The structure of the aglycon of eremomycin--a new antibiotic of the polycyclic glycopeptide group

Eremomycin is shown to be a new representative of the group of polycyclic glycopeptides. By the amino acid composition it is close to vancomycin but by the structure of triphenoxytriaminotricarboxylic acid it differs from vancomycin. Monodechlorovancomycinic acid was detected in eremomycin. On the basis of the data obtained in studies on the amino acid sequence and the molecule functional groups the structural formula of eremomycin aglycon was assigned. It is demonstrated that the chlorine-containing phenylserine fragment of monodechlorovancomycin acid is located in the N-end region of the aglycon peptide chain.     

Isolation and study of the physicochemical properties of the partial acid hydrolysis products of the aglycone actinoidin]

Two new fragments, i.e. products I and II were found in the process of studying the products of acid hydrolysis of actinoidin aglycone. Both compounds were isolated in the form of homogenous preparations by the method of ion exchange chromatography on cellulose KM. Their physico-chemical properties and element composition were studied. It was found that product I was phenylalanine dipeptide (Phe) and oxyaromatic triamiotricarboxylic compound (Y) not described earlier, while product II was tripeptide including diaminodicarboxylic actinoidinic amino acid (B) in addition to phenylalanine and fragment Y.     

Triaminotricarboxylic amino acid oxidation productions of actinoidin and ristomycin]

Aromatic acids with three benzene nuclei bound through oxygen were obtained from actinoidin and ristomycin on their oxydation with permanganates of methylated aglycones and peptides. The structures of the methyl esters of these acids were determined by spectral methods. They are the following: methyl-3,5-bis-(4-methoxycarbonyl-phenoxy)-4-methoxybenzoate (from ristomycin) and methyl-3-(2-chlor-4-methoxycarbonyl-phenoxy)-5-(4-methoxycarbonyl-phenoxy)-4-methoxybenzoate (from actinoidin). The compounds are the aromatic parts of the molecules of the unusual triaminotricarboxylic amino acids present in the aglycones of all antibiotics of the group of polycyclic glycopeptides.     

Solution structure of the nogalamycin-DNA complex

The nogalamycin-d(A-G-C-A-T-G-C-T) complex (two drugs per duplex) has been generated in aqueous solution and its structure characterized by a combined application of two-dimensional NMR experiments and molecular dynamics calculations. Two equivalents of nogalamycin binds to the self-complementary octanucleotide duplex with retention of 2-fold symmetry in solution. We have assigned the proton resonances of nogalamycin and the d(A1-G2-C3-A4-T5-G6-C7-T8) duplex in the complex and identified the intermolecular proton-proton NOEs that define the alignment of the antitumor agent at its binding site on duplex DNA. The analysis was greatly aided by a large number of intermolecular NOEs involving exchangeable protons on both the nogalamycin and the DNA in the complex. The molecular dynamics calculations were guided by 274 intramolecular nucleic acid distance constraints, 90 intramolecular nogalamycin distance constraints, and 104 intermolecular distance constraints between nogalamycin and the nucleic acid protons in the complex. The aglycon chromophore intercalates at (C-A).(T-G) steps with the long axis of the aglycon approximately perpendicular to the long axis of the flanking C3.G6 and A4.T5 base pairs. The aglycon selectively stacks over T5 and G6 on the T5-G6-containing strand with the aglycon edge containing OH-4 and OH-6 substituents directed toward the C3-A4-containing strand. The C3.G6 and A4.T5 base pairs are intact but buckled at the intercalation site with a wedge-shaped alignment of C3 and A4 on the C3-A4 strand compared to the parallel alignment of T5 and G6 on the T5-G6 strand in the complex. The nogalose sugar in a chair conformation, the aglycon ring A in a half-chair conformation, and the COOCH3-10 side chain form a continuous domain that is sandwiched within the walls of the minor groove and spans the three base pair (G2-C3-A4).(T5-G6-C7) segment. The nogalose ring is positioned in the minor groove such that its nonpolar face is directed toward the G6-C7 sugar-phosphate backbone while its polar face containing OCH3 groups is directed toward the G2-C3 sugar-phosphate backbone in the complex. The intermolecular contacts include a nonpolar patch of aglycon (CH3-9) and nogalose (CH3-3') methyl groups forming van der Waals contacts with the base-sugar residues in the minor groove and intermolecular hydrogen bonds involving the amino groups of G2 and G6 with the ether oxygens OCH3-3' and O7, respectively, on the nogalose sugar.(ABSTRACT TRUNCATED AT 400 WORDS)     

Arabinoamidine synthesis and its inhibition toward β-glucosidase (sweet almonds) in comparison to a library of galactonoamidines

Aiming at the development of potent inhibitors of β-glucosidases, a small library of galactonoamidines and one arabinoamidine derived in analogy were studied as inhibitors of sweet almond β-glucosidase. The five-membered glycon in arabinoamidine was shown to interact with the proton donor in the active site of the retaining enzyme, but not with the nucleophile. By contrast, the corresponding galactonoamidine with a six-membered glycon and identical aglycon interacts with both hydrolysis-promoting amino acids in the active site and inhibits the enzymatic hydrolysis of β-glucosides in the low nanomolar concentration range. While both inhibitors are competitive, their inhibition ability is more than 37,000-fold different.     

Mutagenesis and subsite mapping underpin the importance for substrate specificity of the aglycon subsites of glycoside hydrolase family 11 xylanases

Glycoside hydrolase family (GH) 11 xylanase A from Bacillus subtilis (BsXynA) was subjected to site-directed mutagenesis to probe the role of aglycon active site residues with regard to activity, binding of decorated substrates and hydrolysis product profile. Targets were those amino acids identified to be important by 3D structure analysis of BsXynA in complex with substrate bound in the glycon subsites and the + 1 aglycon subsite. Several aromatic residues in the aglycon subsites that make strong substrate–protein interactions and that are indispensable for enzyme activity, were also important for the specificity of the xylanase. In the + 2 subsite of BsXynA, Tyr65 and Trp129 were identified as residues that are involved in the binding of decorated substrates. Most interestingly, replacement of Tyr88 by Ala in the + 3 subsite created an enzyme able to produce a wider variety of hydrolysis products than wild type BsXynA. The contribution of the + 3 subsite to the substrate specificity of BsXynA was established more in detail by mapping the enzyme binding site of the wild type xylanase and mutant Y88A with labelled xylo-oligosaccharides. Also, the length of the cord – a long loop flanking the aglycon subsites of GH11 xylanases – proved to impact the hydrolytic action of BsXynA. The aglycon side of the active site cleft of BsXynA, therefore, offers great potential for engineering and design of xylanases with a desired specificity.     

Differences in active site structure in a family of beta-glucan endohydrolases deduced from the kinetics of inactivation by epoxyalkyl beta-oligoglucosides

The active sites of a spectrum of beta-glucan endohydrolases with distinct, but related substrate specificities have been probed using a series of epoxyalkyl beta-glycosides of glucose, cellobiose, cellotriose, laminaribiose, laminaritriose, 3O-beta-D-glucosyl-cellobiose and 4O-beta-D-glucosyl-laminaribiose with different aglycon chain lengths. The inactivation of each of the endohydrolases by these compounds results from active site-directed inhibitor action, as indicated by the dependence of the inactivation rate on pH, glycosyl chain length and linkage position, aglycon length, and the protective effect of disaccharides derived from the natural substrates. Comparisons of inhibitor specificity between a Bacillus subtilis 1,3;1,4-beta-D-glucan 4-glucanohydrolase (EC 3.2.1.73), a Streptomyces cellulase (EC 3.2.1.4), a Schizophyllum commune cellulase (EC 3.2.1.4), a Rhizopus arrhizus 1,3-(1,3;1,4)-beta-D-glucan 3(4)-glucanohydrolase (EC 3.2.1.6), and a Nicotiana glutinosa 1,3-beta-D-glucan 3-glucanohydrolase (EC 3.2.1.39) demonstrated different tolerances for glycosyl linkage positions in the inactivation process and a critical role of aglycon length reflecting differences in the active site geometry of the enzymes. For the B. subtilis endohydrolase it was concluded that the aglycon residue of the inhibitor spans the glycosyl binding subsite occupied by the 3-substituted glucosyl residue involved in the glucosidic linkage cleaved in the natural substrate. Appropriate positioning of the inhibitor epoxide group with respect to the catalytic amino acids in the active site is crucial to the inactivation step and the number of glucosyl residues in the inhibitor affects aglycon chain length specificity. The importance of this effect differs between the glucanases tested and may be related to the number of glycosyl binding subsites in the active site.     

Structural basis of anthracycline selectivity for unilamellar phosphatidylcholine vesicles: an equilibrium binding study

Fluorescence anisotropy titration was used to determine the equilibrium binding affinities of several anthracycline antitumor antibiotics for sonicated dimyristoylphosphatidylcholine (DMPC) and dipalmitoylphosphatidylcholine (DPPC) vesicles at 27.5 degrees C. Eight daunomycin analogues, all differing from the parent by one structural change in the aglycon portion of the molecule, as well as four anthracycline congeners modified in the amino sugar were studied. Double-reciprocal plots were used to determine overall binding affinities (K). It was shown that structural changes in both the aglycon and amino sugar portions of the daunomycin molecule strongly modulated K values for DMPC and DPPC bilayers. For modifications in the aglycon portion of an anthracycline, a correlation between drug hydrophobicity and membrane affinity was observed. The number of binding sites per phospholipid molecule (n) and the apparent association constant (Kapp) where K = nKapp, were determined at several temperatures for adriamycin, daunomycin, and carminomycin. The n values were found to be independent of temperature for fluid-phase DMPC or solid-phase DPPC bilayers. The Kapp values (25 degrees C) ranged from (0.82-4.4) X 10(5) M-1 for DMPC vesicles to (4.4-7.3) X 10(5) M-1 for DPPC vesicles. Although the Kapp values for the three drugs were similar for a particular bilayer, major differences were noted in the values of n and, therefore, in the overall vesicle affinities (nKapp). van't Hoff plots showed that anthracycline binding was exothermic; in all cases but one binding was accompanied by a decrease in entropy.(ABSTRACT TRUNCATED AT 250 WORDS)     

Two human liver cDNAs encode UDP-glucuronosyltransferases with 2 log differences in activity toward parallel substrates including hyodeoxycholic acid and certain estrogen derivatives.

Two human liver UDP-glucuronosyltransferase cDNA clones, HLUG25 [Jackson, M. R., et al. (1987) Biochem. J. 242, 581-588] and UDPGTh-2 [Ritter, J. K., et al. (1990) J. Biol. Chem. 266, 7900-7906] have previously been shown to encode isozymes active in the glucuronidation of hyodeoxycholic acid (HDCA) and certain estrogen derivatives (estriols and 3,4-catechol estrogens), respectively. Here we report that the UDPGTh-2-encoded isoform (udpgth-2) and the HLUG25-encoded isoform (udpgth-1) have parallel aglycon specificities. Following expression in COS-1 cells, each isoform metabolized three types of dihydroxy- or trihydroxy-substituted ring structures, including the 3,4-catechol estrogen (4-hydroxyestrone), estriol and 17-epiestriol, and HDCA, but the udpgth-2 isozyme is 100-fold more efficient than udpgth-1. udpgth-1 and udpgth-2 are 86% identical overall (76 differences out of 528 amino acids), including 55 differences in the first 300 amino acids of the amino terminus, a domain which confers isoform substrate specificity. The data indicate that a high level of conservation in the amino terminus is not required for the preservation of substrate selectivity. Analysis of glucuronidation activity encoded by UDPGTh-1/UDPGTh-2 chimeric cDNAs constructed at their common restriction sites, SacI (codon 297), NcoI (codon 385), and HhaI (codon 469), showed that nine amino acids between residues 385 and 469 are important for catalytic efficiency, suggesting that this region represents a domain which is critical for catalysis but distinct from that responsible for aglycon selection.(ABSTRACT TRUNCATED AT 250 WORDS)     

The acid hydrolysis of alkyl β-D-galactopyranosides

Twenty-one alkyl β-D-galactopyranosides were synthesised and hydrolysed in hydrochloric acid. Application of the Hammett-Zucker criterion indicates a unimolecular (A-1) mechanism. The activation parameters indicate an isoenthalpic reaction series. Galactosides having secondary-alkyl aglycon groups belong to the same series, but the rate of hydrolysis is slightly increased by the entropy factor. The influence of the aglycon group can be correlated with the Robinson-Matheson Φ parameter.     

Studies on vaccines against cholera. Synthesis of neoglycoconjugates from the hexasaccharide determinant of Vibrio cholerae O:1, serotype Ogawa, by single-point attachment or by attachment of the hapten in the form of clusters

The terminal hexasaccharide of the O-antigen of Vibrio cholerae O:1, serotype Ogawa, has been synthesized in the form of a glycoside whose aglycon (linker) allows conjugation to carrier proteins by reductive amination. The conjugate obtained from direct, single-point attachment of the linker-equipped hapten to chicken serum albumin (CSA) contained seven hapten residues/CSA. A neoglycoconjugate containing the carbohydrate antigen in the form of clusters was obtained using, as a hapten subcarrier, an oligopeptide containing 16 amino groups. It was treated with a limited amount of hapten, to give a hapten-carrying subcarrier (HCS). Subsequent conjugation of HCS to CSA, using squaric acid diethyl ester as a conjugation reagent, gave a cross-linked, glycocluster conjugate containing 51% (w/w) of the carbohydrate.     

DEPBT as an efficient coupling reagent for amide bond formation with remarkable resistance to racemization

3-(Diethoxyphosphoryloxy)-1, 2, 3-benzotriazin-4(3H)-one (DEPBT) is an effective coupling reagent for synthesis of linear and cyclic peptides by both solution and solid-phase peptide synthesis. DEPBT mediates amide bond formation with remarkable resistance to racemization. When DEPBT is used as a coupling reagent, it is not necessary to protect the hydroxy group of the amino component (such as tyrosine, serine, and threonine) and the imidazole group in the case of histidine. The high efficiency of DEPBT and its utility have been demonstrated in the syntheses of complex natural products such as ramoplanin A2, ramoplanose aglycon, ustiloxin, and teicoplanin aglycon.     

Genes and enzymes involved in caffeic acid biosynthesis in the actinomycete Saccharothrix espanaensis

The saccharomicins A and B, produced by the actinomycete Saccharothrix espanaensis, are oligosaccharide antibiotics. They consist of 17 monosaccharide units and the unique aglycon N-(m,p-dihydroxycinnamoyl)taurine. To investigate candidate genes responsible for the formation of trans-m,p-dihydroxycinnamic acid (caffeic acid) as part of the saccharomicin aglycon, gene expression experiments were carried out in Streptomyces fradiae XKS. It is shown that the biosynthetic pathway for trans-caffeic acid proceeds from L-tyrosine via trans-p-coumaric acid directly to trans-caffeic acid, since heterologous expression of sam8, encoding a tyrosine ammonia-lyase, led to the production of trans-p-hydroxycinnamic acid (coumaric acid), and coexpression of sam8 and sam5, the latter encoding a 4-coumarate 3-hydroxylase, led to the production of trans-m,p-dihydroxycinnamic acid. This is not in accordance with the general phenylpropanoid pathway in plants, where trans-p-coumaric acid is first activated before the 3-hydroxylation of its ring takes place.     

Phylogenetic Analysis of Antibiotic Glycosyltransferases

Catalyzed by a family of enzymes called glycosyltransferases, glycosylation reactions are essential for the bioactivities of secondary metabolites such as antibiotics. Due to the special characters of antibiotic glycosyltransferases (AGts), antibiotics can function by attaching some unusual deoxy-sugars to their aglycons. Comprehensive similarity searches on the amino acid sequences of AGts have been performed. We reconstructed the molecular phylogeny of AGts with neighbor-joining, maximum-likelihood, and Bayesian methods of phylogenetic inference. The phylogenetic trees show a distinct separation of polyene macrolide (PEM) AGts and other polyketide AGts. The former are more like eukaryotic glycosyltransferases and were deduced to be the results of horizontal gene transfer from eukaryotes. Protein tertiary structural comparison also indicated that some glycopeptide AGts (Gtf-proteins) have a close evolutionary relationship with MurGs, essential glycosyltransferases involved in maturation of bacterial cell walls. The evolutionary relationship of glycopeptide antibiotic biosynthetic gene clusters was speculated according to the phylogenetic analysis of Gtf-proteins. Considering the fact that polyketide AGts and Gtf-proteins are all GT Family 1 members and their aglycon acceptor biosynthetic patterns are very similar, we deduced that AGts and the synthases of their aglycon acceptors have some evolutionary relevance. Finally, the evolutionary origins of AGts that do not fall into GT Family 1 are discussed, suggesting that their ancestral proteins appear to be derived from various proteins responsible for primary metabolism. [Reviewing Editor: Dr. Niles Lehman]     

The acid-catalyzed hydrolysis of β-d-xylofuranosides

The rate constants for the hydrolysis of six alkyl and four aryl β-d-xylofuranosides in aqueous perchloric acid at various temperatures have been measured. The effects of varying the aglycon structure on the hydrolysis rate are interpreted in terms of two concurrent reactions. Either, the substrate, protonated on the glycosidic oxygen atom, undergoes a rate-limiting heterolysis to form a cyclic oxocarbonium ion, or, an initial rapid protonation of the ring oxygen is followed by a unimolecular cleavage of the five-membered ring, all subsequent reactions being fast. It is suggested that xylofuranosides having strongly electron-attracting aglycon groups react mainly by the former pathway, whereas the latter is more favourable for substrates having electron-repelling aglycon groups. The negative entropies of activation obtained with the latter compounds are attributed to the rate-limiting opening of the five-membered ring. The rate variations of the hydrolyses of alkyl β-d-xylofuranosides in aqueous perchloric acid-methyl sulfoxide mixtures are interpreted as lending further support for the suggested chance in mechanism.     

Detection and structural characterization of amino polyaromatic hydrocarbon-deoxynucleoside adducts using fast atom bombardment and tandem mass spectrometry

Fast atom bombardment (FAB) and tandem mass spectrometry (MS/MS) are shown to be useful methods for the detection and structural characterization of nanogram amounts of amino polyaromatic hydrocarbon-nucleoside DNA adducts. The positive ion spectra of four aromatic amine guanosine adducts were studied in detail. The FAB spectra of these adducts exhibit an [MH]+ ion and a more abundant aglycon fragment ion, [AH2]+, which results from the loss of the deoxyribose sugar. The sensitivity of the adducts to FAB was enhanced by preparing trimethylsilyl (TMS) ether derivatives. High-quality full-scan spectra could be obtained on less than 70 ng of the derivatized adducts without signal averaging. With a B/E-linked scan of the [MH]+ ion for the TMS2 species, these same adducts could be detected by examination of their metastable ion spectra at levels as low as 4-5 ng (S/N greater than 10). Collision-induced dissociation (CID) of the [MH]+ ion yields the aglycon fragment and an ion, S1, which results from cleavage through the sugar. The CID spectrum of the aglycon [AH2]+ ion is much more useful, providing structural information relating to the base, the polyaromatic hydrocarbon, and, possibly, the site of covalent attachment. Differentiation of isomeric aminophenanthrene-guanine adducts was demonstrated on the basis of the CID spectra of their respective [AH2]+ ions. The use of TMS derivatives also improves the sensitivity of these methods.     

Characterization of an antifungal glycolipid secreted by the yeast Sympodiomycopsis paphiopedili

An antifungal glycolipid was purified from the culture liquid of the ustilaginomycetous yeast Sympodiomycopsis paphiopedili by column and thin-layer chromatography. According to nuclear magnetic resonance and mass-spectroscopy experiments it was a cellobioside containing 2,15,16-trihydroxypalmitic acid as an aglycon. The minimal effective concentrations leading to ATP leakage and growth inhibition were 45 and 160 microg ml(-1) for Cryptococcus terreus and Candida albicans, respectively.     

Synthesis and evaluation of vancomycin and vancomycin aglycon analogues that bear modifications in the residue 3 asparagine

The synthesis and biological evaluation of a set of residue 3 analogues of vancomycin and its aglycon are described. These investigations follow from the promising biological activity of a protected and synthetically modified vancomycin aglycon analogue in which the asparagine side chain was modified to possess a nitrile, rather than a carboxamide. Although this modification typically was detrimental to antimicrobial activity, hydrophobic vancomycin aglycon analogues that lack a lipid anchor as well as the disaccharide are detailed that exhibit unusual potency against VanB, but not VanA, resistant bacteria.     

Aglycon specificity profiling of alpha-glucosidases using synthetic probes

We designed and synthesized hydrogen bond based probes 1-8 with the exception of known glycosidase inhibition mechanisms, and aglycon specificity of 11 different sources of alpha-glucosidases were investigated using their probes. Probe 4 (2,6-anhydro-1-deoxy-1-[(1-oxopentyl-5-hydroxy)amino]-D-glycero-D-ido-heptitol) showed a potent inhibition of S. cerevisiae alpha-glucosidase among all alpha-glucosidases. Probe 4 was found to be a competitive inhibitor for S. cerevisiae alpha-glucosidase with Ki 0.13 mM.     

Synthesis and properties of 2,3,4,6-tetra-O-benzyl-1-O-(N-benzyloxycarbonyldipeptidyl)-α- and -β-D-glucopyranoses and 1-O-dipeptidyl-D-glucopyranoses. Piperazinedione formation from 1-O-dipeptidyl-D-glucopyranoses by intramolecular aminolysis

2,3,4,6-Tetra-O-benzyl-1-O-(N-benzyloxycarbonyldipeptidyl)-D-glucopyranoses (1–5) were synthesized from 2,3,4,6-tetra-O-benzyl-α-D-glucopyranose and pentachlorophenyl esters of N-benzyloxycarbonyldipeptides in the presence of imidazole; the anomeric mixtures were resolved and the α and β anomers were characterized. Catalytic hydrogenation of the β anomers of 1–3, having aglycon groups containing aliphatic amino acid residues, afforded the corresponding 1-O-dipeptidyl-β-D-glucopyranoses, which were characterized as the mono-oxalates 6–8; 6 and 7 were converted into the N-acetyl derivatives 9 and 10, which were also prepared by definitive methods. Hydrogenolysis of the β anomers of 4 and 5, having aglycon groups containing Phe-Gly and Gly-Phe residues, led to intramolecular aminolysis with scission of the glycosidic ester bond to give 3-benzylpiperazine-2,5-dione and D-glucose. Selective N-deprotection of 5β afforded 2,3,4,6-tetra-O-benzyl-1-O-(glycyl-DL-phenylalanyl)-β-D-glucopyranose (13β), and complete deprotection of 5α gave 1-O-(glycyl-DL-phenylalanyl)-α-D-glucopyranose (14) as the preponderant products; in both cases, intramolecular cyclisation of the aglycon group was a minor reaction. The results suggest that the balance between the formation of free D-glucosyl ester and the respective piperazinedione derivative depends primarily upon the nature and the sequence of the amino acids involved, and to a lesser extent upon the nature of substituents and the anomeric configuration of the sugar component.