Highly tunable thiosulfonates as a novel class of cysteine protease inhibitors with anti-parasitic activity against Schistosoma mansoni.

The development of a new class of cysteine protease inhibitors utilising the thiosulfonate moiety as an SH specific electrophile is described. This moiety has been introduced into suitable amino acid derived building blocks, which were incorporated into peptidic sequences leading to very potent i.e. sub micromolar inhibitors of the cysteine protease papain in the same range as the vinyl sulfone based inhibitor K11777. Therefore, their inhibitory effect on Schistosoma mansoni, a human blood parasite, that expresses several cysteine proteases, was evaluated. The homophenylalanine side chain containing compounds 27-30 and especially 36 showed promising activities compared with K11777 and warrant further investigations of these peptidic thiosulfonate inhibitors as new potential anti-parasitic compounds.

The presence of C/EBPα and its degradation are both required for TRIB2-mediated leukaemia.

C/EBPα (p42 and p30 isoforms) is commonly dysregulated in cancer via the action of oncogenes, and specifically in acute myeloid leukaemia (AML) by mutation. Elevated TRIB2 leads to the degradation of C/EBPα p42, leaving p30 intact in AML. Whether this relationship is a cooperative event in AML transformation is not known and the molecular mechanism involved remains elusive. Using mouse genetics, our data reveal that in the complete absence of C/EBPα, TRIB2 was unable to induce AML. Only in the presence of C/EBPα p42 and p30, were TRIB2 and p30 able to cooperate to decrease the latency of disease. We demonstrate that the molecular mechanism involved in the degradation of C/EBPα p42 requires site-specific direct interaction between TRIB2 and C/EBPα p42 for the K48-specific ubiquitin-dependent proteasomal degradation of C/EBPα p42. This interaction and ubiquitination is dependent on a critical C terminal lysine residue on C/EBPα. We show effective targeting of this pathway pharmacologically using proteasome inhibitors in TRIB2-positive AML cells. Together, our data show that excess p30 cooperated with TRIB2 only in the presence of p42 to accelerate AML, and the direct interaction and degradation of C/EBPα p42 is required for TRIB2-mediated AML.

Molecular construction of HIV-gp120 discontinuous epitope mimics by assembly of cyclic peptides on an orthogonal alkyne functionalized TAC-scaffold.

Mimics of discontinuous epitopes of for example bacterial or viral proteins may have considerable potential for the development of synthetic vaccines, especially if conserved epitopes can be mimicked. However, due to the structural complexity and size of discontinuous epitopes molecular construction of these mimics remains challeging. We present here a convergent route for the assembly of discontinuous epitope mimics by successive azide alkyne cycloaddition on an orthogonal alkyne functionalized scaffold. Here the synthesis of mimics of the HIV gp120 discontinuous epitope that interacts with the CD4 receptor is described. The resulting protein mimics are capable of inhibition of the gp120-CD4 interaction. The route is convergent, robust and should be applicable to other discontinuous epitopes.

Scaffolded multiple cyclic peptide libraries for protein mimics by native chemical ligation.

The accessibility to collections, libraries and arrays of cyclic peptides is increasingly important since cyclic peptides may provide better mimics of the loop-like structures ubiquitously present in and - especially - on the surface of proteins. The next important step is the preparation of libraries of ensembles of scaffolded cyclic peptides, which upon screening may lead to promising protein mimics. Here we describe the synthesis of a tri-cysteine containing scaffold as well as the simultaneous native chemical ligation of three cyclic peptides thereby affording a clean library of multiple cyclic peptides on this scaffold, representing potential mimics of gp120. Members of this collection of protein mimics showed a decent inhibition of the gp120-CD4 interaction.

Thermodynamics of phosphotyrosine peptide-peptoid hybrids binding to the p56lck SH2 domain.

A frequently used approach to transform peptides into more drug-like compounds is preparation of the corresponding peptoids or peptide-peptoid hybrids. Although peptoids have advantages, there may also be some disadvantages such as their increased flexibility and the reduced ability for hydrogen bond formation due to alkylation of the backbone amide nitrogen, which might affect the free Gibbs energy (DeltaG). To obtain more insight into these contributions to DeltaG, we performed thermodynamic analyses on the interaction between peptide-peptoid hybrids, based on the sequence -pTyr-Glu-Glu-Ile-, and the p56(lck) (Lck) Src homology 2 domain. van't Hoff analysis was performed on binding data obtained from surface plasmon resonance competition experiments in a temperature range of 10-40 degrees C. It is observed that amino acid-peptoid substitutions do not have a systemic negative effect on the entropic contributions to DeltaG. However, loss in hydrogen-bonding capacity of the backbone may strongly reduce the binding enthalpy and contribute to the observed lower binding affinity.

Probing the self-assembly and the accompanying structural changes of hydrophobin SC3 on a hydrophobic surface by mass spectrometry.

The fungal class I hydrophobin SC3 self-assembles into an amphipathic membrane at hydrophilic-hydrophobic interfaces such as the water-air and water-Teflon interface. During self-assembly, the water-soluble state of SC3 proceeds via the intermediate alpha-helical state to the stable end form called the beta-sheet state. Self-assembly of the hydrophobin at the Teflon surface is arrested in the alpha-helical state. The beta-sheet state can be induced at elevated temperature in the presence of detergent. The structural changes of SC3 were monitored by various mass spectrometry techniques. We show that the so-called second loop of SC3 (C39-S72) has a high affinity for Teflon. Binding of this part of SC3 to Teflon was accompanied by the formation of alpha-helical structure and resulted in low solvent accessibility. The solvent-protected region of the second loop extended upon conversion to the beta-sheet state. In contrast, the C-terminal part of SC3 became more exposed to the solvent. The results indicate that the second loop of class I hydrophobins plays a pivotal role in self-assembly at the hydrophilic-hydrophobic interface. Of interest, this loop is much smaller in case of class II hydrophobins, which may explain the differences in their assembly.

Solid-phase synthesis of oligourea peptidomimetics employing the Fmoc protection strategy.

A solid-phase-Fmoc-based-synthesis strategy is described for oligourea peptidomimetics as well as a convenient general synthesis approach for the preparation of the required building blocks 5a-j and 5k. These are suitable for use in peptide or robot synthesizers, which is illustrated by the synthesis of oligourea peptidomimetics of part of Leu-enkephalin (10) and a neurotensin derivative (17).

A selectively deprotectable triazacyclophane scaffold for the construction of artificial receptors.

[reaction: see text]. The synthesis of a triazacylclophane scaffold bearing a set of selectively removable protecting groups is described. This versatile scaffold, which can be linked to a solid support, allows the attachment of three different side chains and can therefore be used for the combinatorial synthesis of libraries of artificial receptor molecules of high structural diversity.

Bio-inspired synthetic receptor molecules towards mimicry of vancomycin.

A 512-member library of bio-inspired synthetic receptor molecules was prepared featuring a triazacyclophane scaffold. The purpose of this scaffold was to orient three (identical) peptide 'binding arms' in order to mimic an antibiotic binding cavity as is present in the vancomycin antibiotics. The library was screened with D-Ala-D-Ala and D-Ala-D-Lac containing ligands, which are present in the cell wall precursors of pathogenic bacteria. Screening and validation led to identification of a synthetic receptor capable of binding these ligands.

Sensitivity of single membrane-spanning alpha-helical peptides to hydrophobic mismatch with a lipid bilayer: effects on backbone structure, orientation, and extent of membrane incorporation.

The extent of matching of membrane hydrophobic thickness with the hydrophobic length of transmembrane protein segments potentially constitutes a major director of membrane organization. Therefore, the extent of mismatch that can be compensated, and the types of membrane rearrangements that result, can provide valuable insight into membrane functionality. In the present study, a large family of synthetic peptides and lipids is used to investigate a range of mismatch situations. Peptide conformation, orientation, and extent of incorporation are assessed by infrared spectroscopy, tryptophan fluorescence, circular dichroism, and sucrose gradient centrifugation. It is shown that peptide backbone structure is not significantly affected by mismatch, even when the extent of mismatch is large. Instead, this study demonstrates that for tryptophan-flanked peptides the dominant response of a membrane to large mismatch is that the extent of incorporation is reduced, when the peptide is both too short and too long. With increasing mismatch, a smaller fraction of peptide is incorporated into the lipid bilayer, and a larger fraction is present in extramembranous aggregates. Relatively long peptides that remain incorporated in the bilayer have a small tilt angle with respect to the membrane normal. The observed effects depend on the nature of the flanking residues: long tryptophan-flanked peptides do not associate well with thin bilayers, while equisized lysine-flanked peptides associate completely, thus supporting the notion that tryptophan and lysine interact differently with membrane-water interfaces. The different properties that aromatic and charged flanking residues impart on transmembrane protein segments are discussed in relation to protein incorporation in biological systems.

Wedgelike glycodendrimers as inhibitors of binding of mammalian galectins to glycoproteins, lactose maxiclusters, and cell surface glycoconjugates.

Galectins are mammalian carbohydrate-binding proteins that are involved in cell-cell and cell-matrix adhesion, cell migration, and growth regulation with relevance to inflammation and tumor spread. These important functions account for the interest to design suitable low molecular weight inhibitors that match the distinct modes of presentation of the carbohydrate recognition domains of the different galectin subfamilies. Using 3,5-di-(2-aminoethoxy)benzoic acid as the branching unit, wedgelike glycodendrimers with two, four, and eight lactose moieties (G1-G3) were synthesized. They were tested in solid-phase competition assays with lactose maxiclusters and various N-glycan branching profiles (miniclusters) as the matrix and also in cell assays. Prototype galectins-1 and -7, chimera-type galectin-3, a plant (AB)(2) toxin, and a lactose-binding immunoglobulin G fraction from human serum were the carbohydrate-binding targets. Potent inhibition and remarkable cluster effects were seen for the homodimeric galectin-1, especially in combination with biantennary N-glycans as the matrix. Remarkably, for the tetravalent G2 glycodendrimer, the inhibitory potency of each lactose unit reached a maximum value of 1667 relative to free lactose. In haemagglutination experiments as a model for cell adhesion, galectin-3 was markedly sensitive to increased sugar valency and a relative potency per lactose of 150 was reached. The spatial orientation of the carbohydrate recognition domains of the endogenous lectins and the branching pattern of the carbohydrates of the glycoprotein matrices used are both important factors in the design and synthesis of glycodendrimers with galectin-selective properties.

Peptoid - peptide hybrids that bind Syk SH2 domains involved in signal transduction.

Peptoid-peptide hybrids are oligomeric peptidomimetics that contain one or more N-substituted glycine residues. In these hybrids, the side chains of one or several amino acids are "shifted" from the alpha-carbon atom to the amide nitrogen atom. A library of phosphorylated peptoid-peptide hybrids derived from the sequence pTyr-Glu-Thr-Leu was synthesized and tested for binding to the tandem SH2 domain of the protein tyrosine kinase Syk. A considerable influence of the side chain position was observed. Compounds 19-21, 24, and 25 comprising a peptoid NpTyr and/or NGlu residue did not show any binding. Compounds 22, 23, and 26 containing an NhThr (hThr=homothreonine) and/or NLeu peptoid residue showed binding with IC(50) values that were only five to eight times higher than that of the tetrapeptide lead compound 18. These data show that side chain shifting is possible with retention of binding capacity, but only at the two C-terminal residues of the tetramer. This method of a peptoid scan using peptoid-peptide hybrids appears to be very useful to explore to what extent a peptide sequence can be transformed into a peptoid while retaining its affinity.

Synthesis of cyclic peptides by ring-closing metathesis.

The synthesis of a series of "amide to amide" cyclized peptides by ring-closing metathesis (RCM) as well as a convenient synthesis for the linear precursors is described. In addition, the influence of the length of the alkene substituents and the influence of the peptide sequence is investigated, leading to a set of general rules to obtain "amide to amide" cyclized peptides by RCM.

Different membrane anchoring positions of tryptophan and lysine in synthetic transmembrane alpha-helical peptides.

Specific interactions of membrane proteins with the membrane interfacial region potentially define protein position with respect to the lipid environment. We investigated the proposed roles of tryptophan and lysine side chains as "anchoring" residues of transmembrane proteins. Model systems were employed, consisting of phosphatidylcholine lipids and hydrophobic alpha-helical peptides, flanked either by tryptophans or lysines. Peptides were incorporated in bilayers of different thickness, and effects on lipid structure were analyzed. Induction of nonbilayer phases and also increases in bilayer thickness were observed that could be explained by a tendency of Trp as well as Lys residues to maintain interactions with the interfacial region. However, effects of the two peptides were remarkably different, indicating affinities of Trp and Lys for different sites at the interface. Our data support a model in which the Trp side chain has a specific affinity for a well defined site near the lipid carbonyl region, while the lysine side chain prefers to be located closer to the aqueous phase, near the lipid phosphate group. The information obtained in this study may further our understanding of the architecture of transmembrane proteins and may prove useful for refining prediction methods for transmembrane segments.

A versatile method for the conjugation of proteins and peptides to poly[2-(dimethylamino)ethyl methacrylate].

Random copolymers of 2-(dimethylamino) ethyl methacrylate (DMAEMA) with aminoethyl methacrylate (AEMA) were synthesized by radical polymerization. The amount of incorporated primary amino groups could be controlled by the feed ratio of AEMA to DMAEMA, and was varied from 2 to 6 mol %. Subsequently, protected thiol groups were introduced in a derivatization step with N-succinimidyl 3-(2-pyridyldithio)propionate (SPDP) and subsequent treatment with dithiothreitol (DTT). The obtained thiolated p(DMAEMA-co-AEMA) was conjugated to transferrin (Tf) or the F(ab') fragment of mAb 323/A3 via a disulfide linkage. Moreover, the maleimide derivative of the nuclear localization signal (NLS) decapeptide Gly-Pro-Lys-Lys-Lys-Arg-Lys-Val-Glu-Asp-NH(2) was coupled to the thiolated polymer via a thioether linkage. The coupling efficiency, as determined by GPC (Tf), SDS-PAGE [F(ab')], or (1)H NMR (NLS peptide) was 90-95% for the Tf conjugate, and more than 95% for the F(ab') conjugate and the NLS conjugate. The synthetic strategy described in this paper is a universal method for the preparation of conjugates of proteins and peptides with pDMAEMA in particular. This method can possibly be used to synthesize protein-polymethacrylate conjugates in general.

Increased stability of peptidesulfonamide peptidomimetics towards protease catalyzed degradation.

Replacement of amide bonds in peptides by sulfonamide moieties resulted in peptidosulfonamides with an increased stability towards protease catalyzed degradation. In addition to protection of the protease cleavage site, it was found that introduction of a sulfonamide also influenced the stability of adjacent amide bonds.

Combinatorial chemistry of hydantoins.

Access to combinatorial chemistry of hydantoins is provided by convenient and versatile methods for the solid phase synthesis of libraries of 3,5-, 1,3- and 1,3,5-substituted hydantoins. The preparation of trisubstituted hydantoins features a Mitsunobu reaction for introduction of the substituent on N-1.

TNF-mediated cytotoxicity of L929 cells: role of staurosporine in enhancement of cytotoxicity and translocation of protein kinase C isozymes.

The role of protein kinase C (PKC) in tumour necrosis factor (TNF)-mediated cytotoxicity was investigated, using the L929 cell line. The PKC activator phorbol-12-myristate 13-acetate (PMA) increased proliferation and inhibited TNF-induced cytotoxicity of L929 cells. A range of specific PKC inhibitors had no effect on TNF-mediated killing, suggesting that PKC does not play a direct role in this response. However, staurosporine enhanced cytotoxicity by TNF in the presence of actinomycin D, a protein synthesis inhibitor. In view of this finding, the authors investigated the role of specific PKC isozymes in both TNF-mediated cytotoxicity and staurosporine-induced sensitization to killing. PKC-alpha, beta, epsilon and zeta were detected in L929 cells. PKC-beta was only weakly detected in the cytoplasm, PKC alpha, epsilon and zeta were all found in resting cytoplasm and membrane. Stimulation with PMA caused a strong translocation of PKC-alpha but not zeta to the membrane. TNF had no effect on these isozymes but interestingly caused a translocation of PKC-epsilon, which also occurred in response to PMA. Staurosporine caused a translocation of PKC-zeta to the plasma membrane and a loss of PKC-epsilon from the cytosol. Although TNF induced PKC-epsilon translocation, this is unlikely to be involved in cytotoxicity as this effect was also induced by PMA which protected against TNF-mediated cytotoxicity. Staurosporine also induced translocation of PKC-zeta, an isozyme whose activity was previously found to be resistant to inhibition by staurosporine. These findings suggest the possibility that the mechanism by which staurosporine potentiates TNF action does not involve inhibition of PKC, but in contrast may involve modulation of PKC-zeta.

Molecular diversity of peptidomimetics: approaches to the solid-phase synthesis of peptidosulfonamides.

In order to use the potential molecular diversity of the peptidosulfonamide peptidomimetics ultimately in libraries, approaches towards the solid-phase synthesis of peptidosulfonamides are a prerequisite. It is shown that peptidosulfonamides can be synthesized by solid-phase synthesis methods using either a Merrifield or a Tentagel resin. Better and more reproducible results are obtained using the latter resin. The possibility to prepare cyclic peptidosulfonamides was illustrated by the synthesis of cyclo-phenylalanyl psi[CH2S(O)2N]-glycine. However, translation of synthesis of peptidosulfonamides in solution to a solid-phase method was rather laborious and still requires careful optimization.

Comparing mass spectrometric characteristics of peptides and peptoids.

The collision-induced dissociation (CID) spectra of the [M+H]+ ions of a pentapeptide and the corresponding peptoid and retropeptoid have been compared. The spectra of the peptide and peptoid both exhibit B- and Y"-type sequence ions at identical m/z values. In contrast to the peptide, the [M+H]+ ion of the peptoid and all sequence ions containing an N-substituted glycine derivative corresponding to a tyrosine amino acid residue can easily lose a C7H6O molecule in a charge-remote fragmentation process. The presence of N-substituted glycine residues in a peptoid is further apparent from the presence of N-substituted immonium ions, which differ significantly in their fragmentation behaviour from the corresponding immonium ions observed in the spectra of common oligopeptides. Loss of the CH2 = NH imine molecule is the dominant fragmentation reaction in the CID spectra of all peptoid immonium ions investigated in this study. The elimination of the CH = NH2 ylide analogue from common peptide immonium ions is energetically less favourable as shown by ab initio calculations. The relative heat of formation of the CH = NH2 ylide neutral appeared to be 168 kJ mol-1 more than that of the CH2 = NH imine molecule.