Selective removal of the 2'- and 3'-O-acyl groups from 2',3',5'-tri-O-acylribonucleoside derivatives with lithium trifluoroethoxide

Selective cleavage of O2' and O3' ester groups from ribonucleoside derivatives has been accomplished with Dowex 1 x 2 (CF3CH2O-) in 2,2,2-trifluoroethanol (TFE) or lithium trifluoroethoxide/TFE. Deacylations with Li+ -OCH2CF3/TFE proceed at ambient temperature (or with mild heating) to give the 5'-O-acyl derivatives in superior yields and higher purity than prior approaches for selective O2' and O3' ester deprotection.     

Superarming the S-benzoxazolyl glycosyl donors by simple 2-O-benzoyl-3,4,6-tri-O-benzyl protection

The strategic placement of common protecting groups led to the discovery of a new method for "superarming" glycosyl donors. Conceptualized from our previous studies on the O-2/O-5 Cooperative Effect, it was determined that S-benzoxazolyl glycosyl donors possessing both a participating moiety at C-2 and an electronically armed lone pair at O-5, such as the superarmed glycosyl donor shown above, were exceptionally reactive.     

Promoting vibrations in human purine nucleoside phosphorylase. A molecular dynamics and hybrid quantum mechanical/molecular mechanical study

Crystallographic studies of human purine nucleoside phosphorylase (hPNP) with several transition-state (TS) analogues in the immucillin family showed an unusual geometric arrangement of the atoms O-5', O-4', and O(P), the nucleophilic phosphate oxygen, lying in a close three-oxygen stack. These observations were corroborated by extensive experimental kinetic isotope effect analysis. We propose that protein-facilitated dynamic modes in hPNP cause this stack, centered on the ribosyl O-4' oxygen, to squeeze together and push electrons toward the purine ring, stabilizing the oxacarbenium character of the TS. As the N-ribosidic bond is cleaved during the reaction, the pK(a) values of N-7 and O-6 increase by the electron density expelled by the oxygen-stack compression toward the purine ring. Increased electron density in the purine ring improves electrostatic interactions with nearby residues and facilitates the abstraction of a proton from a solvent proton or an unidentified general acid, making the purine a better leaving group, and accelerating catalysis. Classical and mixed quantum/classical molecular dynamics (MD) simulations of the Michaelis complex of hPNP with the substrates guanosine and phosphate were performed to assess the existence of protein-promoting vibrations (PPVs). Analogous simulations were performed for the substrates in aqueous solution. In the catalytic site, the O-5', O-4', and O(P) oxygens vibrate at frequencies of ca. 125 and 465 cm(-1), as opposed to 285 cm(-1) in the absence of hPNP. The hybrid quantum mechanical/molecular mechanical method was used to assess whether this enzymatic vibration pushing the oxygens together is coupled to the reaction coordinate, and thus has a direct positive impact on catalysis. The potential energy surface for the phosphorolysis reaction for several snapshots taken from the classical MD simulation showed substantial differences in oxygen compression. Our calculations showed the existence of PPVs coupled to the reaction coordinate, which effect electronic alterations in the active site by pushing the three oxygen centers together in proximity, and accelerate substrate turnover in the phosphorolysis reaction catalyzed by hPNP.     

MicroRNA sequence motifs reveal asymmetry between the stem arms

The processing of micro RNAs (miRNAs) from their stemloop precursor have revealed asymmetry in the processing of the mature and its star sequence. Furthermore, the miRNA processing system between organism differ. To assess this at the sequence level we have investigated mature miRNAs in their genomic contexts. We have compared profiles of mature miRNAs within their genomic context of the 5' and 3' stemloop precursor arms and we find asymmetry between mature sequences of the 5' and 3' stemloop precursor arms. The main observation is that vertebrate organisms have a characteristic motif on the 5' arm which is in contrast to the 3' arm motif which mainly show the conserved U at the position of the mature start. Also the vertebrate 5' arm motif show a semi-conserved G 13 nucleotides upstream from the first position. We compared the 5' and 3' arm profiles using the average log likelihood ratio (ALLR) score, as defined by Wang and Stormo (2003) [Wang T., Stormo, G.D., 2003. Combining phylogenetic data with co-regulated genes to identify regulatory motifs. Bioinformatics 2369-2380.] and computing a p-value we find that the two profiles differs significantly in their 3' end where the 5' arm motif (in contrast to the 3' arm motif) has a semi-conserved GU rich region. Similar findings are also obtained for other organisms, such as fly, worm and plants. The observed similarities and differences between closely and distantly related organisms are discussed and related to current knowledge of miRNA processing.     

Site specificity of metal ions in heterodinuclear complexes derived from an "end-off" compartmental ligand

A phenol-based "end-off" compartmental ligand, 2-[N-[2-(dimethylamino)ethyl]iminomethyl]-6-[N,N-di(2-pyridylmethyl)aminomethyl]-4-methylphenol (HL), having a bidentate arm and a tridentate arm attached to the 2 and 6 positions of the phenolic ring, has afforded the following heterodinuclear M(a)(II)M(b)(II) complexes: [CuM(L)(AcO)(2)]ClO(4) (M = Mn (1), Fe (2), Co (3), Ni (4), Zn (5)), [ZnM(L)(AcO)(2)]ClO(4) (M = Co (6), Ni (7)), and [CuNi(L)(AcO)(NCS)(2)] (8). 1.MeOH (1'), 2.MeOH (2'), 3.MeOH (3'), 4.MeOH (4'), 5.MeOH (5'), and 7.MeOH (7') are isostructural and have a heterodinuclear core bridged by the phenolic oxygen atom of L(-) and two acetate groups. In 1'-5' the Cu(II) is bound to the bidentate arm and has a square-pyramidal geometry with one acetate oxygen at the apical site. The M(II) is bound to the tridentate arm and has a six-coordinate geometry together with two acetate oxygen atoms. In the case of 7' the Zn is bound to the bidentate arm and the Ni is bound to the tridentate arm. 8.2-PrOH (8') has a dinuclear core bridged by the phenolic oxygen atom of L(-) and one acetate group. The Cu bound to the bidentate arm has a square-pyramidal geometry with an isothiocyanate group at the apical site. The Ni bound to the tridentate arm has a six-coordinate geometry with further coordination of an isothiocyanate group. The site specificity of the metal ions is discussed together with the crystal structure of [Cu(4)(L)(2)(AcO)(3)](ClO(4))(3).H(2)O (9) prepared in this work.     

Three new flavonoid glycosides, byzantionoside B 6'-O-sulfate and xyloglucoside of (Z)-hex-3-en-1-ol from Ruellia patula

Three new flavonoid glycosides, demethoxycentaureidin 7-O-β-D-galacturonopyranoside, pectolinarigenin 7-O-α-L-rhamnopyranosyl-(1?→4″)-β-D-glucopyranoside and 7-O-α-L-rhamnopyranosyl-(1?→4″)-β-D-glucuronopyranoside, a new megastigmane glucoside, byzantionoside B 6'-O-sulfate, and a new (Z)-hex-3-en-1-ol O-β-D-xylopyranosyl-(1″→2')-β-D-glucopyranoside, were isolated from leaves of Ruellia patula JACQ., together with 12 known compounds, β-sitosterol glucoside, vanilloside, bioside (decaffeoyl verbascoside), acteoside (verbascoside), syringin, benzyl alcohol O-β-D-xylopyranosyl-(1″→2')-β-D-glucopyranoside, cistanoside E, roseoside, phenethyl alcohol O-β-D-xylopyranosyl-(1″→2')-β-D-glucopyranoside, (+)-lyoniresinol 3α-O-β-D-glucopyranoside, isoacteoside and 3,4,5-trimethoxyphenol O-α-L-rhamnopyranosyl-(1″→6')-β-D-glucopyranoside. Their structures were elucidated by means of spectroscopic analyses.     

2-芳胺基-5-[5’-氨基-1’-(4”-氯苯基)-1’,2’,3’-三唑-4’-基]——1,3,4-噁二唑的合成

利用1-[5’-氨基-1’-(4”-氯苯基)-1’,2’,3’-三唑-4’-甲酰基]-4-芳基氨基硫脲在汞盐Hg(OAc)_2-HOAc中加热缩合,制得11种新的2-芳胺基-5-[5’-氨基-1’-(4”-氯苯基)-1’,2’,3’-三唑-4’-基]-1,3,4-噁二唑。所有化合物的结构经元素分析,IR、MS以及~1HNMR确认。选择代表物作生测试验,结果表明,2b,2k在MIC3.1mg/L时,对大肠杆菌及金黄色葡萄球菌繁殖有明显抑制。     

Studies on macrolide antibiotics I. Synthesis and antibacterial activity of erythromycin A 9-O-substituted oxime ether derivatives against Mycobacterium avium complex

A series of erythromycin A 9-O-substituted oxime ether derivatives have been synthesized and evaluated for antibacterial activity against Mycobacterium avium complex (MAC) and Staphylococcus aureus. These compounds possessed stronger in vitro activity against MAC including macrolide-resistant strains than clarithromycin (2), although in vitro antibacterial activities of these compounds were less than that of 2 against Staphylococcus aureus. Our studies found that several factors contribute to the antibacterial activity against MAC. The length and spatial orientation of the substituent at 9-position were found to significantly influenced the anti-MAC activity, especially against macrolide-resistant strains. Of all the compounds prepared, erythromycin A 9-[O-(4-phenylbutyl)oxime] (12q) and erythromycin A 9-[O-(3-phenoxypropyl)oxime] (12t) possessed 16 times stronger antibacterial activity than 2 against clarithromycin-resistant strains. Surprisingly, the minimum inhibitory concentrations (MICs) of 12q and 12t against the resistant strains were almost same as those against the susceptible strains. These results suggest that the erythromycin A 9-O-substituted oxime ether derivatives would be promising macrolide antibiotics.     

Elucidation of the molecular structure of lipid A isolated from both a rough mutant and a wild strain of Aeromonas salmonicida lipopolysaccharides using electrospray ionization quadrupole time-of-flight tandem mass spectrometry

The chemical structure of lipid A, isolated by mild acid hydrolysis from a rough mutant and a wild strain of Aeromonas salmonicida lipopolysaccharide, was investigated using electrospray ionization quadrupole time-of-flight (QqToF) hybrid tandem mass spectrometry and showed a great degree of microheterogeneity. The chemical structure of the main constituent of this heterogeneous mixture was identified as a beta-D-(1 --> 6) linked D-glucosamine disaccharide substituted by two phosphate groups, one being bound to the non-reducing end at position O-4' and the other to the position O-1 of the reducing end of the D-glucosamine disaccharide. The location of the fatty acids linked to the disaccharide backbone was established by identifying diagnostic ions in the conventional QqToF-MS scan. Low-energy collision tandem mass spectrometry analysis of the selected precursor diagnostic ions confirmed, unambiguously, their proposed molecular structures. We have established that myristyloxylauric (C14:0(3-O(12:0))) acid residues were both N-2' and O-3' linked to the non-reducing end of the D-GlcN residue, and that two 3-hydroxymyristic (C14:0(3-OH)) acid chains acylated the remaining positions of the reducing end. The MS and MS/MS data obtained allowed us to determine the complex molecular structure of lipid A. The QqToF-MS/MS instrument has shown excellent superiority over a conventional quadrupole-hexapole-quadrupole tandem instrument which failed to fragment the selected precursor ion.     

Synthesis and biological properties of conjugates between fluoroquinolones and a N3'-functionalized pyochelin

Pyochelin is a siderophore common to Pseudomonas aeruginosa and several other pathogenic bacteria. A pyochelin functionalized at the N3' position with a propyl-amine extension was previously synthesized. In the present work we proved that this analog binds FptA, the pyochelin outer membrane receptor, and transports iron(III) efficiently into bacteria. This functionalized pyochelin seemed to be a good candidate for antibiotic vectorization in the framework of a Trojan horse prodrug strategy. In this context, conjugates between pyochelin and three fluoroquinolones (norfloxacin, ciprofloxacin and N-desmethyl-ofloxacin) were synthesized with a spacer arm that was either stable or hydrolyzable in vivo. Some pyochelin-fluoroquinolone conjugates had antibacterial activities in growth inhibition experiments on several P. aeruginosa strains. However, these activities were weaker than those of the antibiotic alone. These properties appeared to be related to both the solubility and bioavailability of conjugates and to the stability of the spacer arm used.     

Synthesis of dinucleoside (N3'-->MeP5') methanephosphonamidates

[structure: see text] Three different approaches were used for the synthesis of dinucleoside methanephosphonamidates [3'-NH-P(O)(CH3)O-5'], starting from dichloromethylphosphine or dichloromethanephosphonate as the phosphorus-containing moiety. 5'-DMT-3'-amino-3'-deoxythymidine and N(4)-benzoyl-5'-DMT-3'-amino-2',3'-dideoxycytidine were used as the aminonucleoside precursors and the respective 3'-protected nucleosides (thymidine or N(4)-benzoyl-2'-deoxycytidine) as the 5'-hydroxyl reagents.     

Comprehensive analysis of the substitution pattern in dextran ethers with respect to the reaction conditions

Dextrans from Leuconostoc ssp., α-1,6-linked glucans branched at O-3, were O-methylated in DMSO with lithium dimsyl and methyl iodide under various conditions. Methyl substituent distribution was comprehensively studied in the terminal, internal, and branched glucosyl units and along and over the dextran macromolecules. The order of reactivity was O-2 > O-4 ≥ O-3. The methyl pattern in the glucosyl units significantly deviates from a random distribution with enhanced amounts of un- and trisubstituted moieties. This deviation was found to proceed on macromolecular level by means of ESI-MS of perdeuteromethylated and partially depolymerized methyl dextrans. Heterogeneity was much more pronounced than for methyl amylose prepared under comparable conditions. DS gradients in and over the material are discussed with respect to dextran structure and the mechanism of Li dimsyl alkylation. For comparison, cyanoethyl dextrans were prepared by sodium hydroxide catalyzed addition of acrylonitrile. Monomer analysis of cyanoethyl dextrans revealed that this thermodynamically controlled reaction gave a random substitution pattern with 48% of cyanoethyl groups at O-2, 33% at O-4, and 19% at O-3.      

Coordination properties of cyclam (1,4,8,11-tetraazacyclotetradecane) endowed with two methylphosphonic acid pendant arms in the 1,4-positions

The title ligand, 1,4,8,11-tetraazacyclotetradecane-1,4-diyl-bis(methylphosphonic acid) (H4te2p1,4, H4L), was prepared by an optimized synthetic approach and its complexing properties towards selected metal ions were studied by means of potentiometry. The ligand forms a very stable complex with copper(II) (log beta(CuL) = 27.21), with a high selectivity over binding of other metal ions (e.g. log beta(ZnL) = 20.16, log beta(NiL) = 21.92). The crystal structures of two intermediates in the ligand synthesis and two forms of the nickel(II) complex (obtained by crystallization at different pH) were determined. From acid solution, the crystals of trans-O,O-[Ni(H3L)]Cl.H2O were isolated. In such complex species, one phosphonate pendant arm is double- and the second arm is monoprotonated. The isolation of such species demonstrates a high kinetic inertness of the complex. The central metal ion is surrounded by four in-plane nitrogen atoms (in the ring configuration III) and two oxygen atoms of pendant moieties in the apical positions of octahedral coordination sphere. From neutral solution, the crystals of (trans-O,O-[Ni(H2L)])3.5H2O were isolated. The molecular structures of the complex units found in this structure are analogous to that found in trans-O,O-[Ni(H3L)]Cl.H2O.     

Complete NMR assignments of the antibacterial biflavonoid GB1 from Garcinia kola

From the antibacterial fraction of the roots of Garcinia kola, 3',4',4',5,5',7,7'-heptahydroxy-3,8'-biflavanone (GB1) was isolated as the major constituent, whose interesting conformations were studied on the basis of its 1D and 2D NMR spectra obtained at different temperatures and in different solvents. GB1 showed antibacterial activities against methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci (VRE) with MIC of 32 and 128 microg/ml, respectively.     

Pyromeconic acid derivatives from Conyza canadnsis(L.) Cronq

A new pyromeconic acid derivative,pyromeconic acid-3-O-β-D-glucopyranoside-3′-(O-β-D-glucopyranoside)-6′-(O-4″-hydroxybenzoate) (1),along with two known ones,were isolated from the whole plants of Conyza canadensis.Their structures were elucidated based on the analysis of their spectroscopic data.The in vitro antibacterial testing results showed that all of these three compounds were inactive towards two bacterial strains,Escherichia coli and Staphyloccocus aureus.     

The dimeric "hand-shake" motif in complexes and metallo-supramolecular assemblies of cyclotriveratrylene-based ligands

A series of clathrate and metal complexes with cyclotriveratrylene-like molecular host ligands show a similar dimeric homomeric inclusion motif in which a ligand arm of one host is the intra-cavity guest of another and vice versa. This "hand-shake" motif is found in the trinuclear transition metal complex [Cu(3)Cl(6)(1)]CH(3)CN1.5 H(2)O in which 1 is tris(4-[2,2',6',2'-terpyridyl]benzyl)cyclotriguaiacylene; in the self-included M(4)L(4) tetrahedral metallo-supramolecular assembly [Ag(4)(2)(4)] (BF(4))(4) in which 2 is tris-(2-quinolylmethyl)cyclotriguaiacylene; in the 1D coordination chains [Ag(4)]ReO(4) CH(3)CN and [Ag(5)]SbF(6)3 DMFH(2)O in which 4 is tris(1H-imidazol-1-yl)cyclotriguaiacylene and 5 is tris{4-(2-pyridyl)benzyl}cyclotriguaiacylene; and in the acetone clathrate of tris{4-(2-pyridyl)benzyl-amino}cyclotriguaiacylene. Clathrates of ligands 2 and 5 do not show the same dimeric motif, although 2 has an extended homomeric inclusion motif that gives a hexagonal network.     

New chain-extended analogues of salacinol and blintol and their glycosidase inhibitory activities. Mapping the active-site requirements of human maltase glucoamylase

The synthesis of new chain-extended sulfonium and selenonium salts of 1,4-anhydro-4-thio-(or 4-seleno)-d-arabinitol, analogues of the naturally occurring glycosidase inhibitor salacinol, is described. Nucleophilic attack at the least hindered carbon atom of 4,6-O-benzylidene-2,5-di-O-p-methoxybenzyl-d-mannitol-1,3-cyclic sulfate by 2,3,5-tri-O-p-methoxybenzyl-1,4-anhydro-4-thio-(or 4-seleno)-d-arabinitol gave the sulfonium and selenonium sulfates, respectively. Subsequent deprotection with trifluoroacetic acid yielded the target compounds. In these analogues, an extended polyhydroxylated aliphatic side chain has been incorporated while maintaining the stereochemistry of C-2' and C-3' of salacinol or blintol. These compounds were designed to probe the premise that they would bind with higher affinity to glucosidases than salacinol because the extra hydroxyl groups in the acyclic chain would make favorable polar contacts within the active site. Both target compounds inhibited recombinant human maltase glucoamylase, one of the key intestinal enzymes involved in the breakdown of glucose oligosaccharides in the small intestine, with Ki values in the low micromolar range. Comparison of these values to those of related compounds synthesized in previous studies has provided a better understanding of structure-activity relationships and the optimal stereochemistry at the different stereogenic centers required of an inhibitor of this enzyme. With respect to chain extension, the configurations at C-2' and C-4' are critical for activity, the configuration at C-3', bearing the sulfate moiety, being unimportant. The desired configuration at C-5' is also specified. However, comparison of the activities of the chain-extended analogues with those of salacinol and blintol indicates that there is no particular advantage of the chain-extension relative to salacinol or blintol. These results are similar to those reported earlier for kotalanol, a 7-carbon-extended derivative, versus salacinol against rat intestinal maltase, sucrase, and isomaltase.     

Computational analysis of aza analogues of [2',5'-bis-O-(tert-butyldimethylsilyl)-beta-D-ribofuranose]-3'-spiro-5"-(4"-amino-1",2"-oxathiole-2",2"-dioxide) (TSAO) as HIV-1 reverse transcriptase inhibitors: relevance of conformational properties on the inhibitory activity

We have carried out a theoretical analysis of aza analogues of [2',5'-bis-O-(tert-butyldimethylsilyl)-beta-D-ribofuranosyl]-3'-spiro-5"-(4"-amino-1",2"-oxathiole-2",2"-dioxide) by a variety of computational tools, aimed to account for the effect of the endocyclic amino moiety N-2" on the inhibitory activity against HIV-1. Docking studies suggest that compounds substituted at the N-3 and N-2' ' positions present the same binding mode to the [2',5'-bis-O-(tert-butyldimethylsilyl)-beta-D-ribofuranosyl]-3'-spiro-5"-(4"-amino-1",2"-oxathiole-2",2"-dioxide)thymine prototype, where the endocyclic amino group remains mostly exposed to the solvent. A careful conformational analysis performed through different theoretical levels, from molecular mechanics to high-level quantum mechanical calculations, provides a rationalization based on conformational preferences, which appears as strongly determined by the substitution at N-2", and on electrostatic effects from the bulk water.     

Thermal stability of the crystallisation nucleant

The 2,2',4,4',6,6'hexanitrostilbene, HNS, nucleant, used in the crystallisation of 2,4,6,trinitrotoluene, TNT, was precipitated from molten TNT and examined by differential scanning calorimetry, DSC, at several stages during purification by vacuum sublimation. During purification a broad endotherm, associated with nucleant decomposition, which could be resolved into two endotherms, depending on the sublimation temperature, was observed. Pure nucleant prepared at 70C showed a similar behaviour during thermal annealing for extended periods of time at >85C. Thus TNT, retained in the recrystallised HNS nucleant, may be migrating during the purification process or may occupy a range of lattice sites, which exhibit different activation energies for migration to the surface of the solid during thermal decomposition of the nucleant. Loss of TNT from the nucleant, during purification, could produce some free HNS. The activation energy for nucleant decomposition, which may be a two-stage processes with the initial mobility of the TNT being the limiting reaction, was estimated to be 210 kJ mol^–. The lattice sites available for the TNT in the host HNS nucleant require elucidation and are the subject of further studies to be published at a later date.     

Synthesis and antibacterial activity of novel neamine derivatives: preponderant role of the substituent position on the neamine core

A series of neamine derivatives were prepared from the cyclic carbonate and sulfate of 1,3,2',6'-tetraazido-3',4',-di-O-acetylneamine. Ring opening reactions with diversely substituted amines result in the formation of the corresponding carbamates or sulfonic acids with good overall yields. The antibacterial activities of the synthesized products against E. coli (DH5α) and S. aureus (RN4220) were evaluated. With isolated single regioisomers, the preponderant effect of the 5-positions of the carbamate substituent on the neamine core was demonstrated.