In silico investigation and targeting of amyloid β oligomers of different size

Aggregation of amyloid β (Aβ) peptides into fibrils has been implicated in the pathogenesis of Alzheimer's disease (AD). As a result, in recent years, substantial efforts have been expended in the study of the mechanism of aggregation of the Aβ peptide as well as of its inhibition by potential drug molecules. In this context, we have built a model of the Aβ(17-42) deca-oligomer using the solid-state NMR (ssNMR) structure of the Aβ(17-42) penta-oligomer as a reference. Both the penta- and deca-oligomer systems have been studied by all-atom molecular dynamics (MD) simulations and used as target systems for the investigation of the mechanism of action of a trehalose-derived Aβ aggregation inhibitor. In the deca-oligomer all the main structural features of the putative fibrillar state are retained. Moreover, the simulations reveal a remarkable gain in stability as the oligomer grows. MD studies of the inhibitor in complex with the penta- and deca-oligomers indicate a significant destabilization of the structure beyond the hampering of the addition of successive Aβ peptides at the ends of the fibril due to the presence of the inhibitor molecule. Our work provides an easy and effective approach which could be useful for the in silico development of potential drug molecules acting at different stages of the progression of Aβ-related diseases.

In vitro activity of the αvβ3 integrin antagonist RGDechi-hCit on malignant melanoma cells

BACKGROUND

In malignant melanoma (MM), overexpression of αvβ3 integrin is linked to a more metastatic phenotype. Development of anti-αvβ3 agents able to counteract melanoma progression would be helpful for disease treatment. A new selective ligand of αvβ3, RGDechi-hCit, has anti-angiogenic properties against endothelial cells in animal angiogenesis models. The aim of this study was to evaluate the in vitro effects of the RGDechi-hCit peptide on MM cell lines.

MATERIALS AND METHODS

Cytofluorimetric analysis characterized the cell surface expression of αvβ3 integrin on seven MM cell lines: A375, WM266-4, SK-Mel-28, Sbcl2, LB24Dagi, PR-Mel and PNP-Mel. Cell proliferation, adhesion, and migration assays were carried out using the αvβ3-antagonist RGDechi-hCit.

RESULTS

Proliferation was not significantly inhibited by RGDechi-hCit, although striking morphological changes were detected in MM cell lines highly expressing αvβ3. Conversely, assays on fibronectin-coated plates showed a significant RGDechi-hCit dose-dependent inhibitory effect on both adhesion and migration.

CONCLUSION

The data demonstrate anti-adhesion and anti-migration, but not antiproliferative, activities of RGDechi-hCit against MM cells.

γ Sulphate PNA (PNA S): highly selective DNA binding molecule showing promising antigene activity

Peptide Nucleic Acids (PNAs), nucleic acid analogues showing high stability to enzyme degradation and strong affinity and specificity of binding toward DNA and RNA are widely investigated as tools to interfere in gene expression. Several studies have been focused on PNA analogues with modifications on the backbone and bases in the attempt to overcome solubility, uptake and aggregation issues. γ PNAs, PNA derivatives having a substituent in the γ position of the backbone show interesting properties in terms of secondary structure and affinity of binding toward complementary nucleic acids. In this paper we illustrate our results obtained on new analogues, bearing a sulphate in the γ position of the backbone, developed to be more DNA-like in terms of polarity and charge. The synthesis of monomers and oligomers is described. NMR studies on the conformational properties of monomers and studies on the secondary structure of single strands and triplexes are reported. Furthermore the hybrid stability and the effect of mismatches on the stability have also been investigated. Finally, the ability of the new analogue to work as antigene, interfering with the transcription of the ErbB2 gene on a human cell line overexpressing ErbB2 (SKBR3), assessed by FACS and qPCR, is described.

Effects of decoy molecules targeting NF-kappaB transcription factors in Cystic fibrosis IB3-1 cells: recruitment of NF-kappaB to the IL-8 gene promoter and transcription of the IL-8 gene

One of the clinical features of cystic fibrosis (CF) is a deep inflammatory process, which is characterized by production and release of cytokines and chemokines, among which interleukin 8 (IL-8) represents one of the most important. Accordingly, there is a growing interest in developing therapies against CF to reduce the excessive inflammatory response in the airways of CF patients. Since transcription factor NF-kappaB plays a critical role in IL-8 expression, the transcription factor decoy (TFD) strategy might be of interest. In order to demonstrate that TFD against NF-kappaB interferes with the NF-kappaB pathway we proved, by chromatin immunoprecipitation (ChIP) that treatment with TFD oligodeoxyribonucleotides of cystic fibrosis IB3–1 cells infected with Pseudomonas aeruginosa leads to a decrease occupancy of the Il-8 gene promoter by NF-kappaB factors. In order to develop more stable therapeutic molecules, peptide nucleic acids (PNAs) based agents were considered. In this respect PNA-DNA-PNA (PDP) chimeras are molecules of great interest from several points of view: (1) they can be complexed with liposomes and microspheres; (2) they are resistant to DNases, serum and cytoplasmic extracts; (3) they are potent decoy molecules. By using electrophoretic mobility shift assay and RT-PCR analysis we have demonstrated that (1) the effects of PDP/PDP NF-kappaB decoy chimera on accumulation of pro-inflammatory mRNAs in P.aeruginosa infected IB3–1 cells reproduce that of decoy oligonucleotides; in particular (2) the PDP/PDP chimera is a strong inhibitor of IL-8 gene expression; (3) the effect of PDP/PDP chimeras, unlike those of ODN-based decoys, are observed even in the absence of protection with lipofectamine. These informations are of great impact, in our opinion, for the development of stable molecules to be used in non-viral gene therapy of cystic fibrosis.

Targeting pre-miRNA by peptide nucleic acids: a new strategy to interfere in the miRNA maturation

PNAs conjugated to carrier peptides have been employed for the targeting of miRNA precursor, with the aim to develop molecules able to interfere in the pre-miRNA processing. The capability of the molecules to bind pre-miRNA has been tested in vitro by fluorescence assayes on Thiazole Orange labeled molecules and in vivo, in K562 cells, evaluating the amount of miRNA produced after treatment of cells with two amounts of PNAs.

Gold nanoparticles capped by a GC-containing peptide functionalized with an RGD motif for integrin targeting

Gold nanoparticles were obtained by reduction of a tetrachloroaurate aqueous solution in the presence of a RGD-(GC)(2) peptide as stabilizer. As comparison, the behavior of the (GC)(2) peptide has been studied. The (GC)(2) and RGD-(GC)(2) peptides were prepared ad hoc by Fmoc synthesis. The colloidal systems have been characterized by UV-visible, TGA, ATR-FTIR, mono and bidimensional NMR techniques, confocal and transmission (TEM) microscopy, ζ-potential, and light scattering measurements. The efficient cellular uptake of Au-RGD-(GC)(2) and Au-(GC)(2) stabilized gold nanoparticles into U87 cells (human glioblastoma cells) were investigated by confocal microscopy and compared with the behavior of (GC)(2) capped gold nanoparticles. A quantitative determination of the nanoparticles taken up has been carried out by measuring the pixel brightness of the images, a measure that highlighted the importance of the RGD termination of the peptide. Insight in the cellular uptake mechanism was investigated by TEM microscopy. Various important evidences indicated the selective uptake of RGD-(GC)(2) gold nanoparticles into the nucleus.

Acylpeptide hydrolase inhibition as targeted strategy to induce proteasomal down-regulation

Acylpeptide hydrolase (APEH), one of the four members of the prolyl oligopeptidase class, catalyses the removal of N-acylated amino acids from acetylated peptides and it has been postulated to play a key role in protein degradation machinery. Disruption of protein turnover has been established as an effective strategy to down-regulate the ubiquitin-proteasome system (UPS) and as a promising approach in anticancer therapy.

Here, we illustrate a new pathway modulating UPS and proteasome activity through inhibition of APEH. To find novel molecules able to down-regulate APEH activity, we screened a set of synthetic peptides, reproducing the reactive-site loop of a known archaeal inhibitor of APEH (SsCEI), and the conjugated linoleic acid (CLA) isomers. A 12-mer SsCEI peptide and the trans10-cis12 isomer of CLA, were identified as specific APEH inhibitors and their effects on cell-based assays were paralleled by a dose-dependent reduction of proteasome activity and the activation of the pro-apoptotic caspase cascade. Moreover, cell treatment with the individual compounds increased the cytoplasm levels of several classic hallmarks of proteasome inhibition, such as NFkappaB, p21, and misfolded or polyubiquitinylated proteins, and additive effects were observed in cells exposed to a combination of both inhibitors without any cytotoxicity. Remarkably, transfection of human bronchial epithelial cells with APEH siRNA, promoted a marked accumulation of a mutant of the cystic fibrosis transmembrane conductance regulator (CFTR), herein used as a model of misfolded protein typically degraded by UPS. Finally, molecular modeling studies, to gain insights into the APEH inhibition by the trans10-cis12 CLA isomer, were performed.

Our study supports a previously unrecognized role of APEH as a negative effector of proteasome activity by an unknown mechanism and opens new perspectives for the development of strategies aimed at modulation of cancer progression.

Evaluation of the anti-angiogenic properties of the new selective αVβ3 integrin antagonist RGDechiHCit

Background

Integrins are heterodimeric receptors that play a critical role in cell-cell and cell-matrix adhesion processes. Among them, α_Vβ₃ integrin, that recognizes the aminoacidic RGD triad, is reported to be involved in angiogenesis, tissue repair and tumor growth. We have recently synthesized a new and selective ligand of α_Vβ₃ receptor, referred to as RGDechiHCit, that contains a cyclic RGD motif and two echistatin moieties.

Methods

The aim of this study is to evaluate in vitro and in vivo the effects of RGDechiHCit. Therefore, we assessed its properties in cellular (endothelial cells [EC], and vascular smooth muscle cells [VSMC]) and animal models (Wistar Kyoto rats and c57Bl/6 mice) of angiogenesis.

Results

In EC, but not VSMC, RGDechiHCit inhibits intracellular mitogenic signaling and cell proliferation. Furthermore, RGDechiHCit blocks the ability of EC to form tubes on Matrigel. In vivo, wound healing is delayed in presence of RGDechiHCit. Similarly, Matrigel plugs demonstrate an antiangiogenic effect of RGDechiHCit.

Conclusions

Our data indicate the importance of RGDechiHCit in the selective inhibition of endothelial α_Vβ₃ integrin in vitro and in vivo. Such inhibition opens new fields of investigation on the mechanisms of angiogenesis, offering clinical implications for treatment of pathophysiological conditions such as cancer, proliferative retinopathy and inflammatory disease.

Probing the peptidylglycine alpha-hydroxylating monooxygenase active site with novel 4-phenyl-3-butenoic acid based inhibitors

Specific inhibition of the copper-containing peptidylglycine alpha-hydroxylating monooxygenase (PHM), which catalyzes the post-translational modification of peptides involved in carcinogenesis and tumor progression, constitutes a new approach for combating cancer. We carried out a structure-activity study of new compounds derived from a well-known PHM substrate analogue, the olefinic compound 4-phenyl-3-butenoic acid (PBA). We designed, synthesized, and tested various PBA derivatives both in vitro and in silico. We show that it is possible to increase PBA affinity for PHM by appropriate functionalization of its aromatic nucleus. Compound 2 d, for example, bears a meta-benzyloxy substituent, and exhibits better inhibition features (K(i)=3.9 microM, k(inact)/K(i)=427 M(-1) s(-1)) than the parent PBA (K(i)=19 microM, k(inact)/K(i)=82 M(-1) s(-1)). Docking calculations also suggest two different binding modes for PBA derivatives; these results will aid in the development of further PHM inhibitors with improved features.

gamma-Hydroxymethyl PNAs: Synthesis, interaction with DNA and inhibition of protein/DNA interactions

The ability of PNA to interact with DNA double stranded has been recently investigated. In a decoy approach these interactions are of great importance as may lead to inhibition of interactions of DNA sequences to specific transcription factors and may be employed as a strategy for the inhibition of gene transcription alternative to the antisense strategy (targeting transcription factors mRNAs) and the transcription factor decoy approach (targeting transcription factors). We explored the ability of PNA and PNAs with modified monomers to bind to DNA and to interfere in the formation of DNA/transcription factor complex. We report a procedure for the synthesis of Fmoc-gamma-hydroxymetyl PNA, the synthesis and CD analysis of PNA oligomers containing the modified monomer in different positions and EMSA assays to test the: (a) binding to double stranded DNA and (b) inhibition of DNA-protein interactions.

A novel class of protease targets of phosphatidylethanolamine-binding proteins (PEBP): a study of the acylpeptide hydrolase and the PEBP inhibitor from the archaeon Sulfolobus solfataricus

This work describes the identification and characterization of a Sulfolobus solfataricus acylpeptide hydrolase, named APEH(Ss), recognised as a new protease target of the endogenous PEBP inhibitor, SsCEI. APEH is one of the four members of the prolyl oligopeptidase (POP) family, which removes acylated amino acid residues from the N terminus of oligopeptides. APEH(Ss) is a cytosolic homodimeric protein with a molecular mass of 125 kDa. It displays a similar exopeptidase and endopeptidase activity to the homologous enzymes from Aeropyrum pernix and Pyrococcus horikoshii. Herein we demonstrate that SsCEI is the first PEBP protein found to efficiently inhibit APEH from both S. solfataricus and mammalian sources with IC(50) values in the nanomolar range. The 3D model of APEH(Ss) shows the typical structural features of the POP family including an N-terminal β-propeller and a C-terminal α/β hydrolase domain. Moreover, to gain insights into the binding mode of SsCEI toward APEH(Ss), a structural model of the inhibition complex is proposed, suggesting a mechanism of steric blockage on substrate access to the active site or on product release. Like other POP enzymes, APEH may constitute a new therapeutic target for the treatment of a number of pathologies and this study may represent a starting point for further medical research.

Crystal structure of an S-formylglutathione hydrolase from Pseudoalteromonas haloplanktis TAC125

S-formylglutathione hydrolases (FGHs) constitute a family of ubiquitous enzymes which play a key role in formaldehyde detoxification both in prokaryotes and eukaryotes, catalyzing the hydrolysis of S-formylglutathione to formic acid and glutathione. While a large number of functional studies have been reported on these enzymes, few structural studies have so far been carried out. In this article we report on the functional and structural characterization of PhEst, a FGH isolated from the psychrophilic bacterium Pseudoalteromonas haloplanktis. According to our functional studies, this enzyme is able to efficiently hydrolyze several thioester substrates with very small acyl moieties. By contrast, the enzyme shows no activity toward substrates with bulky acyl groups. These data are in line with structural studies which highlight for this enzyme a very narrow acyl-binding pocket in a typical alpha/beta-hydrolase fold. PhEst represents the first cold-adapted FGH structurally characterized to date; comparison with its mesophilic counterparts of known three-dimensional structure allowed to obtain useful insights into molecular determinants responsible for the ability of this psychrophilic enzyme to work at low temperature.

AKAP121 downregulation impairs protective cAMP signals, promotes mitochondrial dysfunction, and increases oxidative stress

AIMS

The aim of the present study was to determine the function and the role of the scaffold protein AKAP121, tethering cAMP dependent protein kinase A to the outer wall of mitochondria, in neonatal ventricular myocytes and the heart.

METHODS AND RESULTS

Competitive peptides displacing AKAP121 from mitochondria in the tissue and in the cells were used to investigate the role of AKAP121 in mitochondrial function, reactive oxygen species (ROS) generation, and cell survival. Displacement of AKAP121 from mitochondria by synthetic peptides triggers the death program in cardiomyocytes. Under pathological conditions in vivo, in a rat model of cardiac hypertrophy induced by ascending aorta banding, the levels of AKAP121 are significantly down-regulated. Disappearance of AKAP121 is associated with mitochondrial dysfunction, high oxidative stress, and apoptosis. In vivo delocalization of AKAP121 by competitive peptides replicates some of the molecular signatures induced by pressure overload: mitochondrial dysfunction, increased mitochondrial ROS, and apoptosis.

CONCLUSION

These data suggest that AKAP121 regulates the response to stress in cardiomyocytes, and therefore AKAP121 downregulation might represent an important event contributing to the development of cardiac dysfunction.

PNA zipper as a dimerization tool: development of a bZip mimic

The article describes the use of a PNA duplex (PNA zipper) as a tool to dimerize or bring in close proximity two polypeptides or protein domains. The amino acid sequence to be dimerized is covalently bound to complementary PNA sequences. Annealing of the PNA strands results in dimer formation. To test the ability of the "PNA-zipper" as a dimerization tool, we designed a GCN4 mimetic, where the leucine-zipper dimerization domain was replaced by the PNA zipper, whereas the basic DNA-binding domain was covalently attached to the PNA. The molecule was assembled by chemical ligation of the peptide corresponding to the DNA-binding domain of GCN4 modified with a succinyl thioester with two complementary PNAs harboring a cysteine residue. Electromobility-shift experiments show the ability of the PNA zipper-GCN4 to bind selected DNA duplexes. The PNA zipper-GCN4 binds both the TRE and CRE DNA sites, but it does not bind TRE and CRE mutants containing even a single base mutation, as the native GCN4. The ability to fold upon complexation with DNA was investigated by CD. A good correlation between the ability of the PNA zipper-GCN4 to fold into alpha helices and the ability to bind DNA was found.

Imaging of alpha(v)beta(3) expression by a bifunctional chimeric RGD peptide not cross-reacting with alpha(v)beta(5)

PURPOSE

To test whether a novel bifunctional chimeric peptide comprising a cyclic Arg-Gly-Asp pentapeptide covalently bound to an echistatin domain can discriminate alpha(v)beta(3) from alpha(v)beta(5) integrin, thus allowing the in vivo selective visualization of alpha(v)beta(3) expression by single-photon and positron emission tomography (PET) imaging.

EXPERIMENTAL DESIGN

The chimeric peptide was preliminarily tested for inhibition of alpha(v)beta(3)-dependent cell adhesion and competition of 125I-echistatin binding to membrane of stably transfected K562 cells expressing alpha(v)beta(3) (Kalpha(v)beta(3)) or alpha(v)beta(5) (Kalpha(v)beta(5)) integrin. The chimeric peptide was then conjugated with diethylenetriaminepentaacetic acid and labeled with 111In for single-photon imaging, whereas a one-step procedure was used for labeling the full-length peptide and a truncated derivative, lacking the last five C-terminal amino acids, with 18F for PET imaging. Nude mice bearing tumors from Kalpha(v)beta(3), Kalpha(v)beta(5), U87MG human glioblastoma, and A431 human epidermoid cells were subjected to single-photon and PET imaging.

RESULTS

Adhesion and competitive binding assays showed that the novel chimeric peptide selectively binds to alpha(v)beta(3) integrin and does not cross-react with alpha(v)beta(5). In agreement with in vitro findings, single-photon and PET imaging studies showed that the radiolabeled chimeric peptide selectively localizes in tumor xenografts expressing alphavbeta3 and fails to accumulate in those expressing alpha(v)beta(5) integrin. When 18F-labeled truncated derivative was used for PET imaging, alphavbeta3- and alpha(v)beta(5)-expressing tumors were visualized, indicating that the five C-terminal amino acids are required to differentially bind the two integrins.

CONCLUSION

Our findings indicate that the novel chimeric Arg-Gly-Asp peptide, having no cross-reaction with alphavbeta5 integrin, allows highly selective alphavbeta3 expression imaging and monitoring.

Peptides for tumour therapy and diagnosis: current status and future directions

The use of peptides as targeting tools has been validated in different applications. In particular radiolabelled peptides with adequate stability, receptor-binding properties and biokinetic behaviour have been investigated as an important class of radiopharmaceuticals for cancer pathology imaging and therapy. This review focuses on recent progress in design and synthetic modifications of small biologically active peptides used in diagnosis and therapy. In particular, we report the current development and optimization of suitable peptides for targeting three relevant biological receptors (CCK, somatostatin, and integrin receptors) involved in specific tumour diseases.

Selectively functionalized cyclodextrins and their metal complexes

Cyclodextrins (CDs) are cyclic oligomers of alpha-1,4-linked D-glucopyranose. Due to their unique structure, marked by a chiral and hydrophobic cavity, CDs have been extensively used as chiral selectors and drug delivery systems. The functionalization both improve the CD applications and widen their use in many other fields, such as molecular recognition and enzyme mimicking. Moreover, the functionalization highly increases the metal binding properties of the CDs. This critical review is a report of recent applications concerning the CD derivatives and their metal complexes. The metal ion assists the host-guest interaction often increasing the properties of CDs to act as chiral receptors. Furthermore, it can act as a catalytic center in the mimicking of metalloenzymes based on functionalized CDs (164 references).