57 research outputs found
Proteasome Subunit Selective Activity-Based Probes Report on Proteasome Core Particle Composition in a Native Polyacrylamide Gel Electrophoresis Fluorescence-Resonance Energy Transfer Assay
Most
mammalian tissues contain a single proteasome species: constitutive
proteasomes. Tissues able to express, next to the constitutive proteasome
catalytic activities (β1c, β2c, β5c), the three
homologous activities, β1i, β2i and β5i, may contain
numerous distinct proteasome particles: immunoproteasomes (composed
of β1i, β2i and β5i) and mixed proteasomes containing
a mix of these activities. This work describes the development of
new subunit-selective activity-based probes and their use in an activity-based
protein profiling assay that allows the detection of various proteasome
particles. Tissue extracts are treated with subunit-specific probes
bearing distinct fluorophores and subunit-specific inhibitors. The
samples are resolved by native polyacrylamide gel electrophoresis,
after which fluorescence-resonance energy transfer (FRET) reports
on the nature of proteasomes present
Reagent Controlled Stereoselective Synthesis of α‑Glucans
The development of a general glycosylation
method that allows for
the stereoselective construction of glycosidic linkages is a tremendous
challenge. Because of the differences in steric and electronic properties
of the building blocks used, the outcome of a glycosylation reaction
can vary greatly when switching form one glycosyl donor–acceptor
pair to another. We here report a strategy to install <i>cis</i>-glucosidic linkages in a fully stereoselective fashion that is under
direct control of the reagents used to activate a single type of donor
building block. The activating reagents are tuned to the intrinsic
reactivity of the acceptor alcohol to match the reactivity of the
glycosylating agent with the reactivity of the incoming nucleophile.
A protecting group strategy is introduced that is based on the sole
use of benzyl-ether type protecting groups to circumvent changes in
reactivity as a result of the protecting groups. For the stereoselective
construction of the α-glucosyl linkages to a secondary alcohol,
a per-benzylated glusosyl imidate donor is activated with a combination
of trimethylsilyltriflate and DMF, while activation of the same imidate
donor with trimethylsilyl iodide in the presence of triphenylphosphine
oxide allows for the stereoselective <i>cis</i>-glucosylation
of primary alcohols. The effectiveness of the strategy is illustrated
in the modular synthesis of a <i>Mycobacterium tuberculosis</i> nonasaccharide, composed of an α-(1–4)-oligoglucose
backbone bearing different α-glucosyl branches
2,2-Dimethyl-4-(4-methoxy-phenoxy) butanoate and 2,2-Dimethyl-4-azido Butanoate: Two New Pivaloate-ester-like Protecting Groups
The title compounds were developed to extend the available orthogonalities within the class of protecting groups removed by assisted cleavage. The mild, complementary (oxidative vs reductive) reaction conditions for the removal, together with their pivaloate-like character, were exploited, in combination with a levulinoyl-ester functioning as a third orthogonal protecting group, in the assembly of a <i>Streptococcus mutans</i> hexasaccharide built up from a oligorhamnose backbone featuring β-glucosyl appendages
Synthetic Studies on the Preparation of Alanyl Epoxysulfones as Cathepsin Cysteine Protease Electrophilic Traps
A Darzens
reaction between <i>tert</i>-butoxycarbonyl
alaninal and chloromethyl phenyl sulfone afforded chlorohydrins, which
were converted into epoxysulfones by reaction with sodium <i>tert</i>-butoxide. Epoxysulfone <b>10</b> and chloroketone <b>14</b> derived from chlorohydrins by oxidation proved to be inhibitors
of cathepsins H, S, and C as determined by competitive activity-based
protein profiling
Branching of poly(ADP-ribose): Synthesis of the Core Motif
The synthesis of the core motif of
branched poly(adenosine diphosphate
ribose) (poly(ADPr)) is described, and structural analysis reasserted
the proposed stereochemistry for branching. For the synthesis, a ribose
trisaccharide was first constructed with only α-<i>O</i>-glycosidic linkages. Finally, the adenine nucleobase was introduced
via a Vorbrüggen-type glycosylation reaction. The orthogonality
of the selected protecting groups was demonstrated, allowing for the
construction of branched poly(ADPr) oligomers in the near future
Reagent Controlled Stereoselective Synthesis of α‑Glucans
The development of a general glycosylation
method that allows for
the stereoselective construction of glycosidic linkages is a tremendous
challenge. Because of the differences in steric and electronic properties
of the building blocks used, the outcome of a glycosylation reaction
can vary greatly when switching form one glycosyl donor–acceptor
pair to another. We here report a strategy to install <i>cis</i>-glucosidic linkages in a fully stereoselective fashion that is under
direct control of the reagents used to activate a single type of donor
building block. The activating reagents are tuned to the intrinsic
reactivity of the acceptor alcohol to match the reactivity of the
glycosylating agent with the reactivity of the incoming nucleophile.
A protecting group strategy is introduced that is based on the sole
use of benzyl-ether type protecting groups to circumvent changes in
reactivity as a result of the protecting groups. For the stereoselective
construction of the α-glucosyl linkages to a secondary alcohol,
a per-benzylated glusosyl imidate donor is activated with a combination
of trimethylsilyltriflate and DMF, while activation of the same imidate
donor with trimethylsilyl iodide in the presence of triphenylphosphine
oxide allows for the stereoselective <i>cis</i>-glucosylation
of primary alcohols. The effectiveness of the strategy is illustrated
in the modular synthesis of a <i>Mycobacterium tuberculosis</i> nonasaccharide, composed of an α-(1–4)-oligoglucose
backbone bearing different α-glucosyl branches
Mapping the Reactivity and Selectivity of 2‑Azidofucosyl Donors for the Assembly of <i>N</i>‑Acetylfucosamine-Containing Bacterial Oligosaccharides
The synthesis of complex oligosaccharides
is often hindered by
a lack of knowledge on the reactivity and selectivity of their constituent
building blocks. We investigated the reactivity and selectivity of
2-azidofucosyl (FucN<sub>3</sub>) donors, valuable synthons in the
synthesis of 2-acetamido-2-deoxyfucose (FucNAc) containing oligosaccharides.
Six FucN<sub>3</sub> donors, bearing benzyl, benzoyl, or <i>tert</i>-butyldimethylsilyl protecting groups at the C3-<i>O</i> and C4-<i>O</i> positions, were synthesized, and their
reactivity was assessed in a series of glycosylations using acceptors
of varying nucleophilicity and size. It was found that more reactive
nucleophiles and electron-withdrawing benzoyl groups on the donor
favor the formation of β-glycosides, while poorly reactive nucleophiles
and electron-donating protecting groups on the donor favor α-glycosidic
bond formation. Low-temperature NMR activation studies of Bn- and
Bz-protected donors revealed the formation of covalent FucN<sub>3</sub> triflates and oxosulfonium triflates. From these results, a mechanistic
explanation is offered in which more reactive acceptors preferentially
react via an S<sub>N</sub>2-like pathway, while less reactive acceptors
react via an S<sub>N</sub>1-like pathway. The knowledge obtained in
this reactivity study was then applied in the construction of α-FucN<sub>3</sub> linkages relevant to bacterial saccharides. Finally, a modular
synthesis of the <i>Staphylococcus aureus</i> type 5 capsular
polysaccharide repeating unit, a trisaccharide consisting of two FucNAc
units, is described
Stereoselectivity of Conformationally Restricted Glucosazide Donors
Glycosylations of 4,6-tethered glucosazide
donors with a panel
of model acceptors revealed the effect of acceptor nucleophilicity
on the stereoselectivity of these donors. The differences in reactivity
among the donors were evaluated in competitive glycosylation reactions,
and their relative reactivities were found to be reflected in the
stereoselectivity in glycosylations with a set of fluorinated alcohols
as well as carbohydrate acceptors. We found that the 2-azido-2-deoxy
moiety is more β-directing than its C-2-<i>O</i>-benzyl
counterpart, as a consequence of increased destabilization of anomeric
charge development by the electron-withdrawing azide. Additional disarming
groups further decreased the α-selectivity of the studied donors,
whereas substitution of the 4,6-benzylidene acetal with a 4,6-di-<i>tert</i>-butyl silylidene led to a slight increase in α-selectivity.
The C-2-dinitropyridone group was also explored as an alternative
for the nonparticipating azide group, but this protecting group significantly
increased β-selectivity. All studied donors exhibited the same
acceptor-dependent selectivity trend, and good α-selectivity
could be obtained with the weakest acceptors and most reactive donors
Systematic Analyses of Substrate Preferences of 20S Proteasomes Using Peptidic Epoxyketone Inhibitors
Cleavage
analyses of 20S proteasomes with natural or synthetic
substrates allowed to infer the substrate specificities of the active
sites and paved the way for the rational design of high-affinity proteasome
inhibitors. However, details of cleavage preferences remained enigmatic
due to the lack of appropriate structural data. In a unique approach,
we here systematically examined substrate specificities of yeast and
human proteasomes using irreversibly acting α′,β′epoxyketone
(ep) inhibitors. Biochemical and structural analyses provide unique
insights into the substrate preferences of the distinct active sites
and highlight differences between proteasome types that may be considered
in future inhibitor design efforts. (1) For steric reasons, epoxyketones
with Val or Ile at the P1 position are weak inhibitors of all active
sites. (2) Identification of the β2c selective compound Ac-LAE-ep
represents a promising starting point for the development of compounds
that discriminate between β2c and β2i. (3) The compound
Ac-LAA-ep was found to favor subunit β5c over β5i by three
orders of magnitude. (4) Yeast β1 and human β1c subunits
preferentially bind Asp and Leu in their S1 pockets, while Glu and
large hydrophobic residues are not accepted. (5) Exceptional structural
features in the β1/2 substrate binding channel give rise to
the β1 selectivity of compounds featuring Pro at the P3 site.
Altogether, 23 different epoxyketone inhibitors, five proteasome mutants,
and 43 crystal structures served to delineate a detailed picture of
the substrate and ligand specificities of proteasomes and will further
guide drug development efforts toward subunit-specific proteasome
inhibitors for applications as diverse as cancer and autoimmune disorders
Synthetic α- and β‑Ser-ADP-ribosylated Peptides Reveal α‑Ser-ADPr as the Native Epimer
A solid-phase methodology to synthesize
oligopeptides, specifically
incorporating serine residues linked to ADP-ribose (ADPr), is presented.
Through the synthesis of both α- and β-anomers of the
phosphoribosylated Fmoc-Ser building block and their usage in our
modified solid-phase peptide synthesis protocol, both α- and
β-ADPr peptides from a naturally Ser-ADPr containing H2B sequence
were obtained. With these, and by digestion studies using the human
glycohydrolase, ARH3 (hARH3), compelling evidence is obtained that
the α-Ser-ADPr linkage comprises the naturally occurring configuration
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