1,5-Anhydro-D-fructose; a versatile chiral building block: biochemistry and chemistry

There is a steadily increasing need to expand sustainable resources, and carbohydrates are anticipated to play an important role in this respect, both for bulk and fine chemical preparation. The enzyme alpha-(1-->4)-glucan lyase degrades starch to 1,5-anhydro-D-fructose. This compound, which has three different functional properties, a prochiral center together with a permanent pyran ring, renders it a potential chiral building block for the synthesis of valuable and potentially biologically active compounds. 1,5-Anhydro-D-fructose is found in natural materials as a degradation product of alpha-(1-->4)-glucans. The occurrence of lyases and the metabolism of 1,5-anhydro-D-fructose are reviewed in the biological part of this article. In the chemical part, the elucidated structure of 1,5-anhydro-D-fructose will be presented together with simple stereoselective conversions into hydroxy/amino 1,5-anhydro hexitols and a nojirimycin analogue. Synthesis of 6-O-acylated derivatives of 1,5-anhydro-D-fructose substituted with long fatty acid residues is carried out using commercially available enzymes. Those reactions lead to compounds with potential emulsifying properties. The use of protected derivatives of 1,5-anhydro-D-fructose for the synthesis of natural products is likewise reviewed. The potential utilization of this chemical building block is far from being exhausted. Since 1,5-anhydro-D-fructose now is accessible in larger amounts through a simple-enzyme catalyzed degradation of starch by alpha-(1-->4)-glucan lyase, the application of 1,5-anhydro-D-fructose may be considered a valuable contribution to the utilization of carbohydrates as the most abundant resource of sustainable raw materials.     

Preparation of an unprotected phosphotyrosine building block and its application in solid-phase synthesis of phosphopeptides

A new and facile synthesis of tyrosine phosphorylated peptides has been developed. ^N-Fmoc-Tyr^tBu)-OPfp was treated with TFA, phosphorylated with phosphorous oxychloride and the resulting phosphoric acid dichloride was hydrolysed to give N-Fmoc-Tyr(PO₃H₃2)-OPfp 1 in an overall yield of 98%. Compound 1 was used in solid-phase peptide synthesis of phosphopeptides 2, 3 and 4, which are fragments of murine adipocyte lipid binding protein. The advantage of using the Pfp ester was the absence of pyrophosphates and other byproducts.     

Preparation of an unprotected phosphotyrosine building block and its application in solid-phase synthesis of phosphopeptides

Summary A new and facile synthesis of tyrosine phosphorylated peptides has been developed.N ^α-Fmoc-Tyr(tBu)-OPfp was treated with TFA, phosphorylated with phosphorous oxychloride and the resulting phosphoric acid dichloride was hydrolysed to giveN ^α-Fmoc-Tyr(PO₃H₂)-OPfp1 in an overall yield of 98%. Compound1 was used in solid-phase peptide synthesis of phosphopeptides2, 3 and4, which are fragments of murine adipocyte lipid binding protein. The advantage of using the Pfp ester was the absence of pyrophosphates and other byproducts.     

Preparation of a class of versatile, chemoselective, and amorphous polyketoesters

A straightforward and versatile strategy for preparing a class of biodegradable and amorphous polyketoesters is reported. A series of ketone-containing diesters and diacids were combined with di(ethylene glycol) through condensation polymerization, achieving values of up to 10.1 x 10(3) g/mol. Glass transition temperatures ranged from -41 to -6 degrees C, rendering all of the materials liquid at room temperature. By including ketone groups in the repeat unit, facile postpolymerization modifications were possible by reaction with oxyamine-tethered ligands through the formation of an oxime linkage. Upon reaction with molecules that contain oxyamines, under mild conditions, these polymers can easily have a diverse set of side chains appended without coreagents or catalysts. The chemoselective oxime-forming coupling strategy is compatible with physiological conditions and can be done in the presence of a wide range of functional groups and biomolecules, including proteins and nucleic acids. We demonstrate the utility of this strategy by immobilizing a cell adhesive peptide (H2NO-RGD) to polyketoester films, creating cell adhesive elastomers. This immobilization strategy is synthetically flexible for designing and tailoring polymers for targeted biological applications.     

Simultaneous lipidation of a characterized peptide mixture by chemoselective ligation

The modification of a peptide antigen by a fatty acid such as palmitic acid is now recognized as a mean to induce cellular responses. Mixtures of lipopeptides, obtained by combining individually synthesized compounds, were shown to be promising synthetic vaccine candidates. Usually, in lipopeptide synthesis, the fatty acyl moiety is introduced on the crude peptide chain using solid-phase methods. The separation of the target compound from impurities by RP-HPLC is often complicated by the amphiphilic properties of lipopeptides and results in low overall yields. To overcome the difficulties associated with lipopeptide synthesis and mixture preparation, we have developed a method where the fatty acyl moiety is site-specifically and collectively introduced in solution onto a mixture of individually prepurified peptides. The lipidation is based on the quasistoichiometric and high-yielding ligation of a glyoxylyl lipid with hydrazinoacetyl peptides. The hydrazone constructs were prepared in a salt-free medium and could be isolated by direct lyophilization of the reaction mixture. This process is compatible with cysteinyl peptides, and no aggregation nor degradation could be observed.     

Versatile synthesis of Boc protected hydrazinoacetic acid and its application to the chemoselective ligation of TASP molecules

This paper describes a convenient synthesis of protected hydrazine derivatives, i.e. 1,2-bis-Boc-hydrazinoacetic acid, and its application for hydrazone ligation techniques in convergent template assembled synthetic protein (TASP) synthesis.     

Carbopeptides: chemoselective ligation of peptide aldehydes to an aminooxy-functionalized D-galactose template.

Multifunctional, topological template molecules such as linear and cyclic peptides have been used for the attachment of peptide strands to form novel protein models of, for example, 4-alpha-helix bundles. The concept of carbohydrates as templates for de novo design of potential protein models has been previously described and these novel chimeric compounds were termed carbopeptides. Here, a second generation strategy in which carbopeptides are synthesized by chemoselective ligation of a peptide aldehyde to an aminooxy-functionalized alpha-D-galactopyranoside is described. This template was prepared by per-O-acylation of methyl alpha-D-galactopyranoside with N,N-Boc2-aminooxyacetic acid to form a tetra-functionalized template, followed by treatment with TFA-CH2Cl2 to release the aminooxy functionality. The peptide aldehydes Fmoc-Ser-Gly-Gly-H and H-Ala-Leu-Ala-Lys-Leu-Gly-Gly-H were synthesized by a BAL strategy. Four identical copies of peptide aldehyde were smoothly attached to the template by chemoselective ligation to form a 2.1 and a 2.9 kDa carbopeptide, respectively.     

Synthesis of an Fmoc-Asn-heptasaccharide building block and its application to chemoenzymatic glycopeptide synthesis

The Fmoc-protected heptasaccharide asparagine building block β-GlcNAc-(1→2)-α-Man-(1→3)-[β-GlcNAc-(1→2)-α-Man-(1→6)]β-Man-(1→4)-β-GlcNAc-(1→4)-β-GlcNAc-(Fmoc)Asn was obtained by chemical synthesis. Two flexible strategies were developed with optimized conditions for the simultaneous debenzylation of the sugar and the amino acid part. The heptasaccharide asparagine building block is a partial structure of many glycoproteins and can be used for glycopeptide synthesis in solution and on the solid phase. In this work the heptasaccharide asparagine was elongated in solution to an Fmoc-glycopentapeptide methylester. After chemical cleavage of the Fmoc group the methylester was removed enzymatically by chymotrypsin. The use of β-(1→4)-galactosyltransferase and α-(2→6)-sialyltransferase in the presence of alkaline phosphatase allowed the efficient transfer of four sugar units to the acceptor resulting in an undecasaccharide glycopentapeptide.     

Synthesis of a thymine glycol building block and its incorporation into oligonucleotides.

A phosphoramidite building block of thymine glycol, a major oxidative base damage in DNA, was synthesized in four steps from protected thymidine. The two hydroxyl functions of the oxidized base were protected with the tert-butyldimethylsilyl group. Using this building block, oligonucleotides containing this damage were synthesized.     

1,2-Diol and hydrazide phosphoramidites for solid-phase synthesis and chemoselective ligation of 2'-modified oligonucleotides

The preparation of two novel 2'-O-alkyl phosphoramidites bearing 1,2-diol and hydrazide functions for a chemoselective ligation is described. The former amidite was used to obtain 2'-modified oligodeoxyribonucleotides, which can be later oxidised by NaIO4 to generate 2'-aldehyde oligonucleotides. These were successfully conjugated to acceptor molecules. The latter amidite also showed good coupling yields, but the hydrazide function was demonstrated to be labile under basic deprotection conditions.     

Synthesis of an O-alkynyl-chitosan and its chemoselective conjugation with a PEG-like amino-azide through click chemistry

N-Phthaloyl-chitosan O-prop-2-ynyl carbamate was prepared as a biopolymer amenable to undergo chemoselective conjugation by azide-alkyne coupling, while allowing upturn of chitosan's amines after dephthaloylation. N-phthaloylchitosan was prepared according to previously described methods and, due to its low solubility in current organic media, subsequent modifications were run in heterogeneous conditions. Activation of hydroxyls with carbonyl-1,1′-diimidazole and coupling to propargylamine yielded N-phthaloyl-chitosan O-prop-2-ynyl carbamate, then coupled to a model PEG-like azide by azide-alkyne coupling, giving the expected triazolyl conjugate. N-Dephthaloylation allowed recovery of the free amines, responsible for chitosan's bioadhesion and tissue-regeneration properties.The structures of all polymers were confirmed by Fourier-transformed infra-red (FT-IR) and X-ray photoelectron (XPS) spectroscopies, as well as by solid-state nuclear magnetic resonance (SSNMR). All chitosan derivatives were poorly soluble in both aqueous and organic media, which makes them suitable for topical applications or for removal of toxic substances from either the gastric intestinal tract or environmental sources.     

C-Difluoromethylene-containing, C-trifluoromethyl and C-perfluoroalkyl carbohydrates. Synthesis by carbohydrate transformation or building block methods

The synthetic methods for preparing carbohydrates bearing a C-branched substituent of the type CF2-Y, with Y = F, Y = CnF(2n + 1) or Y = a carbon-attached or heteroatom-attached nonfluorinated residues, are reviewed. Both direct introduction of C-branched fluorinated substituents (direct trifluoromethylation, perfluoroalkylation or difluoromethylenation) and building block methods from fluorinated synthons are considered.     

High-resolution electrophoresis in a new polyacrylamide-gel block

A new gel block for electrophoretic separation is offered. When viewed frontally, the block has a form of a trapezium. During electrophoresis a gradient of voltage is formed in such a block, as a result of which the mobility of macromolecules to be separated markedly decreases. The combination of the block with polyacrylamide gel gradient makes it possible to raise the resolving power of electrophoresis up to 300-400 dalton. The new gel block can be applied successfully to the performance of fine biochemical assays and molecular-biological studies of proteins, glycoproteins and nucleic acids.     

Poly-N-acrylylpyrrolidine. A new resin in peptide chemistry.

Entirely beaded poly-N-acrylylpyrrolidine-co-bisacrylyl-1,2-diaminoethane-co-N-acrylyl-1,6-diaminohexane.HCl(PAP), a new resin on which to perform peptide chemistry, has been prepared by reverse phase suspension polymerization in quantitative yield. In addition to being a superior support to polystyrene, albeit readily adaptable to current techniques of peptide synthesis, its versatility has been furthur extended by the introduction and use of new peptide-to-polymer linking groups, which allow the use of the bidirectional approach to peptide chemistry. One such linkage, which connects the side chain of cysteine to PAP via an acid resistant S-carbamoyl bond, was used in a bidirectional synthesis of deamino-oxytocin. PAP solvates and swells in solvents with wide-ranging polarities, including aqueous media. Thus, peptide coupling reactions were performed in organic media of high and of low polarity as well as in aqueous solution.     

Synthesis and application of circularizable ligation probes

We describe a PCR-based approach for the synthesis of circularizable ligation probes (CLiPs). CLiPs are single-stranded probes that consist of target-specific ends separated by a noncomplementary "linker" sequence. When hybridized to a target, the CLiP forms a nicked circle that may be sealed by DNA ligase only if the 5' and 3' ends show perfect Watson-Crick base pairing, thus enabling the discrimination of single nucleotide polymorphisms. Primers incorporating target sequence at their 5' end and plasmid sequence at the 3' end were used in a PCR amplification. In addition, the antisense primer was 5' labeled with biotin, and the amplification was performed in the presence of fluorescently labeled dUTP. The resulting PCR product was captured with streptavidin-coated paramagnetic beads, and the top strand, which forms the CLiP, was alkali eluted. This PCR-based method has allowed the synthesis of CLiPs that are larger and more highly labeled than has previously been possible, with ligation efficiencies similar to those of the purest chemically synthesized padlock probes. Ligations performed in the presence of cognate or mismatched sequence were analyzed by denaturing PAGE using a fluorescent DNA sequencer. Genotyping using target immobilized to nylon membranes was also performed. The CLiPs were readily able to distinguish between mutant and wild-type alleles for the common genetic disorder, 21-hydroxylase deficiency. Additionally, CLiPs of different lengths were synthesized and compared.     

The building block folding model and the kinetics of protein folding.

Here we show that qualitatively, the building blocks folding model accounts for three-state versus the two-state protein folding. Additionally, it is consistent with the faster versus slower folding rates of the two-state proteins. Specifically, we illustrate that the building blocks size, their mode of associations in the native structure, the number of ways they can combinatorially assemble, their population times and the way they are split in the iterative, step-by-step structural dissection which yields the anatomy trees, explain a broad range of folding rates. We further show that proteins with similar general topologies may have different folding pathways, and hence different folding rates. On the other hand, the effect of mutations resembles that of changes in conditions, shifting the population times and hence the energy landscapes. Hence, together with the secondary structure type and the extent of local versus non-local interactions, a coherent, consistent rationale for folding kinetics can be outlined, in agreement with experimental results. Given the native structure of a protein, these guidelines enable a qualitative prediction of the folding kinetics. We further describe these in the context of the protein folding energy landscape. Quantitatively, in principle, the diffusion-collision model for the building block association can be used. However, the folding rates of the building blocks and traps in their formation and association, need to be considered.     

Preparation of ligation intermediates and related polynucleotide pyrophosphates

Unprotected oligonucleotides and oligodeoxynucleotides terminated with an unhindered 5′-phosphate group react with nucleoside 5′-phosphorimidazolides in aqueous solution to give ‘capped’ pyrophosphates in at least 70% yield. If adenosine 5′-phosphorimidazolide is used as a substrate in the reaction, ligase intermediates are obtained as products.     

Microbial production of building block chemicals and polymers

Owing to our increasing concerns on the environment, climate change, and limited natural resources, there has recently been considerable effort exerted to produce chemicals and materials from renewable biomass. Polymers we use everyday can also be produced either by direct fermentation or by polymerization of monomers that are produced by fermentation. Recent advances in metabolic engineering combined with systems biology and synthetic biology are allowing us to more systematically develop superior strains and bioprocesses for the efficient production of polymers and monomers. Here, we review recent trends in microbial production of building block chemicals that can be subsequently used for the synthesis of polymers. Also, recent successful cases of direct one-step production of polymers are reviewed. General strategies for the production of natural and unnatural platform chemicals are described together with representative examples.     

Coordination chemistry of F430. Axial ligation equilibrium between square-planar and bis-aquo species in aqueous solution

X-ray absorption spectroscopic characterization of axial ligand coordination to factor F430, the nickel-tetrapyrrole cofactor of the S-methyl-coenzyme M (CH3SCoM) methyl reductase enzyme from methanogenic bacteria, is presented. The nickel of isolated F430 is hexacoordinate at 10 K in aqueous solution (as is the enzyme-bound cofactor), whereas the epimerized and ring-oxidized derivatives of F430 have four-coordinate nickel. Reduction of the ring-oxidized derivative, F560, with dithionite yields F430 in its native configuration, with axial ligands indistinguishable from those present when the cofactor is obtained directly from the holoenzyme. Thus, we conclude that the axial ligands to F430 in aqueous solution are water molecules. Analysis of the nickel extended x-ray absorption fine structure is consistent with this conclusion. Resonance Raman spectra obtained at room temperature contain features characteristic of both 4- and 6-coordinate forms of the cofactor. We have found that the resonance Raman, optical, and x-ray absorption spectra of aqueous solutions of F430 are temperature-dependent due to a ligand-binding equilibrium involving the square-planar and 6-coordinate bis-aquo forms of the cofactor. At low temperatures (less than 250 K) the 6-coordinate form predominates, whereas higher temperature solutions contain both 4- and 6-coordinate species in a dynamic equilibrium. Similar behavior is observed in other weakly coordinating solvents such as methanol and ethanol. The 4-coordinate form is predominant in solvents with strong electron-withdrawing substituents such as 2,2,2-trifluoroethanol and 2-mercaptoethanol. The relevance of this facile ligand exchange to the active site structure and enzymatic mechanism of the parent enzyme is discussed.