The study of the reaction of terminated oligomerization in the synthesis of oligo-(β1-6)-glucosamines

The applicability of terminated oligomerization to the synthesis of oligo-(β1-6)-glucosamines, fragments of the intercellular polysaccharide adhesin of staphylococci, was studied. The reactions of terminated oligomerization were carried out with mono-, di-, and trisaccharide monomers and N-protected aminopropanol; and spacered mono-and disaccharides as terminating molecules were also attempted. The primary formation of cyclic products of monomer intramolecular glycosylation was observed in almost all the reactions. Only the experiments with the monomer based on the disaccharide bromide under the conditions of the Helferich reaction led to reduced yields (30%) of the cyclic products. However, even in this case, the desired terminated oligosaccharides were generated in approximately 10% yield and mainly were the products of single glycosylation of the terminator by the monomer. These experiments allow the conclusion that, under the examined conditions, the reaction of terminated oligomerization could not result in the synthesis of oligoglucosamines with a high molecular mass.     

Regio- and diastereo-selectivity of montmorillonite-catalyzed oligomerization of racemic adenosine 5'-phosphorimidazolide

Clay is a possible candidate for an effective catalyst in prebiotic chemical evolution of biomolecules. Montmorillonite was reported to effectively catalyze oligomerization of racemic adenosine 5'-phosphorimidazolide (DL-ImpA). In the oligomerization reaction, considerable amounts of cyclic dimers as well as linear dimers were produced in the oligomerization reactions. To assess the regio- and diastereo-selectivities of the oligomerization reaction, the dimer products including cyclic dimers were completely identified by means of enzymatic degradation reactions of the products.     

Regio- and Diastereo-Selectivity of Montmorillonite-Catalyzed Oligomerization of Racemic Adenosine 5′-Phosphorimidazolide

Clay is a possible candidate for an effective catalyst in prebiotic chemical evolution of biomolecules. Montmorillonite was reported to effectively catalyze oligomerization of racemic adenosine 5′-phosphorimidazolide (DL-ImpA). In the oligomerization reaction, considerable amounts of cyclic dimers as well as linear dimers were produced in the oligomerization reactions. To assess the regio- and diastereo-selectivities of the oligomerization reaction, the dimer products including cyclic dimers were completely identified by means of enzymatic degradation reactions of the products.     

Non-Enzymatic Oligomerization of 3’, 5’ Cyclic AMP

Recent studies illustrate that short oligonucleotide sequences can be easily produced from nucleotide precursors in a template-free non-enzymatic way under dehydrating conditions, i.e. using essentially dry materials. Here we report that 3’,5’ cyclic AMP may also serve as a substrate of the reaction, which proceeds under moderate conditions yet with a lower efficiency than the previously reported oligomerization of 3’,5’ cyclic GMP. Optimally the oligomerization requires (i) a temperature of 80°C, (ii) a neutral to alkaline environment and (iii) a time on the order of weeks. Differences in the yield and required reaction conditions of the oligomerizations utilizing 3’,5’ cGMP and cAMP are discussed in terms of the crystal structures of the compounds. Polymerization of 3’,5’ cyclic nucleotides, whose paramount relevance in a prebiotic chemistry context has been widely accepted for decades, supports the possibility that the origin of extant genetic materials might have followed a direct uninterrupted path since its very beginning, starting from non-elaborately pre-activated monomer compounds and simple reactions.     

Template-directed synthesis of oligonucleotides under eutectic conditions

Summary One of the most important sets of model prebiotic experiments consists of reactions that synthesize complementary oligonucleotides from preformed templates under nonenzymatic conditions. Most of these experiments are conducted at 4°C using 0.01–0.1 M concentrations of activated nucleotide monomer and template (monomer equivalent). In an attempt to extend the conditions under which this type of reaction can occur, we have concentrated the reactants by freezing at –18°C, which is close to the NaCl–H₂O eutectic at –21°C.The results from this set of experiments suggest that successful syntheses can occur with poly(C) concentrations as low at 5×10^–4 M and 2MeImpG concentrations at 10^–3 M. It was also anticipated that this mechanism might allow the previously unsuccessful poly(A)-directed synthesis of oligo(U)s to occur. However, no template effect was seen with the poly(A) and ImpU system. The failure of these conditions to allow template-directed synthesis of oligo(U)s supports the previously proposed idea that pyrimidines may not have been part of the earliest genetic material.Because of the low concentrations of monomer and template that would be expected from prebiotic syntheses, this lower temperature could be considered a more plausible geologic setting for template-directed synthesis than the standard reaction conditions.     

Peptide Formation Mechanism on Montmorillonite Under Thermal Conditions

The oligomerization of amino acids is an essential process in the chemical evolution of proteins, which are precursors to life on Earth. Although some researchers have observed peptide formation on clay mineral surfaces, the mechanism of peptide bond formation on the clay mineral surface has not been clarified. In this study, the thermal behavior of glycine (Gly) adsorbed on montmorillonite was observed during heating experiments conducted at 150 °C for 336 h under dry, wet, and dry–wet conditions to clarify the mechanism. Approximately 13.9 % of the Gly monomers became peptides on montmorillonite under dry conditions, with diketopiperazine (cyclic dimer) being the main product. On the other hand, peptides were not synthesized in the absence of montmorillonite. Results of IR analysis showed that the Gly monomer was mainly adsorbed via hydrogen bonding between the positively charged amino groups and negatively charged surface sites (i.e., Lewis base sites) on the montmorillonite surface, indicating that the Lewis base site acts as a catalyst for peptide formation. In contrast, peptides were not detected on montmorillonite heated under wet conditions, since excess water shifted the equilibrium towards hydrolysis of the peptides. The presence of water is likely to control thermodynamic peptide production, and clay minerals, especially those with electrophilic defect sites, seem to act as a kinetic catalyst for the peptide formation reaction.     

Synthesis of inositol glycan cyclic phosphates

An efficient synthesis of tri-, tetra-, and pentasaccharide cyclic phosphates 1-5, structurally related to natural inositol phosphate glycans, is reported. The title compounds were assembled by PhSeOTf-promoted glycosylation of the known glucosamine precursor, t-butyldimethylsilyl 2-azido-3,6-di-O-benzyl-2-deoxy-beta-D-glucopyranoside (8) with protected 1-methylthio mono-, di-, and trimannosides 7a-c, and, after conversion into glycosyl fluorides, Cp2ZrCl2- AgOTf-promoted glycosylation of differentially protected optically pure 1D-myo-inositol 11. The syntheses were completed by installing the cyclic phosphate moieties with methylpyridinium dichlorophosphate and finally, removal of all protecting groups by dissolving-metal reduction.     

The Role of Fluoride in Montmorillonite-Catalyzed RNA Synthesis

The montmorillonite-catalyzed reactions of the 5′-phosphorimidazolide of adenosine in the presence of fluoride were investigated to complete our study on the effect of salts on this type of reaction. Both anions and cations have been found to influence the oligomerization reactions of the activated nucleotides, being used here as a model system for pre-biotic RNA synthesis. However, in total contrast to the behavior of the activated nucleotides in the presence of montmorillonite and other salts, alkali metal fluorides did not yield any detectable oligomerization products except in very dilute (<0.005 M) solutions of fluoride. Instead, 5′-phosphorofluoridates were formed. Their identity was confirmed by a combination of HPLC, mass spectrometry, synthesis, and NMR.     

The effect of cycloheximide on the entry into the S period of the nuclei in heterodikaryons]

Serum-deprived (0.2%) resting NIH 3T3 mouse fibroblasts were fused with serum-stimulated (10%) proliferating cells to elucidate mechanisms of entering into S-period operating in the nuclei of the heterokaryons under the effect of cycloheximide--an inhibitor of protein synthesis. Using radioautography DNA synthesis was investigated in mono-, homo- and heterodikaryons. After short (0.5-3.0 h) depressing of protein synthesis, the nuclei of stimulated cells in heterokaryons were found to enter into S-period. Under these conditions no induction of DNA synthesis was found in the nuclei of resting cells in heterodikaryons. In other experiments, resting cells were under the effect of cycloheximide during 2-4 h before the fusion, that led to a great induction of DNA synthesis in the nuclei of these cells in heterodikaryons. The data obtained are consistent with the idea of fibroblast transition to the rest under the action of labile proteins-repressors.     

Synthesis of a cyanoethylidene derivative of 3,6-anhydro-d-galactose and its application as glycosyl donor

Starting from 1,2,4-tri-O-acetyl-3,6-anhydro-alpha-d-galactopyranose, 4-O-acetyl-3,6-anhydro-1,2-O-(1-cyanoethylidene)-alpha-d-galactopyranose (7) was synthesized by treatment with cyanotrimethylsilane. Additionally, 3,4-di-O-acetyl-1,2-O-(1-cyanoethylidene)-6-O-tosyl-alpha-d-galactopyranose was prepared from the corresponding bromide and both cyanoethylidene derivatives were used as donors in glycosylation reactions. The coupling with benzyl 2,4,6-tri-O-acetyl-3-O-trityl-beta-d-galactopyranoside provided exclusively the beta-linked disaccharides in approximately 30% yield. The more reactive methyl 2,3-O-isopropylidene-4-O-trityl-alpha-l-rhamnopyranoside gave with donors 3 and 7 the corresponding disaccharides in nearly 60% yield. Furthermore, the synthesis of 3,6-anhydro-4-O-trityl-1,2-O-[1-(endo-cyano)ethylidene]-alpha-d-galactopyranose, which can be used as a monomer for polycondensation reaction is described.     

Evidence for the synthesis of soluble peptidoglycan fragments by protoplasts of Streptococcus faecalis.

Growing protoplasts of Streptococcus faecalis 9790 were found to synthesize and excrete soluble peptidoglycan fragments. The presence of soluble peptidoglycan derivatives in culture supernatants was determined by (i) incorporation of three different radioactively labeled precursors (L-lysine, D-alanine, and acetate) into products which, after hen egg-white lysozyme hydrolysis, had the same KD values on gel filtration as muramidase hydrolysis products of isolated walls; (ii) inhibition of net synthesis of these products by cycloserine and vancomycin; and (iii) identification of disaccharide-peptide monomer using the beta-elimination reaction, gel filtration, and high-voltage paper electrophoresis. Under the conditions of these experiments the presence of newly synthesized, acid-precipitable (macromolecular) peptidoglycan was not detected. The predominance of monomer (70 to 80%) in lysozyme digests of peptidoglycan synthesized by protoplasts was in sharp contrast to digest of walls from intact streptococci which contain mostly peptide cross-linked products. Biosynthesis and release of relatively uncross-linked, soluble peptidoglycan fragments by protoplasts was related to the absence of suitable, preexisting acceptor wall.     

Synthesis of alkyl-alpha-L-rhamnosides by water soluble alcohols enzymatic glycosylation

The synthesis of alkyl-alpha-rhamnosides by alpha-rhamnosidase was studied using rhamnose and rhamnosides, particularly the flavonoid naringin, as glycosylation agents, and water soluble alcohols as acceptors. The reaction products were analyzed by HPLC chromatography and identified by 13C y 1H NMR. The glycosylation of alcohols by reverse hydrolysis was maximum for 40% methanol, 30% ethanol, 10% propanol and 20% isopropanol. Under optimum conditions the yield of rhamnose to alkyl-alpha-rhamnoside transformation decreased from 68% for methyl-alpha-rhamnoside to 10% for isopropyl-alpha-rhamnoside. The time course of rhamnosylations produced using naringin as the donor was comparable with that of the reverse hydrolysis obtained at the same molar concentration of the donor. The flavonoids and their derivatives remaining in the solution after the glycosylation were removed by ion exchange QEAE chromatography at pH 10. These results indicate that both, reverse hydrolysis and glycosylation by naringin are acceptable procedures for the enzymatic synthesis of short chain length alkyl-alpha-L-rhamnosides.     

Effects of residual zinc compounds and chain-end structure on thermal degradation of poly(epsilon-caprolactone)

Effects of chain-end structure and residual metal compounds on thermal degradation of poly(epsilon-caprolactone) (PCL) were investigated by means of thermogravimetric and pyrolysis-gas chromatograph mass spectrometric analyses. Four types of PCL samples with different chain-end structures (alpha-carboxylic acid-omega-hydroxyl-PCL, alpha-dodecyl ester-omega-hydroxyl-PCL, alpha-carboxylic acid-omega-acetyl-PCL, and alpha-dodecyl ester-omega-acetyl-PCL) were prepared by ring-opening polymerization of epsilon-caprolactone in the presence of zinc-based catalyst and by subsequent acetylation reaction of polymers with acetic anhydride. PCL samples with different zinc contents were obtained by washing with acetic acid in chloroform solution of polymer. Thermal degradation behaviors of these PCL samples with different chain-end structures were examined under both isothermal and nonisothermal conditions. From both the isothermal and nonisothermal experiments, the thermal degradation of PCL samples containing high amounts of residual zinc compounds from synthesis process revealed the selective unzipping depolymerization step below 300 degrees C producing epsilon-caprolactone exclusively. In contrast, zinc-free PCL samples were stable at temperatures below 300 degrees C, and the thermal degradation occurred only at temperatures above 300 degrees C regardless of the chain-end structure. From (1)H NMR analysis of the residual molecules after isothermal degradation of zinc-free PCL, it was confirmed that the omega-chain-end of residual molecules was 5-hexenoic acid unit. However, the cyclic monomer and oligomers were detected as the volatile products of zinc-free PCL samples. These results suggest that the dominant reaction of thermal degradation for PCL above 300 degrees C is a competition between the random chain scission via cis elimination reaction and the cyclic rupture via intramolecular transesterification of PCL molecules.     

Substrate kinetics and substrate effects on the quaternary structure of barley UDP-glucose pyrophosphorylase

UDP-Glc pyrophosphorylase (UGPase) is an essential enzyme responsible for production of UDP-Glc, which is used in hundreds of glycosylation reactions involving addition of Glc to a variety of compounds. In this study, barley UGPase was characterized with respect to effects of its substrates on activity and quaternary structure of the protein. Its K_m values with Glc-1-P and UTP were 0.33 and 0.25 mM, respectively. Besides using Glc-1-P as a substrate, the enzyme had also considerable activity with Gal-1-P; however, the K_m for Gal-1-P was very high (>10 mM), rendering this reaction unlikely under physiological conditions. UGPase had a relatively broad pH optimum of 6.5–8.5, regardless of the direction of reaction. The enzyme equilibrium constant was 0.4, suggesting slight preference for the Glc-1-P synthesis direction of the reaction. The quaternary structure of the enzyme, studied by Gas-phase Electrophoretic Mobility Macromolecule Analysis (GEMMA), was affected by addition of either single or both substrates in either direction of the reaction, resulting in a shift from UGPase dimers toward monomers, the active form of the enzyme. The substrate-induced changes in quaternary structure of the enzyme may have a regulatory role to assure maximal activity. Kinetics and factors affecting the oligomerization status of UGPase are discussed.     

Abiotic Formation of Valine Peptides Under Conditions of High Temperature and High Pressure

We investigated the oligomerization of solid valine and the stabilities of valine and valine peptides under conditions of high temperature (150–200 °C) and high pressure (50–150 MPa). Experiments were performed under non-aqueous condition in order to promote dehydration reaction. After prolonged exposure of monomeric valine to elevated temperatures and pressures, the products were analyzed by liquid chromatography mass spectrometry comparing their retention times and masses. We identified linear peptides that ranged in size from dimer to hexamer, as well as a cyclic dimer. Previous studies that attempted abiotic oligomerization of valine in the absence of a catalyst have never reported valine peptides larger than a dimer. Increased reaction temperature increased the dissociative decomposition of valine and valine peptides to products such as glycine, β-alanine, ammonia, and amines by processes such as deamination, decarboxylation, and cracking. The amount of residual valine and peptide yields was greater at higher pressures at a given temperature, pressure, and reaction time. This suggests that dissociative decomposition of valine and valine peptides is reduced by pressure. Our findings are relevant to the investigation of diagenetic processes in prebiotic marine sediments where similar pressures occur under water-poor conditions. These findings also suggest that amino acids, such as valine, could have been polymerized to peptides in deep prebiotic marine sediments within a few hundred million years.     

Selectivity of montmorillonite catalyzed prebiotic reactions of D,L-nucleotides

The montmorillonite-catalyzed reactions of the 5′-phosphorimidazolides of D, L-adenosine (D, L-ImpA) (Figure 1a. N = A, R = H) and D, L-uridine (Figure 1a., N = U, R = H) yields oligomers that were as long as 7 mers and 6 mers, respectively. The reactions of dilute solutions of D-ImpA and D-ImpU under the same conditions gave oligomers as long as 9 and 8 mers respectively. This demonstrated that oligomer formation is only partially inhibited by incorporation of both the D- and L-enantiomers. The structures of the dimers, trimers and tetramer fractions formed from D, L-ImpA was investigated by selective enzymatic hydrolysis, comparison with authentic samples and mass spectrometry. Homochiral products were present in greater amounts than would be expected if theoretical amounts of each were formed. The ratio of the proportion of homochiral products to that of the amount of each expected for the dimers (cyclic and linear), trimers and tetramers, was 1.3, 1.6, and 2.1, respectively. In the D, L-ImpU reaction homochiral products did not predominate with ratios of dimers (cyclic and linear), trimers and tetramers 0.8, 0.44, and 1.4, respectively. The proportions of cyclic dimers in the dimer fraction were 52–66% with D, L-ImpA and 44–69% with D, L-ImpU. No cyclic dimers were formed in the absence of montmorillonite. The differences in the reaction products of D, L-ImpA and D, L-ImpU are likely to be due to the difference in the orientations of the activated monomers when bound to the catalytic sites on montmorillonite. The consequences of the selectivity of montmorillonite as a prebiotic catalyst are discussed.     

Lipase-catalyzed copolymerization of dialkyl carbonate with 1,4-butanediol and ω-pentadecalactone: synthesis of poly(ω-pentadecalactone-co-butylene-co-carbonate)

Candida antarctica lipase B (CALB) was successfully used to promote synthesis of aliphatic poly(carbonate-co-ester) copolymers from dialkyl carbonate, diol, and lactone monomers. The polymerization reactions were carried out in two stages: first-stage oligomerization under low vacuum, followed by second-stage polymerization under high vacuum. Therefore, copolymerization of ω-pentadecalactone (PDL), diethyl carbonate (DEC), and 1,4-butanediol (BD) yielded PDL-DEC-BD copolymers with a M(w) of whole product (nonfractionated) up to 33?000 and M(w)/M(n) between 1.2 and 2.3. Desirable reaction temperature for the copolymerization was found to be ～80 °C. The copolymer compositions, in the range from 10 to 80 mol % PDL unit content versus total (PDL + carbonate) units, were effectively controlled by adjusting the monomer feed ratio. Reprecipitation in chloroform/methanol mixture allowed isolation of the purified copolymers in up to 92% yield. (1)H and (13)C NMR analyses, including statistical analysis on repeat unit sequence distribution, were used to determine the polymer microstructures. The synthesized PDL-DEC-BD copolymers possessed near random structures with all possible combinations of PDL, carbonate, and butylene units via either ester or carbonate linkages in the polymer chains and are more appropriately named as poly(PDL-co-butylene-co-carbonate).     

Coupling of DTPA to proteins: a critical analysis of the cyclic dianhydride method in the case of insulin modification.

The reaction between the cyclic dianhydride of diethylenetriaminepentaacetic acid (DTPA), a bifunctional reagent, and proteins under various conditions was studied using porcine insulin as a model protein. The reaction was compared with that between citraconic anhydride, a monofunctional reagent, and insulin. Products were characterized chromatographically and electrophoretically before and after deesterification by hydroxylamine. A DTPA-conjugated product was further characterized by proteolytic fragmentation. The reaction with citraconic anhydride yielded the expected number of products exclusively acylated on amino groups. In contrast, the reaction with the cyclic dianhydride of DTPA under all conditions examined yielded a much higher number of products than expected. Among the products formed were O-acylated ones and products of intermolecular cross-linking. It is concluded that the use of the cyclic dianhydride of DTPA does not allow the reliable preparation of proteins or other macromolecules conjugated with a high number of DTPA molecules in which each molecule of DTPA is linked to one amino group of the macromolecule through a single amide bond.     

Glycosylation of Mono- and Bicyclic Dicarbonic Acid Imides

Abstract

Glycosylation of some mono- and bicyclic dicarbonic acid imides was performed via the Friedel-Crafts-catalyzed silyl Hilbert-Johnson reaction. The occurrence of β-N-ribosylation was established by ¹H and ¹³C NMR spectroscopy. The electron distributions in the lactam region of the N-silylated cyclic imides strongly influence the glycosylation. The N-glycosylated cyclic imides are potential agents for glycoalkylation of lysine residues in proteins.     

Dynamic multiscale metabolic network modeling of Chinese hamster ovary cell metabolism integrating N‐linked glycosylation in industrial biopharmaceutical manufacturing

Experimental and modeling work, described in this article, is focused on the metabolic pathway of Chinese hamster ovary (CHO) cells, which are the preferred expression system for monoclonal antibody protein production. CHO cells are one of the primary hosts for monoclonal antibodies production, which have extensive applications in multiple fields like biochemistry, biology and medicine. Here, an approach to explain cellular metabolism with in silico modeling of a microkinetic reaction network is presented and validated with unique experimental results. Experimental data of 25 different fed‐batch bioprocesses included the variation of multiple process parameters, such as pH, agitation speed, oxygen and CO₂ content, and dissolved oxygen. A total of 151 metabolites were involved in our proposed metabolic network, which consisted of 132 chemical reactions that describe the reaction pathways, and include 25 reactions describing N‐glycosylation and additional reactions for the accumulation of the produced glycoforms. Additional eight reactions are considered for accumulation of the N‐glycosylation products in the extracellular environment and one reaction to correlate cell degradation. The following pathways were considered: glycolysis, pentose phosphate pathway, nucleotide synthesis, tricarboxylic acid cycle, lipid synthesis, protein synthesis, biomass production, anaplerotic reactions, and membrane transport. With the applied modeling procedure, different operational scenarios and fed‐batch techniques can be tested.