Synthesis and applications of a light-fluorous glycosyl donor

Cooperatively Catalyzed Activation of Thioglycosides That Bypasses Intermediacy of Glycosyl Halides

Reported herein is the development of a novel method for activating thioglycosides without a glycosyl halide intermediate. This has been achieved through the use of a silver salt coupled with an acid additive and molecular iodine. The enhanced stereocontrol was achieved via the H-bond mediated aglycone delivery (HAD) method, and the extended trisaccharide synthesis was achieved via iteration of deprotection and glycosylation steps.

Garbage in, garbage out: how reliable training data improved a virtual screening approach against SARS-CoV-2 MPro

Introduction: The identification of chemical compounds that interfere with SARS-CoV-2 replication continues to be a priority in several academic and pharmaceutical laboratories. Computational tools and approaches have the power to integrate, process and analyze multiple data in a short time. However, these initiatives may yield unrealistic results if the applied models are not inferred from reliable data and the resulting predictions are not confirmed by experimental evidence. Methods: We undertook a drug discovery campaign against the essential major protease (MPro) from SARS-CoV-2, which relied on an in silico search strategy -performed in a large and diverse chemolibrary- complemented by experimental validation. The computational method comprises a recently reported ligand-based approach developed upon refinement/learning cycles, and structure-based approximations. Search models were applied to both retrospective (in silico) and prospective (experimentally confirmed) screening. Results: The first generation of ligand-based models were fed by data, which to a great extent, had not been published in peer-reviewed articles. The first screening campaign performed with 188 compounds (46 in silico hits and 100 analogues, and 40 unrelated compounds: flavonols and pyrazoles) yielded three hits against MPro (IC₅₀ ≤ 25 μM): two analogues of in silico hits (one glycoside and one benzo-thiazol) and one flavonol. A second generation of ligand-based models was developed based on this negative information and newly published peer-reviewed data for MPro inhibitors. This led to 43 new hit candidates belonging to different chemical families. From 45 compounds (28 in silico hits and 17 related analogues) tested in the second screening campaign, eight inhibited MPro with IC₅₀ = 0.12-20 μM and five of them also impaired the proliferation of SARS-CoV-2 in Vero cells (EC₅₀ 7-45 μM). Discussion: Our study provides an example of a virtuous loop between computational and experimental approaches applied to target-focused drug discovery against a major and global pathogen, reaffirming the well-known "garbage in, garbage out" machine learning principle.

TsOH-catalyzed acyl migration reaction of the Bz-group: innovative assembly of various building blocks for the synthesis of saccharides

We developed an efficient method to achieve the regioselective acyl migration of benzoyl ester. In all the cases, the reactions required only the commercially available organic acid catalyst TsOH·H₂O. This method enables the benzoyl group to migrate from secondary groups to primary hydroxyl groups, or from equatorial secondary hydroxyl groups to axial hydroxyl groups. The 1,2 or 1,3 acyl migration would potentially occur via five- and six-membered cyclic ortho acid intermediates. A wide range of orthogonally protected monosaccharides, which are useful intermediates for the synthesis of natural oligosaccharides, were synthesized. Finally, to demonstrate the utility of the method, a tetrasaccharide portion from a mycobacterial cell wall polysaccharide was assembled.

Expanding the scope of stereoselective α-galactosylation using glycosyl chlorides

Recently, we reported that silver(I) oxide mediated Koenigs-Knorr glycosylation reaction can be dramatically accelerated in the presence of catalytic acid additives. We have also investigated how well this reaction works in application to differentially protected galactosyl bromides. Reported herein is the stereoselective synthesis of α-galactosides with galactosyl chlorides as glycosyl donors. Chlorides are easily accessible, stable, and can be efficiently activated for glycosylation. In this application, the most favorable reactions conditions comprised cooperative Ag2SO4 and Bi(OTf)3 promoter system.

Bismuth(iii) triflate as a novel and efficient activator for glycosyl halides

Presented herein is the discovery that bismuth(iii) trifluoromethanesulfonate (Bi(OTf)3) is an effective catalyst for the activation of glycosyl bromides and glycosyl chlorides. The key objective for the development of this methodology is to employ only one promoter in the lowest possible amount and to avoid using any additive/co-catalyst/acid scavenger except molecular sieves. Bi(OTf)3 works well in promoting the glycosidation of differentially protected glucosyl, galactosyl, and mannosyl halides with many classes of glycosyl acceptors. Most reactions complete within 1 h in the presence of only 35% of green and light-stable Bi(OTf)3 catalyst.

Stereocontrolled α-Galactosylation under Cooperative Catalysis

A recent discovery of a cooperative catalysis comprising a silver salt and an acid led to a dramatic improvement in the way glycosyl halides are glycosidated. Excellent yields have been achieved, but the stereoselectivity achieved with 2-O-benzylated donors was poor. Reported herein is our first attempt to refine the stereoselectivity of the cooperatively catalyzed galactosylation reaction. Careful optimization of the reaction conditions along with studying effects of the remote protecting groups led to excellent stereocontrol of α-galactosylation of a variety of glycosyl acceptors with differentially protected galactosyl donors.

Stereoselective Synthesis of Iminosugar 2-Deoxy(thio)glycosides from Bicyclic Iminoglycal Carbamates Promoted by Cerium(IV) Ammonium Nitrate and Cooperative Brønsted Acid-Type Organocatalysis

The first examples of iminosugar-type 2-deoxy(thio)glycoside mimetics are reported. The key step is the activation of a bicyclic iminoglycal carbamate to generate a highly reactive acyliminium cation. Cerium(IV) ammonium nitrate efficiently promoted the formation of 2-deoxy S-glycosides in the presence of thiols, probably by in situ generation of catalytic HNO₃, with complete α-stereoselectivity. Cooperative phosphoric acid/Schreiner's thiourea organocatalysis proved better suited for generating 2-deoxy O-glycosides, significantly broadening the scope of the approach.

Synthesis of β-Glucosides with 3-O-Picoloyl-Protected Glycosyl Donors in the Presence of Excess Triflic Acid: Defining the Scope

Excellent β-stereoselectivity for the glycosylation with glucosyl donors equipped with the 3-O-picoloyl (Pico) group, without the use of participating group, was achieved in the presence of NIS/excess TfOH promoter system. A complete investigation of the scope of this reaction was performed, revealing all important attributes of successful glycosylation. While altering the halogen source was tolerated, substitution of the triflate anion resulted in complete loss of stereoselectivity. Protonation of the Pico group was determined to be crucial in this reaction. The stability or extent of the protonated pyridine ring was also found to be another important key factor in obtaining high stereoselectivity. The nucleophilicity of the acceptor was found to be proportional to the stereoselectivity obtained, suggesting an S_N 2-like mechanism.

Defining the Scope of the Acid-Catalyzed Glycosidation of Glycosyl Bromides

Following the recent discovery that traditional silver(I) oxide-promoted glycosidations of glycosyl bromides (Koenigs-Knorr reaction) can be greatly accelerated in the presence of catalytic TMSOTf, reported herein is a dedicated study of all major aspects of this reaction. A thorough investigation of numerous silver salts and careful refinement of the reaction conditions led to an improved mechanistic understanding. This, in turn, led to a significant reduction in the amount of silver salt required for these glycosylations. The progress of this reaction can be monitored by naked eye, and the completion of the reaction can be judged by the disappearance of characteristic dark color of Ag2 O. Further evidence on higher reactivity of benzoylated α-bromides in comparison to that of their benzylated counterparts has been acquired.

Leloir Glycosyltransferases in Applied Biocatalysis: A Multidisciplinary Approach

Enzymes are nature’s catalyst of choice for the highly selective and efficient coupling of carbohydrates. Enzymatic sugar coupling is a competitive technology for industrial glycosylation reactions, since chemical synthetic routes require extensive use of laborious protection group manipulations and often lack regio- and stereoselectivity. The application of Leloir glycosyltransferases has received considerable attention in recent years and offers excellent control over the reactivity and selectivity of glycosylation reactions with unprotected carbohydrates, paving the way for previously inaccessible synthetic routes. The development of nucleotide recycling cascades has allowed for the efficient production and reuse of nucleotide sugar donors in robust one-pot multi-enzyme glycosylation cascades. In this way, large glycans and glycoconjugates with complex stereochemistry can be constructed. With recent advances, LeLoir glycosyltransferases are close to being applied industrially in multi-enzyme, programmable cascade glycosylations.

Investigation of Glycosyl Nitrates as Building Blocks for Chemical Glycosylation

Glycosyl nitrates are important synthetic intermediates in the synthesis of 2-amino sugars, 1,2-orthoesters or, more recently, 2-OH glucose. However, glycosyl nitrates have never been glycosidated. Presented herein is our first attempt to use glycosyl nitrates as glycosyl donors for O-glycosylation. Lanthanide triflates showed good affinity to activate the nitrate leaving group.

Investigation of the H-bond-mediated aglycone delivery reaction in application to the synthesis of β-glucosides

In an attempt to refine the H-bond-mediated Aglycone Delivery (HAD) glycosylation reaction reported herein is the synthesis of β-glucosides using an ethylthio glucoside donor equipped with the remote 6-O-picoloyl substituent. Upon examining various aliphatic, aromatic, and carbohydrate acceptors, it was determined that both electronic and steric factors may greatly affect the stereoselectivity of the HAD reaction with this donor.

"One-Pot" Protection, Glycosylation, and Protection-Glycosylation Strategies of Carbohydrates

Carbohydrates, which are ubiquitously distributed throughout the three domains of life, play significant roles in a variety of vital biological processes. Access to unique and homogeneous carbohydrate materials is important to understand their physical properties, biological functions, and disease-related features. It is difficult to isolate carbohydrates in acceptable purity and amounts from natural sources. Therefore, complex saccharides with well-defined structures are often most conviently accessed through chemical syntheses. Two major hurdles, regioselective protection and stereoselective glycosylation, are faced by carbohydrate chemists in synthesizing these highly complicated molecules. Over the past few years, there has been a radical change in tackling these problems and speeding up the synthesis of oligosaccharides. This is largely due to the development of one-pot protection, one-pot glycosylation, and one-pot protection-glycosylation protocols and streamlined approaches to orthogonally protected building blocks, including those from rare sugars, that can be used in glycan coupling. In addition, new automated strategies for oligosaccharide syntheses have been reported not only for program-controlled assembly on solid support but also by the stepwise glycosylation in solution phase. As a result, various sugar molecules with highly complex, large structures could be successfully synthesized. To summarize these recent advances, this review describes the methodologies for one-pot protection and their one-pot glycosylation into the complex glycans and the chronological developments associated with automated syntheses of oligosaccharides.

Regenerative Glycosylation

Previously, we communicated 3,3-difluoroxindole (HOFox)-mediated glycosylations wherein 3,3-difluoro-3H-indol-2-yl (OFox) imidates were found to be key intermediates. Both the in situ synthesis from the corresponding glycosyl bromides and activation of the OFox imidates could be conducted in a regenerative fashion. Herein, we extend this study to the synthesis of various glycosidic linkages using different sugar series. The main outcome of this study relates to enhanced yields and/or reduced reaction times of glycosylations. The effect of HOFox-mediated reactions is particularly pronounced in case of unreactive glycosyl donors and/or glycosyl acceptors. A multistep regenerative synthesis of oligosaccharides is also reported.

OFox imidates as versatile glycosyl donors for chemical glycosylation

Previously we communicated 3,3-difluoroxindole (HOFox) - mediated glycosylations wherein 3,3-difluoro-3H-indol-2-yl (OFox) imidates were found to be key intermediates. Both the in situ synthesis from the corresponding glycosyl bromides and activation of the OFox imidates could be conducted in a regenerative fashion. Herein, we extend this study with the main focus on the synthesis of various OFox imidates and their investigation as glycosyl donors for chemical 1,2-cis and 1,2-trans glycosylation.

Why Is Direct Glycosylation with N-Acetylglucosamine Donors Such a Poor Reaction and What Can Be Done about It?

The monosaccharide N-acetyl-d-glucosamine (GlcNAc) is an abundant building block in naturally occurring oligosaccharides, but its incorporation by chemical glycosylation is challenging since direct reactions are low yielding. This issue, generally agreed upon to be caused by an intermediate 1,2-oxazoline, is often bypassed by introducing extra synthetic steps to avoid the presence of the NHAc functional group during glycosylation. The present paper describes new fundamental mechanistic insights into the inherent challenges of performing direct glycosylation with GlcNAc. These results show that controlling the balance of oxazoline formation and glycosylation is key to achieving acceptable chemical yields. By applying this line of reasoning to direct glycosylation with a traditional thioglycoside donor of GlcNAc, which otherwise affords poor glycosylation yields, one may obtain useful glycosylation results.

Diastereoselective synthesis of new O-alkylated and C-branched inositols and their corresponding fluoro analogues

Efficient routes were developed for the diastereoselective synthesis of new O-alkylated and C-branched inositols and their corresponding fluoro analogues. The key steps of the synthesis were the easy accessibility of different types of arms in term of configuration (myo and scyllo), the linking method and length, which could modulate the biological properties. These inositol derivatives, bearing an arm terminated either with a hydroxy group or a fluorine atom, could be interesting candidates for diastereoisomeric intermediates and biological evaluations, especially for PET imaging experiments.

Convergent synthesis of oligosaccharides on the gram-scale using cetyl thioglycoside based on a hydrophobically assisted switching phase method

A hydrophobically assisted switching phase (HASP) method is an efficient strategy for the synthesis of carrier-loaded oligosaccharides.

Assembly of a Complex Branched Oligosaccharide by Combining Fluorous-Supported Synthesis and Stereoselective Glycosylations using Anomeric Sulfonium Ions

There is an urgent need to develop reliable strategies for the rapid assembly of complex oligosaccharides. This paper presents a set of strategically selected orthogonal protecting groups, glycosyl donors modified by a (S)-phenylthiomethylbenzyl ether at C-2, and a glycosyl acceptor containing a fluorous tag, which makes it possible to rapidly prepare complex branched oligosaccharides of biological importance. The C-2 auxiliary controlled the 1,2-cis anomeric selectivity of the various galactosylations. The orthogonal protecting groups, 2-naphthylmethyl ether (Nap) and levulinic ester (Lev), made it possible to generate glycosyl acceptors and allowed the installation of a crowded branching point. After the glycosylations, the chiral auxiliary could be removed using acidic conditions, which was compatible with the presence of the orthogonal protecting groups Lev and Nap, thereby allowing the efficient installation of 1,2-linked glycosides. The light fluorous tag made it possible to purify the compounds by a simple filtration method using silica gel modified by fluorocarbons. The set of building blocks was successfully employed for the preparation of the carbohydrate moiety of the GPI anchor of Trypanosoma brucei, which is a parasite that causes sleeping sickness in humans and similar diseases in domestic animals.

Efficient assembly of oligomannosides using the hydrophobically assisted switching phase method

The hydrophobically assisted switching phase (HASP) method was applied in the assembly of oligomannosides. A new mannosyl donor with high reactivity was selected after a series of optimization studies, which was suitable for the synthesis of oligomannosides via the HASP method. The practicability of the HASP method towards the synthesis of branched oligosaccharides was explored and two branched penta-mannosides were assembled efficiently.

Synthesis and biological evaluation of a novel MUC1 glycopeptide conjugate vaccine candidate comprising a 4'-deoxy-4'-fluoro-Thomsen-Friedenreich epitope

The development of selective anticancer vaccines that provide enhanced protection against tumor recurrence and metastasis has been the subject of intense research in the scientific community. The tumor-associated glycoprotein MUC1 represents a well-established target for cancer immunotherapy and has been used for the construction of various synthetic vaccine candidates. However, many of these vaccine prototypes suffer from an inherent low immunogenicity and are susceptible to rapid in vivo degradation. To overcome these drawbacks, novel fluorinated MUC1 glycopeptide-BSA/TTox conjugate vaccines have been prepared. Immunization of mice with the 4’F-TF-MUC1-TTox conjugate resulted in strong immune responses overriding the natural tolerance against MUC1 and producing selective IgG antibodies that are cross-reactive with native MUC1 epitopes on MCF-7 human cancer cells.

Synthesis of fluorous photolabile aldehyde and carbamate and alkyl carbamate protecting groups for carbohydrate-associated amines

Two new fluorous photolabile-protecting groups (FNBC and FNB) and a new base-labile protecting group (FOC) for the masking of amines are reported. The protecting groups survive a wide range of common reaction conditions used in oligosaccharide synthesis and render the attached molecules amenable to fluorous solid-phase extraction (FSPE). A glycosyl acceptor containing the FNB group is shown to be useful in the synthesis of carbohydrates tagged with free deactivated secondary amines.

Highly efficient one-pot multienzyme (OPME) synthesis of glycans with fluorous-tag assisted purification

Oligo(ethylene glycol)-linked light fluorous tags have been found to be optimal for conjugating to glycans for both high-yield enzymatic glycosylation reactions using one-pot multienzyme (OPME) systems and quick product purification using fluorous solid-phase extraction (FSPE) cartridges. The combination of OPME glycosylation systems and the FSPE cartridge purification scheme provides a highly effective strategy for facile synthesis and purification of glycans.

A new approach for the synthesis of O-glycopeptides through a combination of solid-phase glycosylation and fluorous tagging chemistry (SHGPFT)

A new and efficient hybrid approach has been developed for the synthesis and purification of O-linked glycopeptides with high purity.

Fluorous supported modular synthesis of heparan sulfate oligosaccharides

The modular synthesis of heparan sulfate fragments is greatly facilitated by employing an anomeric aminopentyl linker protected by a benzyloxycarbonyl group modified by a perfluorodecyl tag, which made it possible to purify highly polar intermediates by fluorous solid phase extraction. This tagging methodology made it also possible to perform repeated glycosylations to drive reactions to completion.

Efficient activation of thioglycosides with N-(p-methylphenylthio)-ε-caprolactam-TMSOTf

N-(p-Methylphenylthio)-ε-caprolactam (1) in combination with trimethylsilyl trifluoromethanesulfonate (TMSOTf) provides an efficient thiophilic promoter system, capable of activating different thioglycosides. Both 'armed' and 'disarmed' thioglycosyl donors were activated for glycosidic bond formation. Notably, this reagent combination works well in reactivity-based one-pot oligosaccharide assembly strategy.

Toward automated oligosaccharide synthesis

Carbohydrates have been shown to play important roles in biological processes. The pace of development in carbohydrate research is, however, relatively slow due to the problems associated with the complexity of carbohydrate structures and the lack of general synthetic methods and tools available for the study of this class of biomolecules. Recent advances in synthesis have demonstrated that many of these problems can be circumvented. In this Review, we describe the methods developed to tackle the problems of carbohydrate-mediated biological processes, with particular focus on the issue related to the development of the automated synthesis of oligosaccharides. Further applications of carbohydrate microarrays and vaccines to human diseases are also highlighted.

On the stereoselectivity of glycosidation of thiocyanates, thioimidates, and thioglycosides

Comparative side-by-side glycosylation studies demonstrated that glycosyl thiocyanates, thioimidates, and thioglycosides provide comparative stereoselectivities in glycosylations. Very high α-stereoselectivity that was previously recorded for glycosyl thiocyanates can be achieved, but only if glycosyl acceptors are equipped with electron-withdrawing acyl substituents. Partially benzylated glycosyl acceptors provided relatively modest stereoselectivity, which was on a par with other common glycosyl donors. Accordingly, thioimidates and thioglycosides showed high stereoselectivity similarly to that of thiocyanates with different classes of acylated primary and secondary glycosyl acceptors.

Fluorous-Assisted One-Pot Oligosaccharide Synthesis

A new method for oligosaccharide assembly that combines the advantages of one-pot synthesis and fluorous separation is described. After one-pot glycosylations are completed, a fluorous tag is introduced into the reaction mixture to selectively "catch" the desired oligosaccharide, which is rapidly separated from non-fluorous impurities by fluorous solid-phase extraction (F-SPE). Subsequent "release" of the fluo rous tag and F-SPE achieved the purification of the desired oligosaccharide without the use of time- and solvent-consuming silica gel chromatography. Linear and branched oligosaccharides have been synthesized with this approach in just a few hours (for the overall oligosaccharide assembly and purification process).