Human proteasomes are validated targets in oncology and are promising targets in immune related diseases. A number of peptide-based proteasome inhibitors have reached the clinic and several others are currently investigated in clinical trials. Despite these achievements, peptide-based inhibitors may be susceptible to protease-mediated degradation. In this paper, we report on our results on the introduction of 5-methylpyridin-2-one moiety in peptide vinyl sulfone and peptide epoxy ketone-based proteasome inhibitors. Pyridin-2-ones have previously been used as constrained peptide isosteres capable to act as a hydrogen-bond acceptor. Our results demonstrate that 5-methylpyridin-2-one can be introduced into proteasome inhibitors, but that the activity of the resulting compounds is compromised compared to their parent peptide vinyl sulfones and peptide epoxy ketones.

Three fluorescent cathepsin inhibitor glycoconjugates have been designed, synthesized, and evaluated in terms of their cell internalization and cathepsin inhibitory properties. The conjugates are composed of a peptide epoxysuccinate, capable of covalent and irreversible binding to cysteine proteases, coupled to a fluorescent BODIPY dye and functionalized with a mono-, tri-, or heptamannoside. Mannose-receptor-dependent uptake of the probes in live dendritic cells is shown to depend on the type of carbohydrate attached. Where uptake of the monomannoside is poor and mannose-receptor-independent, the intracellular labeling of cathepsins by the probes equipped with a tri- or heptamannoside conjugate appeared concentration- and mannose-receptor-dependent.

The synthesis and evaluation as activity-based probes (ABPs) of three configurationally distinct, fluorescent N-alkyl cyclophellitol aziridine isosteres for profiling GH1 β-glucosidase (GBA), GH27 α-galactosidase (GLA) and GH29 α-fucosidase (FUCA) is described. In comparison with the corresponding acyl aziridine ABPs reported previously, the alkyl aziridine ABPs are synthesized easily and are more stable in mild acidic and basic media, and are thus easier to handle. The β-glucose-configured alkyl aziridine ABP proves equally effective in labeling GBA as its N-acyl counterpart, whereas the N-acyl aziridines targeting GLA and FUCA outperform their N-alkyl counterparts. Alkyl aziridines can therefore be an attractive alternative in retaining glycosidase ABP design, but in targeting a new retaining glycosidase both N-alkyl and N-acyl aziridines are best considered at the onset of a new study.

Glucosylceramide metabolism and the enzymes involved have attracted significant interest in medicinal chemistry, because aberrations in the levels of glycolipids that are derived from glucosylceramide are causative in a range of human diseases including lysosomal storage disorders, type 2 diabetes, and neurodegenerative diseases. Selective modulation of one of the glycoprocessing enzymes involved in glucosylceramide metabolism—glucosylceramide synthase (GCS), acid glucosylceramidase (GBA1), or neutral glucosylceramidase (GBA2)—is therefore an attractive research objective. In this study we took two established GCS inhibitors, one based on deoxynojirimycin and the other a ceramide analogue, and merged characteristic features to obtain hybrid compounds. The resulting 39-compound library does not contain new GCS inhibitors; however, a potent (200 nm) GBA1 inhibitor was identified that has little activity toward GBA2 and might therefore serve as a lead for further biomedical development as a selective GBA1 modulator.

Cyclophellitol and cyclophellitol aziridine are potent and irreversible mechanism-based inhibitors of retaining β-glucosidases. Alterations in the configuration of these compounds can lead to irreversible inhibition of different classes of retaining glycosidases. We have recently reported on the design of a set of α-galactopyranose-configured cyclophellitol and cyclophellitol aziridine derivatives that inhibit human retaining α-galactosidases. Moreover, we have shown that fluorescently labeled derivatives enable the activity-based profiling of these enzymes in vitro. In this report we describe in detail the synthetic strategies that were used to obtain these epoxide- and aziridine-based probes. In addition, we describe the parallel synthesis of a set of β-galactopyranose-configured cyclophellitol isomers as putative inhibitors of retaining β-galactosidases.

Activity-based protein profiling has emerged as a powerful discovery tool in chemical biology and medicinal chemistry research. Success of activity-based protein profiling hinges on the presence of compounds that can covalently and irreversibly bind to enzymes, do so selectively in the context of complex biological samples, and subsequently report on the selected pool of proteins. Such tagged molecules featuring an electrophilic trap, termed activity-based probes, have been developed with most success for serine hydrolases and various protease families (serine proteases, cysteine proteases, proteasomes). This concept presents the current progress and future directions in the design of activity-based probes targeting retaining glycosidases, enzymes that employ a double displacement mechanism in the hydrolysis of glycosidic bonds with overall retention. In contrast to inverting glycosidases, retaining glycosidases form a covalent intermediate with their substrates during the catalytic process and are therefore amenable to activity-based protein profiling studies.

The ubiquitously expressed mannose-6-phosphate receptors (MPRs) are a promising class of receptors for targeted compound delivery into the endolysosomal compartments of a variety of cell types. The development of a synthetic, multivalent, mannose-6-phosphate (M6P) glycopeptide-based MPR ligand is described. The conjugation of this ligand to fluorescent DCG-04, an activity-based probe for cysteine cathepsins, enabled fluorescent readout of its receptor-targeting properties. The resulting M6P-cluster–BODIPY–DCG-04 probe was shown to efficiently label cathepsins in cell lysates as well as in live cells. Furthermore, the introduction of the 6-O-phosphates leads to a completely altered uptake profile in COS and dendritic cells compared to a mannose-containing ligand. Competition with mannose-6-phosphate abolished all uptake of the probe in COS cells, and we conclude that the mannose-6-phosphate cluster targets the MPR and ensures the targeted delivery of cargo bound to the cluster into the endolysosomal pathway.

The ubiquitously expressed mannose-6-phosphate receptors (MPRs) are a promising class of receptors for targeted compound delivery into the endolysosomal compartments of a variety of cell types. The development of a synthetic, multivalent, mannose-6-phosphate (M6P) glycopeptide-based MPR ligand is described. The conjugation of this ligand to fluorescent DCG-04, an activity-based probe for cysteine cathepsins, enabled fluorescent readout of its receptor-targeting properties. The resulting M6P-cluster–BODIPY–DCG-04 probe was shown to efficiently label cathepsins in cell lysates as well as in live cells. Furthermore, the introduction of the 6-O-phosphates leads to a completely altered uptake profile in COS and dendritic cells compared to a mannose-containing ligand. Competition with mannose-6-phosphate abolished all uptake of the probe in COS cells, and we conclude that the mannose-6-phosphate cluster targets the MPR and ensures the targeted delivery of cargo bound to the cluster into the endolysosomal pathway.

Eight configurational 1-deoxynojirimycin isomers have been synthesized starting from a chiral cyanohydrin as the common precursor. The cyanohydrin chiral pool building block is easily accessible in large quantities by using almond hydroxynitrile lyase as the chiral catalyst in condensing hydrogen cyanide and crotonaldehyde. Our work complements the large body of literature on the synthesis of 1-deoxynojirimycin derivatives with the distinguishing feature that eight stereoisomers of this important class of glycosidase inhibitors can be derived from a common precursor in an efficient manner.

We report the tandem Staudinger/aza-Wittig/Ugi three-component reaction mediated synthesis of a 64-member compound library of aza-C-glycosides. The library is composed of four pyrrolidine and three piperidine scaffolds, onto which a number of functional groups is grafted to form seven sublibraries. Variation in the library is achieved by transformation of two pentoses and a hexose into the corresponding 4-azidopentanal and 5-azidohexanal derivatives as precursors for the Staudinger/aza-Wittig process. Further variation is achieved by using different isocyanides as well as protective- and functional-group manipulations on the fully protected Ugi-3CR intermediates. Preliminary biological evaluation of the compound library revealed several low micromolar inhibitors of human acid glucosylceramidase.

In this paper we describe the concise synthesis of D-erythro-sphingosine starting from the readily available chiral building block D-ribo-phytosphingosine. The title compound is the ubiquitous sphingolipid from which most mammalian ceramides are derived. Our work is based on the existing literature in which the same sphingoid base is used as a starting point and culminates in what we believe is the most efficient synthesis of D-erythro-sphingosine reported to date.

Metalloproteases (ADAMs, MMPs) are multidomain proteins that play key roles in extracellular matrix remodelling and degradation, in cell–cell and cell–matrix interactions and in the proteolytic liberation of membrane-anchored proforms of cytokines and growth factors, the so-called ectodomainshedding. In this work we describe the development ofphotoactivatable activity-based probes with which active metalloproteases can be visualised. Our probes are based on the succinyl hydroxamate motif and differ in the positioning of the trifluoromethylphenyldiazirine photoreactive group. We demonstrate that directing the photoactivatable group towards the S1′ pocket yields activity-based probes more effective than the corresponding probe with the photoactivatable group directed towards the S2′ pocket.

The structure–activity relationship of lipophilic aza-C-glycosides as inhibitors of the three enzymes of glucosylceramide metabolism is investigated. A library of β-aza-C-glycosides was synthesized with variations in N-alkylation and the linker length/type to the lipophilic moiety. A cross-metathesis reaction was used to prepare a second library of α-aza-C-glycosides with D-gluco, L-ido and D-xylo iminosugar cores possessing analogous linker variations. Evaluation of both libraries did not reveal a potent or selective inhibitor of glucosylceramide synthase. However, β-aza-C-glycoside 43 was found to be a selective inhibitor of β-glucosidase 2. The α-aza-C-glycosides – especially with a D-xylo core (e.g. 80) – proved to be very potent and selective inhibitors of glucocerebrosidase.

A ligation strategy based on the Diels–Alder [4+2] cycloaddition for the two-step activity-based labeling of endogenously expressed enzymes in complex biological samples has been developed. A panel of four diene-derivatized proteasome probes was synthesized, along with a dienophile-functionalized BODIPY(TMR) tag. These probes were applied in a Diels–Alder labeling procedure that enabled us to label active proteasome β-subunits selectively in cellular extracts and in living cells. We were also able to label the activity of cysteine proteases in cell extracts by utilizing a diene-derivatized cathepsin probe. Importantly, the Diels–Alder strategy described here is fully orthogonal with respect to the Staudinger–Bertozzi ligation, as demonstrated by the independent labeling of different proteolytic activities by the two methods in a single experiment.

Proteolysis, or the processing and degradation of proteins, has emerged as one of the most widely studied processes in biology today. Long viewed as a dead end process, of importance only for the removal of obsolete peptides and proteins, proteolytic events are now associated with numerous biological events. The main proteolytic pathway in the eukaryotic cytoplasm and nucleus, responsible for the degradation of 80–90 % of all cellular proteins is known as the Ubiquitin Proteasome System (UPS). Proteasomes are the central proteases in this tightly controlled ATP- and ubiquitin-dependent proteolytic pathway. Proteasomes are multicatalytic, compartmentalized proteinase complexes. Their substrates include abnormal and damaged proteins, cell-cycle regulators, oncogens and tumor suppressors. Furthermore, proteasomal degradation is imperative for the generation of MHC class I antigenic peptides. The recent approval of a proteasome inhibitor as a cancer drug has boosted proteasome research. This microreview highlights the recent advances in the development of chemical tools to study proteasome activity.(© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009)

A series of homo- and heterodimeric compounds encompassing the follicle-stimulating hormone receptor (FSHR) antagonist (R)-1 and its inactive conformer (S)-1 connected through ethylene glycol spacers of various lengths is described. Evaluation of these compounds reveals that dimeric compounds, with a spacer of sufficient length, bearing two active copies of the antagonist are more potent relative to dimeric compounds in which one of the active pharmacophores is replaced by an inactive conformer. Interestingly, the opposite trend is observed if a short spacer is used, indicating that these compounds may be valuable tools to study FSHR dimerization in greater detail.

Die Entdeckung der Glycosphingolipide wird im Allgemeinen Johan L. W. Thudichum zugeschrieben, der 1884 über die chemische Zusammensetzung des Gehirns publizierte. In seinen Studien isolierte er aus ethanolischen Hirnextrakten mehrere Verbindungen, die er als Cerebroside bezeichnete. Eine dieser Verbindungen, Phrenosin (heute als Galactosylceramid bekannt), unterwarf er einer sauren Hydrolyse, aus der drei Komponenten hervorgingen. Eine Komponente identifizierte er als Fettsäure, eine andere als Isomer zur D-Glucose, heute als D-Galactose bekannt. Die dritte Komponente mit “alkaloidaler Natur” gab Thudichum “viele Rätsel” auf, weshalb er sie Sphingosin nannte, nach dem mythologischen Rätsel der Sphinx. Derzeit sind Sphingolipide und ihre glycosidierten Derivate Gegenstand intensiver Forschung mit dem Ziel, ihre Funktion für die strukturelle Integrität der Zellmembran, ihre Teilnahme in Erkennungs- und Signalübertragungsvorgängen und besonders ihre Beteiligung an pathologischen Prozessen, die als Ursache menschlicher Krankheiten (z. B. von Sphingolipidosen und Typ-2-Diabetes) gelten, aufzuklären. Dieser Aufsatz wird auf neuere Befunde zur Biosynthese, Funktion und zum Abbau von Glycosphingolipiden im Menschen eingehen, mit Fokus auf das Glycosphingolipidglucosylceramid. Besondere Aufmerksamkeit richtet sich auf die klinische Bedeutung von Verbindungen, die mit den Faktoren des Glycosphingolipid-Metabolismus wechselwirken.

The discovery of the glycosphingolipids is generally attributed to Johan L. W. Thudichum, who in 1884 published on the chemical composition of the brain. In his studies he isolated several compounds from ethanolic brain extracts which he coined cerebrosides. He subjected one of these, phrenosin (now known as galactosylceramide), to acid hydrolysis, and this produced three distinct components. One he identified as a fatty acid and another proved to be an isomer of D-glucose, which is now known as D-galactose. The third component, with an “alkaloidal nature”, presented “many enigmas” to Thudichum, and therefore he named it sphingosine, after the mythological riddle of the Sphinx. Today, sphingolipids and their glycosidated derivatives are the subjects of intense study aimed at elucidating their role in the structural integrity of the cell membrane, their participation in recognition and signaling events, and in particular their involvement in pathological processes that are at the basis of human disease (for example, sphingolipidoses and diabetes type 2). This Review details some of the recent findings on the biosynthesis, function, and degradation of glycosphingolipids in man, with a focus on the glycosphingolipid glucosylceramide. Special attention is paid to the clinical relevance of compounds directed at interfering with the factors responsible for glycosphingolipid metabolism.

A library of polyhydroxylated pyrrolidines was obtained by performing a tandem Staudinger/aza-Wittig/Ugi three-component reaction on a L-ribose-derived 4-azido aldehyde. In this paper we describe the effect of Lewis acids on the diastereoselectivity of the final Ugi three-component reaction step that the intermediate (D-lyxo-pyrroline) cyclic imine undergoes. When the Ugi reaction was performed in methanol almost exclusively pyrrolidines with a 2,3-cis relationship were formed. However, a significant amount of 2,3-trans product was formed upon addition of Lewis acids to the Ugi reaction mixture. The scope of this effect is explored by evaluating a diverse set of Lewis acids in combination with variation of other reaction parameters and the carboxylic acid/isocyanide component. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008)