA method in drug design. Examination of each component of the free energy leads to the construction of van der Waals interaction energy profiles for each ligand as well as for wild-type and mutant Sem-5 proteins. The profiles and free energy calculations indicate that the van der Waals interactions between the ligands and the receptor determine whether an N- or a Calpha-substituted residue is favored at each site. A VC value (defined as a product of the conservation percentage of each residue and its van der Waals interaction energy with the ligand) is used to identify several residues on the receptor that are critical for specificity and binding affinity. This VC value may have a potential use in identifying crucial residues for any ligand-protein or protein-protein system. Mutations at two of those crucial residues, N190 and N206, are examined. One mutation, N190I, is predicted to reduce the selectivity of the N-substituted residue at site -1 of the ligand and is shown to bind similarly with N- and Calpha-substituted residues at that site.