19F NMR monitoring of a SNAr reaction on solid support

Protecting-group-based colorimetric monitoring of fluorous-phase and solid-phase synthesis of oligoglucosamines

A new hydroxyl protecting group, nitrophthalimidobutyric (NPB) acid, has been synthesized in one solvent-free step for colorimetric monitoring of reaction cycles upon its facile removal with hydrazine acetate in the solid-phase and fluorous-phase syntheses of antigenic oligoglucosamines associated with infectious Staphylococcus aureus. The NPB group serves as a convenient hydroxyl protecting group that is stable to the basic conditions required for the synthesis of the common trichloroacetimidate protecting groups, the strongly acidic conditions used in glycosylation reactions, as well as conditions commonly used to remove silicon-based protecting groups.

Parallel solid-phase synthesis and high-throughput 1H NMR evaluation of a 96-member 1,2,4-trisubstituted-pyrimidin-6-one-5-carboxylic acid library

A solid-phase organic synthesis method has been developed for the preparation of trisubstituted pyrimidin-6-one carboxylic acids 12, which allows elaboration to a 3-dimensional combinatorial library. Three substituents are introduced by initial Knoevenagel condensation of an aldehyde and malonate ester resin 7 to give resin bound 1. Cyclization of 1 with an N-substituted amidine 10, oxidation, and cleavage afforded pyrimidinone 12. The initial solid-phase reaction sequence was followed by gel-phase (19)FNMR and direct-cleavage (1)H NMR of intermediate resins to determine the optimal conditions. The scope of the method for library production was determined by investigation of a 3 x 4 pilot library of twelve compounds. Cyclocondensation of N-methylamidines and 7 followed by CAN oxidation gave mixtures of the resin bound pyrimidin-6-one 11 and the regioisomeric pyrimidin-4-one 15, which after cleavage from the resin afforded a nearly 1:1 mixture of pyrimidin-6-one and pyrimidin-4-one carboxylic acids 12 and 16, respectively. The regiochemical assignment was confirmed by ROESY1D and gHMBC NMR experiments. A library was prepared using 8 aldehydes, 3 nitriles, and 4 amines to give a full combinatorial set of 96 pyrimidinones 12. Confirmation of structural identity and purity was carried out by LCMS using coupled ELS detection and by high-throughput flow (1)H NMR.

Gel-phase19F NMR spectral quality for resins commonly used in solid-phase organic synthesis; a study of peptide solid-phase glycosylations

The spectroscopic properties for seven different commercial resins used in solid-phase synthesis were investigated with (19)F NMR spectroscopy. A fluorine-labeled dipeptide was synthesized on each resin, and the resolution of the (19)F resonances in CDCl(3), DMSO-d(6), benzene-d(6) and CD(3)OD were measured with a conventional NMR spectrometer, i.e. without using magic angle spinning. In general, resins containing poly(ethylene glycol) chains (ArgoGel, TentaGel and PEGA) were found to be favorable for the (19)F NMR spectral quality. Three serine containing tri-, penta-, and heptapeptides were then prepared on an ArgoGel resin functionalized with a fluorine-labeled linker. The resin bound peptides were glycosylated utilizing a thiogalactoside glycosyl donor carrying fluorine-labeled protective groups. Monitoring of the glycosylations with gel-phase (19)F NMR spectroscopy allowed each glycopeptide to be formed in similar 80% yield, using a minimal amount of glycosyl donor (3 x 2 equivalents). In addition, it was found that the glycosylation yields were independent of peptide length.

Solid-phase synthesis of alpha-Gal epitopes: on-resin analysis of solid-phase oligosaccharide synthesis with 19F NMR spectroscopy

A route for solid-phase synthesis of the alpha-Gal epitopes Gal(alpha1-3)Gal(beta1-4)Glc and Gal(alpha1-3)Gal(beta1-4)GlcNAc is described. These trisaccharide antigens are responsible for hyperacute rejection in xenotransplantation of porcine organs. Optimization of the solid-phase synthesis relied on use of fluorinated protective groups for the carbohydrate building blocks and use of a fluorinated linker. This allowed convenient on-resin analysis of the reactions with gel-phase (19)F NMR spectroscopy. Conditions were established which allowed reductive ring-opening of 4,6-O-benzylidene acetals to be performed on the solid phase with high regioselectivity to furnish the corresponding 6-O-benzyl ethers. It was found that glycosylations could be conveniently carried out by using thioglycosides as donors with N-iodosuccinimide and trifluoromethanesulfonic acid as the promoter system. With use of these conditions a challenging alpha-glycosidic linkage was successfully installed with complete stereoselectivity in the final glycosylation. It was also established that fluorinated benzoates, benzyl ethers, and benzylidene acetals display almost identical chemical properties as their nonfluorinated counterparts, a finding that is essential for future use of fluorinated protective groups in solid-phase oligosaccharide synthesis.

Analytical methods for the monitoring of solid phase organic synthesis

Solid phase synthesis (SPS) is a powerful technique to assemble compound libraries in high-throughput parallel and combinatorial synthesis. The widespread applications of these techniques required the development of analytical methods for both structural elucidation and reaction monitoring. This review covers some recently developed techniques for on-bead analyses together with solution-state ones. Particular emphasis is devoted to software and hardware improvements for automated high-throughput analysis.

Development and application of a carbonyl-(13)C-enriched backbone amide linker for solid-phase reaction monitoring

The synthesis and application of a carbonyl-(13)C backbone amide linker are described. The labeled unit is conveniently mixed with commercial resins, providing a rapid means of monitoring chemistry performed with this linker on solid support using conventional (13)C NMR methods.

High resolution MAS-NMR in combinatorial chemistry

High-resolution magic angle spinning (hr-MAS) NMR is a powerful tool for characterizing organic reactions on solid support. Because magic angle spinning reduces the line-broadening due to dipolar coupling and variations in bulk magnetic susceptibility, line widths approaching those obtained in solution-phase NMR can be obtained. The magic angle spinning method is amenable for use in conjunction with a variety of NMR-pulse sequences, making it possible to perform full-structure determinations and conformational analysis on compounds attached to a polymer support. Diffusion-weighted MAS-NMR methods such as SPEEDY (Spin-Echo-Enhanced Diffusion-Filtered Spectroscopy) can be used to remove unwanted signals from the solvent, residual reactants, and the polymer support from the MAS-NMR spectrum, leaving only those signals arising from the resin-bound product. This review will present the applications of high-resolution magic angle spinning NMR for use in combinatorial chemistry research.

Use of fluorobenzoyl protective groups in synthesis of glycopeptides: beta-elimination of O-linked carbohydrates is suppressed

Fluorobenzoyl groups have been investigated as alternatives to acetyl and benzoyl protective groups in carbohydrate and glycopeptide synthesis. D-Glucose and lactose were protected with different fluorobenzoyl groups and then converted into glycosyl bromides in high yields (>80% over two steps). Glycosylation of protected derivatives of serine with these donors gave 1,2-trans glycosides in good yields (approximately 60--70%) and excellent stereoselectivity without formation of ortho esters. The resulting glycosylated amino acid building blocks were then used in solid-phase synthesis of two model O-linked glycopeptides known to be unusually sensitive to beta-elimination on base-catalyzed deacylation. When either a 3-fluoro- or a 2,5-difluorobenzoyl group was used for protection of each of the two model glycopeptides the extent of beta-elimination decreased from 80% to 10% and from 50% to 0%, respectively, as compared to when using the ordinary benzoyl group. Fluorobenzoyl groups thus combine the advantages of the benzoyl group in formation of glycosidic bonds (i.e., high stereoselectivity and low levels of ortho ester formation) with the ease of removal characteristic of the acetyl group.

Quantitative Determination of Resin Loading in Solid-Phase Organic Synthesis Using (13)C MAS NMR

The use of quantitative carbon nuclear magnetic resonance spectroscopy ((13)C NMR) for the determination of resin loadings has been investigated. Magic angle spinning (MAS) NMR spectra have been obtained for solvent-swollen resins on a conventional 7 mm CP/MAS probe using the two pulse phase modulation (TPPM) proton decoupling sequence. Loadings of resin-bound organic compounds were evaluated via addition of tetrakis(trimethylsilyl)silane as reference or using the carbon resonances of the polymeric resin material as an internal standard. Results for several functionalized Wang and trityl resins are consistent with those obtained using well-established analytical methods. The (13)C NMR method has interesting applications in the field of solid-phase organic synthesis (SPOS), since no functional group acting as a support for the attachment of a quantifiable chromophore must be available in the material of interest.

Development of an easy-to-use mass spectrometric technique to monitor solid-phase reactions on polystyrene supports

By using mass spectrometry as an analytical tool to characterise substituted, cross-linked polystyrene resins, it is possible to directly monitor the progress of the solid-phase reactions performed on these resins without prior cleavage of the resin-bound molecules. Therefore, this is a true on-resin analytical method. The mass-to-charge ratios observed in the mass spectra are readily assigned to fragments of the polymer that include the chemically bound substituents. This is the first time that the formation and breaking of bonds have been directly observed on the polymeric support. Furthermore, the relative intensities of the signals in the mass spectra provide a measure of the completeness of the reaction. Because these measurements are rapidly performed without further chemical transformations or cleavage procedures, and because only minimal amounts of material are needed, this technique could become the solid-phase equivalent of thin-layer chromatography used in classical liquid-phase chemistry.

Polymer-supported tetrafluorophenol: a new activated resin for chemical library synthesis

A new tetrafluorophenol activated resin that facilitates the use of 19F NMR to quantitate loading is presented. This new resin provides a useful tool for acylation, and a novel activated polymeric sulfonate ester to generate sulfonamides. This activated resin reacts with a wide scope of N-nucleophiles including primary and secondary amines, and anilines. This new activated resin methodology provides a powerful tool for pure single-compound library synthesis.

Preparation of fluorinated linkers: use of 19F NMR spectroscopy to establish conditions for solid-phase synthesis of pilicide libraries

Three fluorinated linkers which are analogues of linkers commonly used in solid-phase peptide synthesis have been prepared. One of the linkers was used in combination with gel-phase 19F NMR spectroscopy to develop conditions for solid-phase synthesis of two libraries of pilicides, i.e. compounds designed to inhibit assembly of adhesive pili in uropathogenic Escherichia coli. Attachment to and cleavage from the linker could be monitored based on the chemical shift of the fluorine atom of the linker. In addition, use of the linker as internal standard allowed quantification and optimization of reactions occurring further away from the linker when fluorinated building blocks were employed. Importantly, high-quality 19F NMR spectra were obtained for compounds linked to a TentaGel resin in a standard NMR tube using an ordinary NMR instrument.

Combined application of analytical techniques for the characterization of polymer supported species

The combined application of a diverse range of analytical techniques is described for the complete analysis of polymer supported molecules. These techniques permit complete description of the FTIR, (1)H NMR, and (13)C NMR spectra. The comparison of supported bicyclo[2.2.2]octane derivatives with analogous species prepared using polymer supported reagents is made.

Combinatorial liquid-phase synthesis of structurally diverse benzimidazole libraries

An expedient liquid-phase synthesis for construction of the diverse benzimidazole libraries is described. Nucleophilic aryl substitution of poly(ethylene glycol)-supported 4-fluoro-3-nitrobenzoic acid 3 with several primary amines under basic conditions, followed by Zn/NH(4)Cl mediated nitro group reduction, gave the PEG bound diamines 5. Subsequent cyclization of immobilized o-phenylenediamine 5 using thiocarbonyldiimidazole (TCD) or thiophosgene in dichloromethane furnished benzimidazole-2-thiones 6. Treatment of 6 with alkyl halides and benzylic halides in the presence of triethylamine provided 1-substituted-2-alkylthio-5-carbamoylbenzimidazoles on the support. The desired products 8 were severed from the PEG under mild conditions in high yield and high purity.

Combinatorial chemistry as a tool for drug discovery

The question 'will combinatorial chemistry deliver real medicines' has been posed [96]. First it is important to realise that the chemical part of the drug discovery process cannot stand alone; the integration of synthesis and biological assays is fundamental to the combinatorial approach. The results presented in Tables 3.1 to 3.8 suggest that so far smaller directed combinatorial libraries have obtained equivalent results to those obtained previously from traditional medicinal chemistry analogue programs. Unfortunately, because of the long time it takes to develop pharmaceutical drugs there are no examples yet of marketed drugs discovered by combinatorial methods. There are interesting examples where active leads have been discovered from the screening of the same library against multiple targets (e.g. libraries 13, 39, 43, 66, 71 and 76). It is now possible to handle much larger libraries of non-oligomeric structures and the chemistry required for such applications is becoming available. Whether combinatorial approaches can also be adapted to deal with all the other requirements of a successful pharmaceutical (lack of toxicity, bioavailability etc.) is open to question but there are already examples such as cassette dosing [235-237]. However we can still be optimistic about the possibility of larger libraries producing avenues of investigation for the medicinal chemist to develop into real drugs. Combinatorial chemistry is an important tool for the medicinal chemist.

On-resin macrocyclization of peptides via intramolecular SnAr reactions

On-resin macrocyclization via an SNAr reaction is employed in the synthesis of tocinoic acid analogs. Specifically, an N-terminal nitrofluorobenzene is attacked by a nucleophilic C-terminal sidechain. The remaining nitro group can be reduced and acylated. NMR is used to compare the conformation of the new macrocyclic peptides to tocinoic acid.

Magic Angle Spinning NMR for Reaction Monitoring and Structure Determination of Molecules Attached to Multipin Crowns

The first example of magic angle spinning NMR on crowns has been demonstrated. The ability to monitor a reaction on a crown and to confirm the structure of the reaction product directly on the crown without resorting to chemical cleavage should greatly enhance the utility of this convenient format for combinatorial chemistry.