Toward fully synthetic N-linked glycoproteins

Solid-Phase Synthesis of Head to Side-Chain Tyr-Cyclodepsipeptides Through a Cyclative Cleavage From Fmoc-MeDbz/MeNbz-resins

Cyclic depsipeptides constitute a fascinating class of natural products. Most of them are characterized by an ester formed between the β-hydroxy function of Ser/Thr -and related amino acids- and the carboxylic group of the C-terminal amino acid. Less frequent are those where the thiol of Cys is involved rendering a thioester (cyclo thiodepsipeptides) and even less common are the cyclo depsipeptides with a phenyl ester coming from the side-chain of Tyr. Herein, the preparation of the later through a cyclative cleavage using the Fmoc-MeDbz/MeNbz-resin is described. This resin has previously reported for the synthesis of cyclo thiodepsipeptides and homodetic peptides. The use of that resin for the preparation of all these peptides is also summarized.

Straightforward Synthesis of N-Glycan Polymers from Free Glycans via Cyanoxyl Free Radical-Mediated Polymerization

We report a straightforward synthesis of N-glycan polymers from free glycans via glycosylamine intermediates followed by acrylation and polymerization via cyanoxyl-mediated free radical polymerization (CMFRP) in one-pot fashion. No protection and deprotection were used in either glycomonomer or glycopolymer synthesis. A typical synthetic procedure for N-glycan polymers from free monosaccharide and disaccharide, Glc, Gal, Man, GlcNAc, and Lac, was demonstrated. In addition, enzymatic sialylation of the Lac-containing N-glycan polymers and their anti-influenza virus hemagglutination activities were investigated.

Glycopeptide synthesis on an ionic liquid support

An ionic liquid-supported synthetic method for the construction of glycopeptides in high yields is reported. This method avoids the use of large excesses of reagents and chromatographic purification and, therefore, represents a useful addition to existing approaches for the ionic liquid-supported synthesis of oligosaccharides and peptides.

Chemical synthesis of highly congested gp120 V1V2 N-glycopeptide antigens for potential HIV-1-directed vaccines

Critical to the search for an effective HIV-1 vaccine is the development of immunogens capable of inducing broadly neutralizing antibodies (BnAbs). A key first step in this process is to design immunogens that can be recognized by known BnAbs. The monoclonal antibody PG9 is a BnAb that neutralizes diverse strains of HIV-1 by targeting a conserved carbohydrate-protein epitope in the variable 1 and 2 (V1V2) region of the viral envelope. Important for recognition are two closely spaced N-glycans at Asn(160) and Asn(156). Glycopeptides containing this synthetically challenging bis-N-glycosylated motif were prepared by convergent assembly, and were shown to be antigenic for PG9. Synthetic glycopeptides such as these may be useful for the development of HIV-1 vaccines based on the envelope V1V2 BnAb epitope.

The winding pathway to erythropoietin along the chemistry-biology frontier: a success at last

The total synthesis of a homogeneous erythropoietin (EPO), possessing the native amino acid sequence and chitobiose glycans at each of the three wild-type sites of N glycosylation, has been accomplished in our laboratory. We provide herein an account of our decade-long research effort en route to this formidable target compound. The optimization of the synergy of the two bedrock sciences we now call biology and chemistry was central to the success of the synthesis of EPO.

Synthesis of small glycopeptides by decarboxylative condensation and insight into the reaction mechanism

The chemical synthesis of homogeneous glycoproteins and glycopeptides facilitates progress toward understanding the functional role of carbohydrates attached to proteins and is important in the preparation of glycopeptide-based therapeutics. A series of protected and unprotected glycosyl dipeptides, glycopeptide I, which contained the alpha-ketoacid moiety at the C-terminus, were synthesized and ligated with a series of O-tert-butyl-protected N-hydroxylamino acids to afford O-tert-butyl-protected glycosyl tripeptides, glycopeptide II. The reactions were carried out under both anhydrous and aqueous conditions at neutral pH to produce glycopeptide products in yields ranging from 15% to 86% depending on the amino acids present at the ligation junction. The best yields were obtained when both the alpha-ketoacid and the N-hydroxylamino acid contained medium-sized side chains. In addition to the expected tripeptide product, 2,5-substituted oxazoles were isolated when O-tert-butyl protected N-hydroxylamines of glycine were employed in the reaction. The formation of the oxazole is believed to result from an intramolecular cyclization of the O-tert-butyl ester on a nitrilium ion intermediate followed by aromatization. A decarboxylative condensation between O(18)-labeled phenyl pyruvic acid and N-hydroxyphenethylamine oxalate salt resulted in amide products lacking the O(18)-label, providing further support for the nitrilium ion in the reaction pathway.

Discovery and design of carbohydrate-based therapeutics

IMPORTANCE OF THE FIELD

Till now, the importance of carbohydrates has been underscored, if compared with the two other major classes of biopolymers such as oligonucleotides and proteins. Recent advances in glycobiology and glycochemistry have imparted a strong interest in the study of this enormous family of biomolecules. Carbohydrates have been shown to be implicated in recognition processes, such as cell-cell adhesion, cell-extracellular matrix adhesion and cell-intruder recognition phenomena. In addition, carbohydrates are recognized as differentiation markers and as antigenic determinants. Due to their relevant biological role, carbohydrates are promising candidates for drug design and disease treatment. However, the growing number of human disorders known as congenital disorders of glycosylation that are being identified as resulting from abnormalities in glycan structures and protein glycosylation strongly indicates that a fast development of glycobiology, glycochemistry and glycomedicine is highly desirable.

AREAS COVERED IN THIS REVIEW

The topics give an overview of different approaches that have been used to date for the design of carbohydrate-based therapeutics; this includes the use of native synthetic carbohydrates, the use of carbohydrate mimics designed on the basis of their native counterpart, the use of carbohydrates as scaffolds and finally the design of glyco-fused therapeutics, one of the most recent approaches. The review covers mainly literature that has appeared since 2000, except for a few papers cited for historical reasons.

WHAT THE READER WILL GAIN

The reader will gain an overview of the current strategies applied to the design of carbohydrate-based therapeutics; in particular, the advantages/disadvantages of different approaches are highlighted. The topic is presented in a general, basic manner and will hopefully be a useful resource for all readers who are not familiar with it. In addition, in order to stress the potentialities of carbohydrates, several examples of carbohydrate-based marketed therapeutics are given.

TAKE HOME MESSAGE

Carbohydrates are a rich class of natural compounds, possessing an intriguing and still not fully understood biological role. This richness offers several strategies for the design of carbohydrate-based therapeutics.

Expressed protein ligation: a resourceful tool to study protein structure and function

This review outlines the use of expressed protein ligation (EPL) to study protein structure, function and stability. EPL is a chemoselective ligation method that allows the selective ligation of unprotected polypeptides from synthetic and recombinant origin for the production of semi-synthetic protein samples of well-defined and homogeneous chemical composition. This method has been extensively used for the site-specific introduction of biophysical probes, unnatural amino acids, and increasingly complex post-translational modifications. Since it was introduced 10 years ago, EPL applications have grown increasingly more sophisticated in order to address even more complex biological questions. In this review, we highlight how this powerful technology combined with standard biochemical analysis techniques has been used to improve our ability to understand protein structure and function.

Recent Departures in the Synthesis of Peptides and Glycopeptides

In this account, we describe the results of a research program directed to the proposition that chemical synthesis can play a valuable role in identifying biologic level molecules worthy of pharma level development. We recount our journey towards the chemical synthesis of homogeneous erythropoietin, the challenges we encountered, and our efforts to address deficiencies in the current "state of the art" of glycopeptide synthesis. Here we describe new methods for the synthesis of glycopeptides that have emerged from the erythropoietin adventure, including the development of unique C-terminal acyl donors, novel amide bond forming methods, and new ligation and coupling strategies.

Toward fully synthetic homogeneous beta-human follicle-stimulating hormone (beta-hFSH) with a biantennary N-linked dodecasaccharide. synthesis of beta-hFSH with chitobiose units at the natural linkage sites

A highly convergent synthesis of the sialic acid-rich biantennary N-linked glycan found in human glycoprotein hormones and its use in the synthesis of a fragment derived from the beta-domain of human Follicle-Stimulating Hormone (hFSH) are described. The synthesis highlights the use of the Sinay radical glycosidation protocol for the simultaneous installation of both biantennary side-chains of the dodecasaccharide as well as the use of glycal chemistry to construct the tetrasaccharide core in an efficient manner. The synthetic glycan was used to prepare the glycosylated 20-27aa domain of the beta-subunit of hFSH under a Lansbury aspartylation protocol. The proposed strategy for incorporating the prepared N-linked dodecasaccharide-containing 20-27aa domain into beta-hFSH subunit was validated in the context of a model system, providing protected beta-hFSH subunit functionalized with chitobiose at positions 7 and 24.

Toward homogeneous erythropoietin: chemical synthesis of the Ala1-Gly28 glycopeptide domain by "alanine" ligation

The Ala(1)-Gly(28) glycopeptide fragment (28) of EPO was prepared by chemical synthesis as a single glycoform. Key steps in the synthesis include attachment of a complex dodecasaccharide (7) to a seven amino acid peptide via Lansbury aspartylation, native chemical ligation to join peptide 19 with the glycopeptide domain 18, and a selective desulfurization at the ligation site to reveal the natural Ala(19). This glycopeptide fragment (28) contains both the requisite N-linked dodecasaccharide and a C-terminal (alpha)thioester handle, the latter feature permitting direct coupling with a glycopeptide fragment bearing N-terminal Cys(29) without further functionalization.

Chemoenzymatic synthesis of glycopeptides and glycoproteins through endoglycosidase-catalyzed transglycosylation

Homogeneous glycopeptides and glycoproteins are indispensable for detailed structural and functional studies of glycoproteins. It is also fundamentally important to correct glycosylation patterns for developing effective glycoprotein-based therapeutics. This review discusses a useful chemoenzymatic method that takes advantage of the endoglycosidase-catalyzed transglycosylation to attach an intact oligosaccharide to a polypeptide in a single step, without the need for any protecting groups. The exploration of sugar oxazolines (enzymatic reaction intermediates) as donor substrates has not only expanded substrate availability, but also has significantly enhanced the enzymatic transglycosylation efficiency. Moreover, the discovery of a novel mutant with glycosynthase-like activity has made it possible to synthesize homogeneous glycoproteins with full-size natural N-glycans. Recent advances in this highly convergent chemoenzymatic approach and its application for glycopeptide and glycoprotein synthesis are highlighted.

Mechanism of thio acid/azide amidation

A combined experimental and computational mechanistic study of amide formation from thio acids and azides is described. The data support two distinct mechanistic pathways dependent on the electronic character of the azide component. Relatively electron-rich azides undergo bimolecular coupling with thiocarboxylates via an anion-accelerated [3+2] cycloaddition to give a thiatriazoline. Highly electron-poor azides couple via bimolecular union of the terminal nitrogen of the azide with sulfur of the thiocarboxylate to give a linear adduct. Cyclization of this intermediate gives a thiatriazoline. Decomposition to amide is found to proceed via retro-[3+2] cycloaddition of the neutral thiatriazoline intermediates. Computational analysis (DFT, 6-31+G(d)) identified pathways by which both classes of azide undergo [3+2] cycloaddition with thio acid to give thiatriazoline intermediates, although these paths are higher in energy than the thiocarboxylate amidations. These studies also establish that the reaction profile of electron-poor azides is attributable to a prior capture mechanism followed by intramolecular acylation.

Nanoporous magnets of chiral and racemic [{Mn(HL)}2Mn{Mo(CN)7}2] with switchable ordering temperatures (TC = 85 K <--> 106 K) driven by H2O sorption (L = N,N-dimethylalaninol)

Molecule-based solids represent a rare opportunity to combine, adjust, and interrelate structural and physical functionalities to develop multifunctional materials. Here we report on a series of porous supramolecular magnets whose magnetic properties are related to their sorption state. A family of magnets of the formula [{Mn(HL)(H2O)}2Mn{Mo(CN)7}2].2H2O have been obtained by assembling the heptacyano-metalate building unit {Mo(CN)7}4- with Mn(II) in the presence of protonated N,N-dimethylalaninol (L) as ligand, the latter being either as a racemic mixture or as a chiral R- or S-enantiomer. The resulting magnets possess an open framework structure and exhibit a TC with a switching behavior (TC = 85 K <--> 106 K) as a function of the hydration state. Moreover, chiral magnets are formed with the optically active ligands. The H2O and gas (N2, CO2, CO) sorption features, the magnetic behavior of both the hydrated and dehydrated magnets, and the crystal structures of the hydrated chiral (S) and racemic magnets are described.

Synthesis of a beta-(1-->3)-D-rhamnotetraose by a one-pot, multiple radical fragmentation

A naturally occurring beta-(1-->3)-D-rhamnotetraose has been constructed under conditions of sequential beta-selective mannosylation controlled by the 4,6-O-[1-cyano-2-(2-iodophenyl)-ethylidene] protecting group. The route is concise, proceeding through a late-stage radical deoxygenation that successfully uncovers all four deoxy subunits at once.

Recent progress in the field of glycopeptide synthesis

Glycosylation is a common post-translational modification of proteins. Although its significance in biological system is well recognized, approaches to analyze carbohydrate function are limited. This is because of difficulty in obtaining homogeneous glycoproteins from natural sources. Due to the progress of the carbohydrate and peptide chemistry, syntheses of various homogeneous glycopeptides and glycoproteins, which are suitable for biological studies, have been achieved by chemical means. In this review, we briefly summarize recent advances in the field of glycopeptide synthesis after 1999.

Clathrate formation mechanism of supercritical hydrogen adsorption on copper(II) benzoate pyrazine

The adsorption isotherms of supercritical hydrogen on [Cu2(bz)4(pyz)]n were measured at 77 K up to 10 MPa. The amount of supercritical hydrogen adsorbed on [Cu2(bz)4(pyz)]n at 77 K was 1.4 wt % at 10 MPa. The adsorption isotherms of supercritical hydrogen on [Cu2(bz)4(pyz)]n showed a stepwise adsorption that suggests clathrate formation between [Cu2(bz)4(pyz)]n and hydrogen molecules.

An approach for a synthesis of asparagine-linked sialylglycopeptides having intact and homogeneous complex-type undecadisialyloligosaccharides

This paper describes synthesis of asparagine-linked sialylglycopeptides. The typical feature of our strategy for the synthesis of a sialylglycopeptide is to employ undecadisialyloligosaccharyl Fmoc-asparagine (Fmoc-Asn(CHO)-OH) 1 without protecting groups on its hydroxyl groups except for the benzyl ester of the NeuAc residues. Our synthetic methodology solved the problem of esterification toward sugar hydroxyl groups by activated amino acids during the elongation of a peptide chain. When employing high concentrations of the Fmoc-amino acid, esterification markedly occurred, but the esterification scarcely occurred when employing low concentrations of reactants. Taking advantage of these findings, we examined the synthesis of a high molecular sialylglycopeptide, CTLA-4 fragment (113-150) 13 having two complex-type sialyloligosaccharides by use of native chemical ligation (NCL). As a result, we succeeded in the synthesis of a sialylglycopeptide having a cysteine residue at the N-terminus (CTLA-4: 129-150 fragment) 11 and a sialylglycopeptide-thioester (CTLA-4: 113-128 fragment) 12. Finally, the sialylglycopeptides synthesized were applied to NCL reactions. The reaction successfully afforded the desired product, CTLA-4 (113-150) 13 containing mature and pure complex-type sialyloligosaccharides in excellent purity.

Site-Specific Incorporation of Glycosylated Serine and Tyrosine Derivatives into Proteins

Glycosylation of proteins can have a dramatic effect on their physical, chemical, and biological properties. Analogues of dihydrofolate reductase and firefly luciferase containing glycosylated amino acids at single, predetermined sites have been elaborated. Misacylated suppressor tRNAs activated with glycosylated serine and tyrosine derivatives were used for suppression of the nonsense codons in a cell-free protein biosynthesizing system, thereby permitting the preparation of the desired glycosylated proteins. In this fashion, it was possible to obtain proteins containing both mono- and diglycosylated amino acids, including glycosylated serine and tyrosine moieties. For the modified firefly luciferases, the effect of these substitutions on the wavelength of the light emitted by firefly luciferase was investigated. The maximum wavelength for mutants containing peracetylated glycosylated serine derivatives at position 284 showed a red shift in the emission spectra. For mutants containing glycosylated tyrosines, the red shift was observed only when the carbohydrate moiety was fully deacetylated.

Promising agents at the interface of biology and oncology derived through chemical synthesis

This account traces the development of our synthetic glycopeptide- and glycoprotein-based research program over the past decade. We recount the syntheses of a number of biologically relevant, natural product-inspired glycopeptide constructs, including those associated with prostate specific antigen (PSA) and with the gp120 surface envelope protein of HIV. We also describe our progress toward the synthesis of the multiply glycosylated protein, erythropoietin (EPO). Particular emphasis is placed on the development of enabling methodologies which allow for the ligation of complex glycopeptide fragments, thus rendering it possible to access, through purely synthetic means, homogeneous, multidomainal glycopeptide and glycoprotein constructs.

Novel expansion/shrinkage modulation of 2D layered MOF triggered by clathrate formation with CO(2) molecules

Crystal-to-crystal transformation from a 3D interpenetrated-type MOF {[Cu(BF(4))(2)(bpy)(H(2)O)(2)] (bpy)} (1) to a 2D square-grid-type [Cu(BF(4))(2)(bpy)(2)] (2) (bpy = 4,4'-bipyridine) was observed. It was derived from dehydration and confirmed by in situ FT-IR, TG, and elemental analysis. Moreover, we elucidate the novel expansion/shrinkage dynamic modulation of 2 triggered by clathrate formation with gas molecules.

Functionalities of One-Dimensional Dynamic Ultramicropores in Nickel(II) Coordination Polymers

Ni(II) coordination polymers with a 4,4'-azobis(pyridine) (azpy) ligand, {[Ni2(NCX)4(azpy)4].G}n (X = S, G (guest molecule) = MeOH (1.MeOH); X = S, G = EtOH (1.EtOH); X = S, G = H2O (1.H2O); X = S, G = no guest (1); X = Se, G = MeOH (2.MeOH); X = Se, G = H2O (2.H2O); X = Se, G = no guest (2)), have been synthesized and structurally characterized with their porosity. These compounds have one-dimensional periodic ultramicropores that contain the small guest molecules, H2O, MeOH, or EtOH, whose hydroxy groups interact with the S or Se atoms of isothiocyanate or isoselenocyanate, respectively, via -S(Se)...HO- hydrogen bonds. Although the molecular dimensions of the MeOH guest are considerably larger than the window size of the ultramicropore, 1.MeOH and 2.MeOH easily release their guest molecules without decomposition of the framework to form 1 and 2 without any guest molecules. This shows that 1 and 2 have dynamic ultramicropores constructed from the interpenetrating framework. The guest desorption experiments using 1.MeOH and 1.EtOH reveal that the difference in the desorption behavior is due to van der Waals interactions that depend on the molecular shape of the guest molecule in the ultramicropores and/or an entrance blocking effect that depends on the minimum dimensions of the guest molecule for the pore windows. A marked difference in the N2 and CH4 adsorption isotherms was observed and is associated with the strength of the host-guest interaction.

Porous Metal−Organic Framework with Coordinatively Unsaturated MnIISites:Sorption Properties for Various Gases

A 3D porous metal-organic framework generating 1D channels, [Mn(NDC)(DEF)]n (1), has been prepared from the solvothermal reaction of Mn(II) and 2,6-naphthalenedicarboxylic acid (H2NDC) in diethylformamide (DEF). When DEF molecules coordinating Mn(II), which occupy the channels, are removed from 1 by heating the crystal of 1 at 250 degrees C under vacuum for 18 h, structural change occurs as evidenced by X-ray powder diffraction patterns. Desolvated solid [Mn(NDC)]n (2), which contains coordinatively unsaturated Mn(II) sites, reveals remarkable sorption capabilities for N2, H2, CO2, and CH4 gases and exhibits type I sorption behavior indicative of permanent microporosity.