Spin labeling of oligonucleotides with the nitroxide TPA and use of PELDOR, a pulse EPR method, to measure intramolecular distances

In this protocol, we describe the facile synthesis of the nitroxide spin-label 2,2,5,5-tetramethyl-pyrrolin-1-oxyl-3-acetylene (TPA) and then its coupling to DNA/RNA through Sonogashira cross-coupling during automated solid-phase synthesis. Subsequently, we explain how to perform distance measurements between two such spin-labels on RNA/DNA using the pulsed electron paramagnetic resonance method pulsed electron double resonance (PELDOR). This combination of methods can be used to study global structure elements of oligonucleotides in frozen solution at RNA/DNA amounts of approximately 10 nmol. We especially focus on the Sonogashira cross-coupling step, the advantages of the ACE chemistry together with the appropriate parameters for the RNA synthesizer and on the PELDOR data analysis. This procedure is applicable to RNA/DNA strands of up to approximately 80 bases in length and PELDOR yields reliably spin-spin distances up to approximately 6.5 nm. The synthesis of TPA takes approximately 5 days and spin labeling together with purification approximately 4 days. The PELDOR measurements usually take approximately 16 h and data analysis from an hour up to several days depending on the extent of analysis.     

Rapid preparation of the mitotic kinesin Eg5 inhibitor monastrol using controlled microwave-assisted synthesis

We present here a protocol for the synthesis of the dihydropyrimidine (DHPM) derivative monastrol, which is known to be a specific mitotic kinesin Eg5 inhibitor. By applying controlled microwave heating under sealed-vessel conditions, the synthesis via the one-pot three-component Biginelli condensation can be performed in a shorter reaction time (30 min) compared with conventional heating methods that normally require several hours of reflux heating. For the purification of the crude target compound, two different methods are presented. The first protocol includes a simple precipitation/filtration step to provide monastrol in 76% isolated yield and high purity so that no recrystallization step is necessary. This can be ascribed to the microwave heating technology in which less side-product formation is typically one of the advantages. In an alternative purification step, column chromatography is performed, which provides the product in a slightly higher yield (86%). Monastrol synthesis can be conducted in approximately 2 h by employing the precipitation/filtration purification method.     

Regioselective one-pot protection of glucose

Detailed protocols for the regioselective protection of individual hydroxyls in monosaccharide units are described here. This expedient methodology incorporates up to seven reaction sequences, obviating the necessity to carry out intermittent tedious work-ups and time-consuming purifications. Using this TMSOTf-catalyzed one-pot protocol, the 2,3,4,6-tetra-O-trimethylsilylated hexopyranosides bearing an anomeric group could be transformed into a whole set of differentially protected 2-alcohols, 3-alcohols, 4-alcohols, 6-alcohols and fully protected monosaccharides in high yields. These tailor-made glycosyl donors and acceptors can then be used for stereoselective one-pot glycosylation for oligosaccharide synthesis. The total time for the preparation of a purified protected sugar unit ranges between 1 and 2 d. This process would otherwise take 1-2 weeks.     

DNA containing side chains with terminal triple bonds: Base-pair stability and functionalization of alkynylated pyrimidines and 7-deazapurines

The synthesis of a series of oligonucleotides containing 5-substituted pyrimidines as well as 7-substituted 7-deazapurines bearing diyne groups with terminal triple bonds is reported. The modified nucleosides were prepared from the corresponding iodo nucleosides and diynes by the Sonogashira cross-coupling reaction. They were converted into phosphoramidites and employed in solid-phase synthesis of oligonucleotides. The effect of the diyne modifications on the duplex stability was investigated. The modified nucleosides were used for further functionalization using the protocol of Huisgen-Sharpless [2+3] cycloaddition ('click chemistry').     

Rapid microwave-enhanced synthesis of C5-alkynyl pyranonucleosides as novel cytotoxic antitumor agents

A microwave-assisted, one-pot, coupling reaction for the synthesis of C5-alkynyl-uracil and cytosine glucopyranonucleosides has been developed. The reaction is carried out under standard Sonogashira coupling conditions from glucopyranonucleosides of 5-iodouracil or 5-iodocytosine and various terminal alkynes. All compounds were evaluated for their cytostatic and antiviral activity. The 5-phenylethynyluracil pyranonucleoside derivative 6a showed the most promising cytostatic activity (50% inhibitory concentration in the lower micromolar range). No meaningful antiviral activity was recorded.     

Regioselective monodeprotection of peracetylated carbohydrates

This protocol describes the regioselective deprotection of single hydroxyls in peracetylated monosaccharides and disaccharides by enzymatic or chemoenzymatic strategies. The introduction of a one-pot enzymatic step by using immobilized biocatalysts obviates the requirement to carry out tedious workups and time-consuming purifications. By using this straightforward protocol, different per-O-acetylated glycopyranosides (mono- or disaccharides, 1-substituted or glycals) can be transformed into a whole set of differentially monodeprotected 1-alcohols, 3-alcohols, 4-alcohols and 6-alcohols in high yields. These tailor-made glycosyl acceptors can then be used for stereoselective glycosylation for oligosaccharide and glycoderivative synthesis. They have been successfully used as building blocks to synthesize tailor-made di- and trisaccharides involved in the structure of lacto-N-neo-tetraose and precursors of the tumor-associated carbohydrate antigen T and the antitumoral drug peracetylated β-naphtyl-lactosamine. We are able to prepare a purified monoprotected carbohydrate in between 1 and 4 d. With this protocol, the small library of monodeprotected products can be synthesized in 1-2 weeks.     

Optimized synthesis of phosphatidylserine

The synthesis of phosphatidyl serine containing saturated fatty acids was thoroughly studied and optimized in order to establish a protocol amenable to large-scale synthesis. The key step was a one-pot multicomponent reaction involving an O-benzyl phosphorodiamidite, protected serine and diacylglycerol, followed by in situ oxidation of the resulting phosphite. In order to replace expensive and poorly stable tetrazole, a screening of substitutes was carried out and imidazolium chloride was selected as the best suited one.     

2-pyrones possessing antimicrobial and cytotoxic activities

The 2-pyrone sub-unit is found in a number of natural products possessing broad spectrum biological activity. Such compounds are validated as being capable of binding to specific protein domains and able to exert a remarkable range of biological effects. In an effort to identify synthetic 2-pyrones with interesting biological effects, herein we report the synthesis and biological evaluation of 4-substituted-6-methyl-2-pyrones. Synthetic routes to 4-alkyl/alkenyl/aryl/alkynyl-6-methyl-2-pyrones have been developed utilising Sonogashira, Suzuki and Negishi cross-coupling starting from readily available 4-bromo-6-methyl-2-pyrone. Specific conditions for each organometallic protocol were required for successful cross-coupling. In particular, a triethylamine/acetonitrile--base/solvent mixture was crucial to Sonogashira alkynylation of 4-bromo-6-methyl-2-pyrone, whereas thallium carbonate was a mandatory base for the Suzuki cross-coupling of trialkylboranes. The 2-pyrones demonstrate potent inhibitory activity against Bacillus subtilis, Escherichia coli, Staphylococcus aureus, Schizosaccharomyces pombe and Botrytis cinerea. The growth inhibitory activities of selected 2-pyrones were determined in A2780 human ovarian carcinoma and K562 human chronic myelogenous leukaemia cell lines using an in vitro cell culture system (MTT assay). These studies demonstrate that 4-phenylethynyl-, 4-tetrahydropyranylpropargyl ether- and 4-ethynyl-6-methyl-2-pyrones have excellent potential as a new class of anticancer agents.     

An expedient, facile and simple one-pot synthesis of 2-methylenealkanoates and alkanenitriles from the Baylis-Hillman bromides in aqueous media

This protocol is for an expedient and operationally simple one-pot synthesis of 2-methylenealkanoates and alkanenitriles in high yields from the corresponding Baylis-Hillman bromides. The reaction proceeds via the successive treatment with 1,4-diazabicyclo(2.2.2)octane (DABCO) for 15 min and sodium borohydride for 15 min in aqueous media [tetrahydrofuran (THF):H2O (1:1)] at room temperature.     

2-Nitroglycals: versatile intermediates for efficient and highly stereoselective base-catalyzed glycoside bond formations

This protocol describes the O-glycosyl trichloroacetimidate-based glycosylation of protected galactal 1 as acceptor under Sn(OTf)(2) catalysis to give disaccharide 4. Nitration of the galactal moiety using nitric acid-acetic acid as nitrating agent followed by base-promoted acetic acid elimination affords the 2-nitro derivative 6 in a one-pot procedure. These types of intermediates can be used in the stereoselective synthesis of glycosides via Michael-type addition of alcohols as nucleophiles to 2-nitroglycals. Here, the base-catalyzed alpha-selective addition of N-Boc-protected Ser and Thr esters (7a, b) is described, which leads stereoselectively to adducts 8a, b. Transformation into the corresponding 2a-acetylamino derivates 9a, b provides versatile mucin core 1 building blocks (the total time for synthesizing 9a, b starting from 1 to 2 is typically 7 d with an overall yield of 18-25%). Also various other types of nucleophiles are amenable to this Michael-type addition 2-nitroglycals.     

Direct one-pot conversion of acylated carbohydrates into their alkylated derivatives under heterogeneous reaction conditions using solid NaOH and a phase transfer catalyst

A convenient one-pot protocol for the direct conversion of acyl-protected carbohydrates into their alkylated counterparts has been developed by using alkyl halides in the presence of solid sodium hydroxide and a phase transfer catalyst. These economically convenient, mild, two-phase reaction conditions allow the preparation of a variety of monosaccharide intermediates for use in the synthesis of complex oligosaccharides.     

Microwave-assisted, one-pot syntheses and fungicidal activity of polyfluorinated 2-benzylthiobenzothiazoles

Polyfluorinated 2-benzylthiobenzothiazoles 3a–l are prepared via a microwave-assisted, one-pot procedure. The advantages, such as good to excellent yields, shorter reaction time (14–21 min), readily available starting material, and simple purification procedure, distinguish the present protocol from other existing methods used for the synthesis of 2-benzylthiobenzothiazoles. Bioassay indicated that most of the compounds showed significant fungicidal activity against Rhizoctonia solani, Botrytis cinereapers, and Dothiorella gregaria at a dosage of 50 μg/mL. Interestingly, compared to the control of commercial fungicide, triadimefon, compound 3c exhibited much higher activities against R. solani, B. cinereapers, and D. gregaria, which showed that the polyfluorinated 2-benzylthiobenzothiazoles can be used as lead compound for developing novel fungicides.     

Synthesis of an acromelic acid A analog-based 11C-labeled PET tracer for exploration of the site of action of acromelic acid A in allodynia induction

A novel ¹¹C-labeled PET (positron emission tomography) tracer, which was designed based on the (phenylthio)pyrrolidine derivative that can competitively block the acromelic acid A-induced allodynia, was synthesized. A protocol in which methylation by palladium-mediated coupling of the boronate derivative with [¹¹C]CH₃I and deprotection of the protected amino acid moiety are successively performed in one-pot within 5 min was established for the synthesis of the tracer. The tracer is potentially useful as a tool to investigate the mode of action of acromelic acid A in the induction of allodynia.     

Iodine-catalyzed one-pot synthesis and antimalarial activity evaluation of symmetrically and asymmetrically substituted 3,6-diphenyl[1,2,4,5]tetraoxanes

A novel iodine-catalyzed one-pot synthesis of symmetrically and asymmetrically substituted 3,6-diphenyl-[1,2,4,5]tetraoxanes is described. The synthetic protocol is general with substituted benzaldehydes and proceeds well under acidic conditions. Total 17 tetraoxanes have been prepared during this study and some of these compounds exhibit promising antimalarial activity. None of the compounds shows any toxicity against vero cells.     

Modified PNAs: a simple method for the synthesis of monomeric building blocks

The synthesis of PNA-monomers with variations in the substitution pattern using the Ugi-Reaction is described. The one-pot procedure leads to new totally protected PNA-monomers which can be selectively cleaved to N-protected monomeric building blocks for PNA synthesis.     

Programmable reactivity-based one-pot oligosaccharide synthesis

A detailed protocol is described for the application of a programmable one-pot oligosaccharide synthesis methodology to the synthesis of fucosyl GM1. This serves as a general example of the application of this method to the synthesis of any desired oligosaccharide. The method relies on a large database of relative reactivities for differentially protected tolyl thioglycoside donor molecules and a computer program to suggest the best order of addition for assembly of the oligosaccharide in optimal yield and with the fewest operations. The product is a protected form of the desired oligosaccharide isolated in 47% yield, which is then deprotected using standard procedures to provide fucosyl GM1 oligosaccharide (1) in 44% yield. The total time for synthesis of 1 from building blocks 3, 4 and 5 is approximately 4 d, whereas synthesis of the same compound by traditional stepwise procedures would take significantly longer. Protocols for the synthesis of thioglycoside building blocks 3 and 4 are also described.     

An efficient Mitsunobu protocol for the one-pot synthesis of S-glycosyl amino-acid building blocks and their use in combinatorial spot synthesis of glycopeptide libraries

Complex glycosylation patterns on cell surfaces are involved in many fundamental biological processes like specific cell-cell interactions and signal transduction. Furthermore, the glycon part of glycopeptides and glycosylated proteins play a crucial role in numerous ligand-receptor interactions of biological significance. However, the distinct function of complex carbohydrate structures associated with cell surfaces and proteins is still only poorly understood at a molecular level with regard to specific carbohydrate-protein interaction. Here, we present an efficient Mitsunobu protocol for the convenient chemical one-pot preparation of S-glycosyl amino-acid building blocks suitable for automated combinatorial syntheses of highly glycosylated beta-peptides, which, in turn, can serve as potential mimics for complex oligosaccharides or for studying carbohydrate-protein interactions. The protocol also describes the use of the S-glycosyl amino-acid building blocks for combinatorial spot syntheses of glycopeptide libraries and can be used for the construction of other combinatorial peptide libraries as well. This is a procedure that can be completed in approximately 7 days.     

Chemoenzymatic synthesis and antibody detection of DNA glycoconjugates

A chemoenzymatic approach for the efficient synthesis of DNA-carbohydrate conjugates was developed and applied to an antibody-based strategy for the detection of DNA glycoconjugates. A phosphoramidite derivative of N-acetylglucosamine (GlcNAc) was synthesized and utilized to attach GlcNAc sugars to the 5'-terminus of DNA oligonucleotides by solid-phase DNA synthesis. The resulting GlcNAc-DNA conjugates were used as substrates for glycosyl transferase enzymes to synthesize DNA glycoconjugates. Treatment of GlcNAc-DNA with beta-1,4-galactosyl transferase (GalT) and UDP-Gal produced N-acetyllactosamine-modified DNA (LacNAc-DNA), which could be converted quantitatively to the trisaccharide Lewis X (LeX)-DNA conjugate by alpha-1,3-fucosyltransferase VI (FucT) and GDP-Fuc. The facile enzymatic synthesis of LeX-DNA from GlcNAc-DNA also was accomplished in a one-pot reaction by the combined action of GalT and FucT. The resulting glycoconjugates were characterized by gel electrophoresis, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS), and glycosidase digestion experiments. Covalent modification of the 5'-terminus of DNA with carbohydrates did not interfere with the ability of DNA glycoconjugates to hybridize with complementary DNA, as indicated by UV thermal denaturation analysis. The trisaccharide DNA glycoconjugate, LeX-DNA, was detected by a dual DNA hybridization/monoclonal antibody (mAb) detection protocol ("Southwestern"): membrane-immobilized LeX-DNA was visualized by Southern detection with a radiolabeled complementary DNA probe and by Western chemiluminescence detection with a mAb specific for the LeX antigen. The efficient chemoenzymatic synthesis of DNA glycoconjugates and the Southwestern detection protocol may facilitate the application of glycosylated DNA to cellular targeting and DNA glycoconjugate detection strategies.     

Reaction modelling and simulation to assess the integrated use of transketolase and ω-transaminase for the synthesis of an aminotriol

The most attractive, as well as challenging, multistep organic syntheses would preferably be carried out in a single reactor, as a one-pot synthesis. For biocatalytic syntheses, multistep reactions in one-pot mode bring a number of advantages, while at the same time raising unique challenges such as the compatibility of different biocatalysts. In this paper, we have developed a transketolase-transaminase (TK-TAm) two-step one-pot aminotriol synthesis reaction model, which integrates reaction kinetic models with process characterization (consisting of component degradation as a function of pH and concentration, aldehyde toxicity towards the enzyme, and ketol donor and acceptor side-reactions with TAm). Based on the analysis of the effect of the TAm/TK activity ratio on product yield, simulations provided guidance for further process and biocatalyst development.     

Reaction modelling and simulation to assess the integrated use of transketolase and ω-transaminase for the synthesis of an aminotriol

The most attractive, as well as challenging, multistep organic syntheses would preferably be carried out in a single reactor, as a one-pot synthesis. For biocatalytic syntheses, multistep reactions in one-pot mode bring a number of advantages, while at the same time raising unique challenges such as the compatibility of different biocatalysts. In this paper, we have developed a transketolase–transaminase (TK-TAm) two-step one-pot aminotriol synthesis reaction model, which integrates reaction kinetic models with process characterization (consisting of component degradation as a function of pH and concentration, aldehyde toxicity towards the enzyme, and ketol donor and acceptor side-reactions with TAm). Based on the analysis of the effect of the TAm/TK activity ratio on product yield, simulations provided guidance for further process and biocatalyst development.