Protecting Group Strategy Research Articles

Synthesis and anion binding properties of (thio)urea functionalized Ni(II)-salen complexes.

Salen ligands (salen = N,N'-ethylenebis(salicylimine)) are well-known for their versatility and widespread utility in chelating metal complexes. However, installation of hydrogen-bonding units on the salen framework, particularly functional groups that require amine-based precursors such as (thio)ureas, is difficult to achieve without the use of protecting group strategies. In this report, we show that the phenylketone analog of salicyladehyde is a stable alternative that enables the facile installation of hydrogen bonding (thio)urea groups on the salen scaffold, thus imparting anion binding abilities to a metal salen complex. Synthesis of symmetric N-phenyl(thio)urea salen ligands functionalized at the 3,3'-position and an unsymmetric salen ligand with N-phenylurea at the 5-position was achieved. Subsequent metalation with nickel(II) acetate afforded the nickel(II) complexes that were investigated for their anion binding properties towards F-, Cl-, Br-, CH3COO-, and H2PO4-. Solid-state structures of the nickel(II) complexes as well as the Cl- bound dimer of the symmetric urea complex were obtained. The unusual acidity of the (thio)urea groups is reflected in the pKa-dependent anion binding behavior of the nickel(II) complexes, as elucidated by 1H and 19F Nuclear Magnetic Resonance (NMR) spectroscopy and Diffusion Ordered Spectroscopy (DOSY) experiments.

Benzoylation of Tetrols: A Comparison of Regioselectivity Patterns for O- and S-Glycosides of d-Galactose.

Efficient protecting group strategies are important for glycan synthesis and represent a unique synthetic challenge in differentiating sugar ring hydroxyl groups. Direct methods to enable regioselective protecting group installation are thus desirable. Herein, we explore a one-step regioselective benzoylation to deliver 2,3,6-protected d-galactose building blocks from tetrols across a variety of α- and β-, O- and S-glycoside substrates. We focus on benzoyl chloride as the esterifying reagent and a reaction temperature of -40 °C to screen the regioselectivity outcome for twenty-two different glycosides, based on isolated yields. Using this methodology, we demonstrate the capability for α-linked aryl and alkyl glycosides (O- and S- d-galactosides, d-galactosamines, and l-fucose), delivering consistent isolated yields (>65%) for 2,3,6-benzoylated products. We extend to explore β-linked systems, where the observed regioselectivity is not paralleled. We posit that both steric and electronic factors from the anomeric substituent contribute to modulating the reactivity competition between 2-OH and 4-OH, enabling the formation of regioisomeric mixtures. However, a certain balance of these factors within the aglycon can deliver 2,3,6-regioselectivity, notably for β-O-Et and β-O-CH2CF3 glycosides. The methodology contributes toward understanding the peculiarities of regioselective carbohydrate-protecting group installation, exploring the importance of the anomeric substituent upon ring hydroxyl group reactivity.

Tuning the Solubility of Soluble Support Constructs in Liquid Phase Oligonucleotide Synthesis.

Solubility of the growing oligonucleotide-soluble support constructs in the liquid phase oligonucleotide synthesis (LPOS) is a critical parameter, which affects coupling efficiency, purity, and recovery of the growing oligonucleotides during the chain elongation. In the present study, oligonucleotides have been assembled on a 4-oxoheptanedioic acid (OHDA) linker-derived tetrapodal soluble support using 5'-O-(2-methoxyprop-2-yl)-protected 2'-deoxyribonucleotide phosphoroamidite building blocks with different nucleobase protecting groups [isobutyryl (Gua), 1-butylpyrrolidin-2-ylidene (Gua, Cyt), 2,4-dimethylbenzoyl (Ade, Cyt), and Bz (Thy)]. The solubility of the oligonucleotide-soluble support constructs (molecular mass varying between 3 and 10 kDa) as models of protected tetra-, octa-, dodeca-, hexadeca-, and eicosa-nucleotides was measured in different solvent systems and in potential antisolvents. By tuning the nucleobase protecting group scheme, the solubility can be improved in aprotic organic solvent systems, while the recovery of the constructs in the precipitation, used for the isolation and purification of the growing oligonucleotide intermediates in a protic antisolvent (2-propanol), remained near quantitative. The precipitation-based yield of the protected tetrapodal oligonucleotides varied from a quantitative to 90% yield. Overall yield (for di-: 95%, tri-: 79-96%, tetra-: 82-88%, and pentanucleotides: 68-75%) and purity of the LPOS were evaluated by RP HPLC and MS-spectroscopy of the released oligonucleotide aliquots. In addition, the orthogonality of the OHDA linker was applied to release authentic protected nucleotides from the soluble supports.

Orthogonal Deprotection of Photolabile Protecting Groups and Its Application in Oligosaccharide Synthesis.

We herein report for the first time the inter- and intramolecular orthogonal cleavage of two ortho-nitrobenzyl (NB) analogues. It is shown that the nitroveratryl (NV) group can be photolyzed with high priority when NV and ortho-nitrobenzyl carbonate (oNBC) are used together as the protecting groups of glycans. Notably, the photolytic products could be used directly in the subsequent glycosylation without further purification. With the above-mentioned orthogonal photolabile protecting group strategy in hand, a Mycobacterium tuberculosis tetrasaccharide and a derivative of glucosyl glycerol were rapidly prepared.

Selective Macrocyclization of Unprotected Peptides with an Ex Situ Gaseous Linchpin Reagent.

Peptide cyclization has dramatic effects on a variety of important properties, enhancing metabolic stability, limiting conformational flexibility, and altering cellular entry and intracellular localization. The hydrophilic, polyfunctional nature of peptides creates chemoselectivity challenges in macrocyclization, especially for natural sequences without biorthogonal handles. Herein, we describe a gaseous sulfonyl chloride derived reagent that achieves amine-amine, amine-phenol, and amine-aniline crosslinking through a minimalist linchpin strategy that affords macrocyclic urea or carbamate products. The cyclization reaction is metal-mediated and involves a novel application of sulfine species that remains unexplored in aqueous or biological contexts. The aqueous method delivers unique cyclic or bicyclic topologies directly from a variety of natural bioactive peptides without the need for protecting-group strategies.

Scalable Total Synthesis of (+)-Desmethylxestospongin B.

Herein, the execution of synthetic strategies solving scalability issues observed in the original route is reported, increasing the total yield by 50% compared to the previously disclosed synthesis. A notable restructuring of the route's initial steps to reach a common allylic alcohol intermediate employs a highly stereoselective epoxidation method and avoids superfluous protecting group manipulations while limiting dependence on kinetic resolution in establishing stereochemistry for four of the six chiral centers in (+)-desmethylxestospongin B. Different protecting group strategies to avoid problems with their subsequent removal were considered and enacted; to this end, material was retained as byproducts were suppressed. While the lactam semireduction under Birch conditions requires further investigation, the updated synthesis of (+)-desmethylxestospongin B reported here made it more scalable, affording 0.37 g of this natural product for continued biological studies.

Chemical Synthesis of Fucosylated Chondroitin Sulfate Tetrasaccharide with Fucosyl Branch at the 6-OH of GalNAc Residue.

Fucosylated chondroitin sulfate is a unique glycosaminoglycan isolated from sea cucumbers, with excellent anticoagulant activity. The fucosyl branch in FCS is generally located at the 3-OH of D-glucuronic acid but, recently, a novel structure with α-L-fucose linked to the 6-OH of N-acetyl-galactosamine has been found. Here, using functionalized monosaccharide building blocks, we prepared novel FCS tetrasaccharides with fucosyl branches both at the 6-OH of GalNAc and 3-OH of GlcA. In the synthesis, the protective group strategy of selective O-sulfation, as well as stereoselective glycosylation, was established, which enabled the efficient synthesis of the specific tetrasaccharide compounds. This research enriches knowledge on the structural types of FCS oligosaccharides and facilitates the exploration of the structure-activity relationship in the future.

Versatile approach towards fully desymmetrized trehalose with a novel set of orthogonal protecting groups.

Trehalose-containing glycans play an essential role in bacterial pathogenesis, host-pathogen interaction, and cell signaling. The investigation of trehalose uptake and metabolism in Mycobacteria using synthetic desymmetrized trehalose probes is an important approach for the development of diagnostic tools and potential therapeutics for tuberculosis. Trehalose-derived mycobacterial glycolipids activate the innate immune response through recognition by the C-type lectin Mincle, justifying efforts to develop novel trehalose-based Mincle-dependent adjuvants. The chemical synthesis of trehalose-based glycoconjugates, glycolipids, and small-molecule trehalose probes requires the challenging chemical desymmetrization of eight hydroxyl groups in a C 2-symmetric disaccharide αGlc(1↔1)αGlc. Using a novel set of orthogonal protecting groups, we developed a flexible multiscale synthetic approach to a collection of differently and variably protected fully desymmetrized trehalose derivatives, ready for final chemical modification with relevant functional or reporter groups. Using a regioselective and site-specific protecting group strategy, we performed multiple symmetry-breaking operations, resulting in a library of trehalose-derived orthogonally protected building blocks as a versatile source for the synthesis of complex trehalose-containing glycans.

Sensor Absorbents for Heavy Metal Ions By Low-Cost Functionalization of Porous Carbons

Porous carbons are key materials in electrodes for electrochemical energy storage as well as in water purification. Methods to modify porous carbons to enhance their properties as charge storing or water purification materials have been explored during the past decades [1,2]. The main application fields if porous carbon, water purification and energy storage, are highly cost sensitive. For this reason, there is a need to develop low-cost methods to modify porous carbons. Here, the use of benzoxazine chemistry to modify porous carbons is explored. Benzoxazine chemistry can be considered a protection group strategy for phenols, where the phenols from which the benzoxazines are synthesized, are deprotected upon benzoxazine polymerization. Further, benzoxazine polymerization produces Mannich bridges located near phenol groups, motifs that can be used to capture heavy metal ions. More specifically, in the first step, the porous carbons are partially impregnated with benzoxazine monomers, from melt or solutions to afford powders impregnated far below the liquid saturation level of the particles. That is, the particles retain porosity after the impregnation but still have a dry appearance. After impregnation, the particles are heated over the polymerization temperature of the benzoxazine to afford the porous carbon with immobilized functionalities. As phenols can initiate benzoxazine polymerization and be incorporated in the polymer, this method offers a simple route to produce polymerized and immobilized structure at a carbon interface. Here, results on metal ion absorption and the electrochemical response after exposure are presented for carbons modified by impregnation-polymerization of benzoxazines with or without incorporation of phenols. Inks were manufactured from the modified carbons. The electrochemical characterizations were performed on printed arrays of electrochemical cells on a substrate having dimensions of well plates and intended for automatized testing and where the carbon inks were deposited on the working electrodes. This methodology has a potential of simplifying the development of sensor materials and absorbents and can be automatized and potentially be supported with machine learning schemes. The electrochemical responses of exposure of the modified carbon electrodes to metal salt solutions show that impregnation-polymerization of functional benzoxazine can produce absorbents responding electrochemically to metal ion absorption with a scalable process starting from low-cost materials.

Practical Synthesis of N-Formylmethionylated Peptidyl-tRNA Mimics.

Hydrolysis-resistant RNA-peptide conjugates that mimic peptidyl-tRNAs are frequently needed for structural and functional studies of protein synthesis in the ribosome. Such conjugates are accessible by chemical solid-phase synthesis, allowing for the utmost flexibility of both the peptide and the RNA sequence. Commonly used protection group strategies, however, have severe limitations with respect to generating the characteristic Nα-formylmethionyl terminus because the formyl group of the conjugate synthesized at the solid support is easily cleaved during the final basic deprotection/release step. In this study, we demonstrate a simple solution to the problem by coupling appropriately activated Nα-formyl methionine to the fully deprotected conjugate. The structural integrity of the obtained Nα-formylmethionyl conjugate─and hence the chemoselectivity of the reaction─were verified by Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry sequence analysis. Additionally, we confirmed the applicability of our procedure for structural studies by obtaining two structures of the ribosome in complex with either fMAI-nh-ACCA or fMFI-nh-ACCA in the P site and ACC-PMN in the A site of the bacterial ribosome at 2.65 and 2.60 Å resolution, respectively. In summary, our approach for hydrolysis-resistant Nα-formylated RNA-peptide conjugates is synthetically straightforward and opens up new avenues to explore ribosomal translation with high-precision substrate mimics.

Total Synthesis and Structural Studies of Zwitterionic Bacteroides fragilis Polysaccharide A1 Fragments.

Zwitterionic polysaccharides (ZPSs) are exceptional carbohydrates, carrying both positively charged amine groups and negatively charged carboxylates, that can be loaded onto MHC-II molecules to activate T cells. It remains enigmatic, however, how these polysaccharides bind to these receptors, and to understand the structural features responsible for this "peptide-like" behavior, well-defined ZPS fragments are required in sufficient quantity and quality. We here present the first total synthesis of Bacteroides fragilis PS A1 fragments encompassing up to 12 monosaccharides, representing three repeating units. Key to our successful syntheses has been the incorporation of a C-3,C-6-silylidene-bridged "ring-inverted" galactosamine building block that was designed to act as an apt nucleophile as well as a stereoselective glycosyl donor. Our stereoselective synthesis route is further characterized by a unique protecting group strategy, built on base-labile protecting groups, which has allowed the incorporation of an orthogonal alkyne functionalization handle. Detailed structural studies have revealed that the assembled oligosaccharides take up a bent structure, which translates into a left-handed helix for larger PS A1 polysaccharides, presenting the key positively charged amino groups to the outside of the helix. The availability of the fragments and the insight into their secondary structure will enable detailed interaction studies with binding proteins to unravel the mode of action of these unique oligosaccharides at the atomic level.

New method for peptide purification based on selective removal of truncation peptide impurities after SPPS with orthogonal capping.

Peptide purification by high-performance liquid chromatography (HPLC) is associated with high solvent consumption, relatively large effort and lack of efficient parallelization. As an alternative, many catch-and-release (c&r) purification methods have been developed over the last decades to enable the efficient parallel purification of peptides originating from solid-phase peptide synthesis (SPPS). However, with one exception, none of the c&r systems has been widely established in industry and academia until today. Herein, we present an entirely new chromatography-free purification concept for peptides synthesized on a solid support, termed reactive capping purification (RCP). The RCP method relies on the capping of truncation peptides arising from incomplete coupling of amino acids during SPPS with a reactive tag. The reactive tag contains a masked functionality that, upon liberation during cleavage from the resin, enables straightforward purification of the peptide by incubation with a resin-bound reactive moiety. In this work, two different reactive tags based on masked thiols were developed. Capping with these reactive tags during SPPS led to effective modification of truncated sequences and subsequent removal of the latter by chemoselective reaction with a maleimide-functionalized solid support. By introducing a suitable protecting group strategy, the thiol-based RCP method described here could also be successfully applied to a thiol-containing peptide. Finally, the purification of a 15-meric peptide by the RCP method was demonstrated. The developed method has low solvent consumption, has the potential for efficient parallelization, uses readily available reagents, and is experimentally simple to perform.

Highly stereoselective synthesis of heparin tri- and tetra-saccharide derivatives

<p indent="0mm">Heparin, a naturally highly sulfated glycosaminoglycan, mediates various physiologic and pathophysiologic processes, and is mainly used for the prevention and treatment of venous thrombosis in clinic. Here we report an efficient synthesis of heparin oligosaccharides with different degrees of 6-<italic>O</italic>-sulfonation modification, employing orthogonal protective group strategy. <italic>tert</italic>-Butyldiphenylsilyl (TBDPS) group is used as the protective group of 6-OH of the 2-azide-glucose donors, and highly α-selective construction of the key GlcN-(1→4)-GlcUA glycosidic bond was achieved with the corresponding <italic>N</italic>-phenyl trifluoroacetimidate donors. Thus, tri- and tetra-saccharides are synthesized by the convergent [1 + 2] and [2 + 2] glycosylation. The fully elaborated oligosaccharides have then been successfully transformed into the target heparin oligosaccharides <bold>28</bold>–<bold>34</bold> <italic>via</italic> an optimal sequence of manipulation of the protecting groups. The post-assembly manipulations include desilylation with HF·Py (for removal of TBDPS group), delevulinoylation with hydrazine hydrate (for removal of levulinoyl group), saponification under Zemplén conditions (for removal of methyl ester and benzoyl group), <italic>O</italic>-sulfonation with sulfur trioxide pyridine complex (for hydroxyl groups), reduction and <italic>N</italic>-sulfonation (for azido group), and atmospheric pressure hydrogenation (for removal of benzyl and Cbz groups). The availability of these heparin oligosaccharide derivatives which bear amino linker shall facilitate the preparation of glycan chips for studies on the interaction between heparin oligosaccharides with proteins, such as the heparanase.

Divergent Synthesis of Six Recent Berkeleylactones.

The six recently isolated berkeleylactones E, J, K, M, N, and O were synthesized for the first time by a divergent strategy starting from a common intermediate in our synthesis of berkeleylactone A. Key features were the stereoselective formation of the γ,δ-dihydroxy-α,β-unsaturated ester moiety and the development of a general protection group strategy. Along the way we also established a short high-yielding formal synthesis of the often-synthesized antibiotic A26771B.

Synthesis of Bifunctional Lipoxin‐Derived Enzyme‐Triggered CO‐Releasing Molecules (LipET‐CORMs)

AbstractIn an attempt to develop new anti‐inflammatory agents which act by co‐release of carbon monoxide (CO) and a specialized pro‐resolving mediator, we designed conjugates of a lipoxin A4 analogue and an acyloxycyclohexadiene‐Fe(CO)3 complex as an esterase‐triggered CO‐releasing molecule (ET‐CORM). After adjustment of the protecting group strategy, two of such compounds were successfully prepared by total synthesis (12 steps; 4–5 % overall yield) starting from deoxy‐d‐ribose and exploiting a Wittig olefination and an intermolecular Heck reaction as key C−C bond‐forming steps. A crucial late reduction of an aryl‐ketone moiety in the presence of a highly sensitive dienol ester functionality was achieved with BH3‐SMe2 in the presence of catalytic amounts of NaBH4. Both target compounds were dose‐dependently toxic towards cultured human umbilical vein endothelial cells (HUVEC), with LipET‐CORM 1‐A being slightly more toxic. While induction of heme oxygenase 1 (HO‐1) in HUVEC was observed for both compounds, they did not inhibit TNF‐α‐mediated VCAM‐1 expression in these cells. In M2 polarized macrophages HO‐1 expression was more pronounced as compared to M1 polarized macrophages. In both types of macrophages HO‐1 expression was downregulated by lipopolysaccharide, but only in M2 macrophages HO‐1 expression was rescued by LipET‐CORM. 15‐Lipoxygenase (15‐LO) was only expressed in M2 macrophages and was not influenced by LipET‐CORM. Collectively our data demonstrate that LipET‐CORMs induce HO‐1 expression in endothelial cells and M2 polarized macrophages. The role of the intra‐cellular released lipoxin A4 in resolution of inflammation, however, remains to be assessed.

A safety-catch protecting group strategy compatible with Boc-chemistry for the synthesis of peptide nucleic acids (PNAs).

Peptide Nucleic Acids (PNAs) are an intriguing class of synthetic biomolecules with great potential in medicine. Although PNAs could be considered analogs of oligonucleotides, their synthesis is more like that of peptides. In both cases, a Solid-Phase Synthesis (SPS) approach is used. Herein, the advantage using Boc as a temporal protecting group has been demonstrated to be more favored than Fmoc. In this context, a new PNA SPS strategy has been developed based on a safety-catch protecting group scheme for the exocyclic nitrogen of the side-chain bases and the linker. Sulfinyl (sulfoxide)-containing moieties are fully stable to the trifluoroacetic acid (TFA) used to remove the Boc group, but they can be reduced to the corresponding sulfide derivatives, which are labile in the presence of TFA. The efficiency of this novel synthetic strategy has been demonstrated in the synthesis of the PNA pentamer H-PNA(TATCT)-βAla-OH.

Total Synthesis of a Pentasaccharide O-Glycan from Acinetobacter baumannii.

Acinetobacter baumannii is a Gram-negative bacteria associated with drug resistance and infection in healthcare settings. An understanding of both the biological roles and antigenicity of surface molecules of this organism may provide an important step in the prevention and treatment of infection through vaccination or the development of monoclonal antibodies. With this in mind, we have performed the multistep synthesis of a conjugation-ready pentasaccharide O-glycan from A. baumannii with a longest linear synthetic sequence of 19 steps. This target is particularly relevant due to its role in both fitness and virulence across an apparently broad range of clinically relevant strains. Synthetic challenges include formulating an effective protecting group scheme as well as the installation of a particularly difficult glycosidic linkage between the anomeric position of a 2,3-diacetamido-2,3-dideoxy-D-glucuronic acid and the 4-position of D-galactose.

From Peptide Nucleic Acids to Supramolecular Structures of Nucleic Acid Derivatives.

Nucleic acids play a pivotal role in life processes. The endeavours to shed light on the essential properties of these intriguing building blocks led us to the synthesis of different analogues and the investigation of their properties. First various peptide nucleic acid monomers and oligomers have been synthesized, using an Fmoc/acyl protecting group strategy, and their properties studied. The serendipitous discovery of a side reaction of coupling agents led us to the elaboration of a peptide sequencing method. The capricious behaviour of guanine derivatives spurred the determination of their substitution pattern using 13 C, 15 N NMR, and mass spectrometric methods. The properties of guanines initiated the logical transition to the study of supramolecular systems composed of purine analogues. Thus, xanthine and uracil derivatives have been obtained and their supramolecular self-assembly properties scrutinized in gas, solid, and liquid states and at solid-liquid interfaces.

Three-Component Stereoselective Enzymatic Synthesis of Amino-Diols and Amino-Polyols.

Amino-polyols represent attractive chemical building blocks but can be challenging to synthesize because of the high density of asymmetric functionalities and the need for extensive protecting-group strategies. Here we present a three-component strategy for the stereoselective enzymatic synthesis of amino-diols and amino-polyols using a diverse set of prochiral aldehydes, hydroxy ketones, and amines as starting materials. We were able to combine biocatalytic aldol reactions, using variants of d-fructose-6-phosphate aldolase (FSA), with reductive aminations catalyzed by IRED-259, identified from a metagenomic library. A two-step process, without the need for intermediate isolation, was developed to avoid cross-reactivity of the carbonyl components. Stereoselective formation of the 2R,3R,4R enantiomers of amino-polyols was observed and confirmed by X-ray crystallography.

Carbonylative Suzuki Coupling Catalyzed by Pd Complexes Based on [N,P]‐Pyrrole Ligands: Direct Access to 2‐Hydroxybenzophenones

AbstractThe Suzuki‐Miyaura cross‐coupling is one of the most useful synthetic tools to build C−C bonds, but the use of hydroxyaryl halides to direct access hydroxy‐byaryls still remains a challenge. For the carbonylative version of the reaction, the synthesis of hydroxybiaryl ketones is commonly solved by protecting group strategies. In this work, we report a protocol of carbonylative Suzuki‐ Miyaura coupling catalysed by a [N,P]‐PdCl2complex using aryl halides, various aryl boronic acids and CO. We were able at first to obtain biphenyls, finding a singular reactivity towards 2‐bromophenol, that later was extended to the carbonylation reaction, resulting in methodology that allows the obtention of 2‐hydroxybiaryl ketones, with a functional group tolerance toward amines, alkoxy, ketones, esters, and halides.magnified image