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Biomedical subjects

Jacques H van Boom

Publications and source records attributed to Jacques H van Boom.

At least 37 records · Page 2Linked to original sources
PubMed2003

The interaction of peptide-tethered platinum(II) complexes with DNA.

The sequence specificity and intensity of DNA damage induced by six peptide-tethered platinum complexes was compared to cisplatin and Pt(en)Cl(2). DNA damage was investigated in pUC19 plasmid and in intact HeLa cells, and quantitatively analyzed using a Taq DNA polymerase/linear amplification assay. The DNA sequence specificity of the peptide-platinum compounds was found to be very similar to cisplatin and Pt(en)Cl(2), with runs of consecutive guanines being the most intensely damaged sites. The observed reactivity of the peptide-platinum complexes towards plasmid DNA was lower compared to cisplatin and Pt(en)Cl(2), with the glycine-tethered complex 3 and the phenylalanine-tethered complex 4 producing the highest relative damage intensity, followed by (in decreasing order) lysine-tethered (5), arginine-tethered (6), serine-tethered (7) and glutamate-tethered (8). The reactivity of the peptide-platinum complexes towards cellular DNA was also lower compared to cisplatin and Pt(en)Cl(2). For most investigated complexes, the relative damage intensities were found to be similar in cells compared to plasmid DNA, but were greatly reduced for 3 and 4. The lysine-tethered 5 complex produced the highest DNA damage intensity in cells followed by (in decreasing order) 6, 7, 3, 4 and 8.

Antineoplastic Agents↗
PubMed2003

Transglycosidase activity of chitotriosidase: improved enzymatic assay for the human macrophage chitinase.

Chitotriosidase is a chitinase that is massively expressed by lipid-laden tissue macrophages in man. Its enzymatic activity is markedly elevated in serum of patients suffering from lysosomal lipid storage disorders, sarcoidosis, thalassemia, and visceral Leishmaniasis. Monitoring of serum chitotriosidase activity in Gaucher disease patients during progression and therapeutic correction of their disease is useful to obtain insight in changes in body burden on pathological macrophages. However, accurate quantification of chitotriosidase levels by enzyme assay is complicated by apparent substrate inhibition, which prohibits the use of saturating substrate concentrations. We have therefore studied the catalytic features of chitotriosidase in more detail. It is demonstrated that the inhibition of enzyme activity at excess substrate concentration can be fully explained by transglycosylation of substrate molecules. The potential physiological consequences of the ability of chitotriosidase to hydrolyze as well as transglycosylate are discussed. The novel insight in transglycosidase activity of chitotriosidase has led to the design of a new substrate molecule, 4-methylumbelliferyl-(4-deoxy)chitobiose. With this substrate, which is no acceptor for transglycosylation, chitotriosidase shows normal Michaelis-Menten kinetics, resulting in major improvements in sensitivity and reproducibility of enzymatic activity measurements. The novel convenient chitotriosidase enzyme assay should facilitate the accurate monitoring of Gaucher disease patients receiving costly enzyme replacement therapy.

Catalysis↗
PubMed2003

Improvement of hepatocyte-specific gene expression by a targeted colchicine prodrug.

Colchicine, an established tubulin inhibitor, interferes with the trafficking of endocytotic vesicles and thereby promotes the escape of lysosome-entrapped compounds. To improve its potency and cell specificity, a targeted prodrug of colchicine was synthesized by conjugation to a high-affinity ligand (di-N(alpha),N(epsilon)-(5-(2-acetamido-2-deoxy-beta-D-galactopyranosyloxy)pentanomido)lysine, K(GalNAc)(2)) for the asialoglycoprotein receptor on parenchymal liver cells. The resulting colchicine-K(GalNAc)(2) conjugate bound to this receptor with an affinity of 4.5 nM. Confocal microscopy studies confirmed rapid uptake and receptor dependency of a prodrug conjugated with fluorescein isothiocyanate. Colchicine-K(GalNAc)(2) substantially increased the transfection efficiency of polyplexed DNA in parenchymal liver cells in a concentration- and receptor-dependent fashion. Colchicine-K(GalNAc)(2) was found to enhance the transfection efficiency by 50-fold at 1 nM, whereas the parental colchicine was ineffective. In conclusion, this nontoxic colchicine-K(GalNAc)(2) conjugate can be a useful tool to improve the transfection efficiency of hepatic nonviral gene transfer vehicles.

Animals↗
PubMed2003

Sequential one-pot glycosylations using 1-hydroxyl and 1-thiodonors.

[reaction: see text] A novel sequential glycosylation procedure is described that combines the use of 1-hydroxyl and thiodonors. The Ph(2)SO/Tf(2)O-mediated dehydrative condensation of 1-hydroxyl donors with thioglycosides affords in good yield the thiodisaccharides, which in turn can be activated by the same activator system to furnish trisaccharides. The alpha-Gal epitope and a hyaluronan trisaccharide were efficiently assembled in a one-pot procedure.

Carbohydrate Sequence↗
PubMed2003

Ph2SO/Tf2O: a powerful promotor system in chemoselective glycosylations using thioglycosides.

Diphenylsulfoxide in combination with triflic anhydride provides a very potent thiophilic glycosylation promotor system, capable of activating disarmed thioglycosides. The usefulness of this novel thiophilic activator is illustrated in a successful chemoselective glycosylation sequence in which the donor thioglycoside in the first condensation step may be either armed or disarmed. [reaction: see text]

Anhydrides↗
PubMed2003

A versatile approach towards regioselective platinated DNA sequences.

Undesired N(7) platination of 2'-deoxyguanosine residues at predetermined sites in an oligodeoxynucleotide (ODN) sequence is prevented by applying the sterically demanding diphenylcarbamoyl (DPC) as an O(6)-protecting group. The presence of a base-labile oxalyl linker between the immobilized 3'-nucleotide and controlled pore glass (CPG) allows cleavage of the protected ODN from the support and leaves DPC protection unaffected. This method provides an ODN with specifically blocked guanine-N(7) sites for platination. In the hexanucleotides prepared in this study, 5'-GGBGGT-3'(for B=T, C and A), a platinum GG adduct is introduced at G4,G5. These site-specific platinated hexamers were isolated in a yield of 65 %, and were fully characterized by using reversed-phase HPLC (high performance liquid chromotography), LCMS (liquid chromatography-mass spectrometry), MALDI-TOF MS (matrix-assisted laser desorption/ionization time-of-flight mass spectrometry), PAGE (polyacrylamide gel electrophoresis) and Maxam-Gilbert sequencing analysis.

Base Sequence↗
PubMed2003

Solid-phase synthesis of cyclic RGD-furanoid sugar amino acid peptides as integrin inhibitors.

The solid-phase synthesis of cyclic RGD peptides containing either one or two furanoid sugar amino acids (SAAs) is reported. Using a cyclization-cleavage approach five peptides were successfully assembled and consecutively tested on their ability to bind to the integrin receptors alpha(v)beta(3) and alpha(IIb)beta(3). The cyclic tetrapeptide c[RGD-SAA] (1) showed the most promising activity in an inhibition assay with an IC(50) of 1.49 microM for the alpha(v)beta(3) receptor and 384 nM for the alpha(IIb)beta(3) receptor.

Binding, Competitive↗
PubMed2003

Biochemical and genetic studies of the VPg uridylylation reaction catalyzed by the RNA polymerase of poliovirus.

The first step in poliovirus (PV) RNA synthesis is the covalent linkage of UMP to the terminal protein VPg. This reaction can be studied in vitro with two different assays. The simpler assay is based on a poly(A) template and requires synthetic VPg, purified RNA polymerase 3D(pol), UTP, and a divalent cation. The other assay uses specific viral sequences [cre(2C)] as a template for VPg uridylylation and requires the addition of proteinase 3CD(pro). Using one or both of these assays, we analyzed the VPg specificities and metal requirements of the uridylylation reactions. We determined the effects of single and double amino acid substitutions in VPg on the abilities of the peptides to serve as substrates for 3D(pol). Mutations in VPg, which interfered with uridylylation in vitro, were found to abolish viral growth. A chimeric PV containing the VPg of human rhinovirus 14 (HRV14) was viable, but substitutions of HRV2 and HRV89 VPgs for PV VPg were lethal. Of the three rhinoviral VPgs tested, only the HRV14 peptide was found to function as a substrate for PV1(M) 3D(pol) in vitro. We also examined the metal specificity of the VPg uridylylation reaction on a poly(A) template. Our results show a strong preference of the RNA polymerase for Mn(2+) as a cofactor compared to Mg(2+) or other divalent cations.

Amino Acid Sequence↗
PubMed2002

Monofunctionally trans-diammine platinum(II)-modified peptide nucleic acid oligomers: a new generation of potential antisense drugs.

A solid-phase approach is described that provides facile access to monofunctionally trans-PtII-modified PNA oligomers of arbitrary sequence for potential use both in antigene and antisense strategies. The approach includes the synthesis of a platinated building block 1 and its subsequent incorporation into three different PNA oligomers 5-7 by solid-phase synthesis. In a model cross-linking reaction one of the latter is found to recognize sequence-specifically a target oligonucleotide 8 and to cross-link to it. The resulting structure is the trans-PtII-cross-linked PNA/DNA duplex 9 as revealed by mass spectrometry in combination with a Maxam-Gilbert sequencing experiment.

Antineoplastic Agents↗
PubMed2002

Confirmation of the D configuration of the 2-substituted arabinitol 1-phosphate residue in the capsular polysaccharide from Streptococcus pneumoniae Type 17F.

The absolute configuration of the 2-substituted arabinitol 1-phosphate residue present in the repeating unit of the capsular polysaccharide (CPS) from Streptococcus pneumoniae Type 17F is confirmed as D, based on a comparison of proton and carbon chemical shifts in a synthetic oligosaccharide and in an oligosaccharide derived from the CPS by degradation.

Carbohydrate Conformation↗
PubMed2002

Antiproliferative effect in chronic myeloid leukaemia cells by antisense peptide nucleic acids.

Peptide nucleic acid (PNA) is a synthetic DNA analogue that is resistant to nucleases and proteases and binds with exceptional affinity to RNA. Because of these properties PNA has the potential to become a powerful therapeutic agent to be used in vivo. Until now, however, the use of PNA in vivo has not been much investigated. Here, we have attempted to reduce the expression of the bcr/abl oncogene in chronic myeloid leukaemia KYO-1 cells using a 13mer PNA sequence (asPNA) designed to hybridise to the b2a2 junction of bcr/abl mRNA. To enhance cellular uptake asPNA was covalently linked to the basic peptide VKRKKKP (NLS-asPNA). Moreover, to investigate the cellular uptake by confocal microscopy, both PNAs were linked by their N-terminus to fluorescein (FL). Studies of uptake, carried out at 4 and 37 degrees C on living KYO-1 cells stained with hexidium iodide, showed that both NLS-asPNA-FL and asPNA-FL were taken up by the cells, through a receptor-independent mechanism. The intracellular amount of NLS-asPNA-FL was about two to three times higher than that of asPNA-FL. Using a semi-quantitative RT- PCR technique we found that 10 micro M asPNA and NLS-asPNA reduced the level of b2a2 mRNA in KYO-1 cells to 20 +/- 5% and 60 +/- 10% of the control, respectively. Western blot analysis showed that asPNA promoted a significant inhibition of p210(BCR/ABL) protein: residual protein measured in cells exposed for 48 h to asPNA was approximately 35% of the control. Additionally, asPNA impaired cell growth to 50 +/- 5% of the control and inhibited completion of the cell cycle. In summary, these results demonstrate that a PNA 13mer is taken up by KYO-1 cells and is capable of producing a significant and specific down-regulation of the bcr/abl oncogene involved in leukaemogenesis.

Antineoplastic Agents↗
PubMed2002

The C-terminal region of Escherichia coli UvrC contributes to the flexibility of the UvrABC nucleotide excision repair system.

Nucleotide excision repair in Escherichia coli involves formation of the UvrB-DNA complex and subsequent DNA incisions on either site of the damage by UvrC. In this paper, we studied the incision of substrates with different damages in varying sequence contexts. We show that there is not always a correlation between the incision efficiency and the stability of the UvrB-DNA complex. Both stable and unstable UvrB-DNA complexes can be efficiently incised. However some lesions that give rise to stable UvrB-DNA complexes do result in a very low incision. We present evidence that this poor incision is due to sterical hindrance of the damage itself. In its C-terminal region UvrC contains two helix-hairpin-helix (HhH) motifs. Mutational analysis shows that these motifs constitute one functional unit, probably folded as one structural unit; the (HhH)2 domain. This (HhH)2 domain was previously shown to be important for the 5' incision on a substrate containing a (cis-Pt).GG adduct, but not for 3' incision. Here we show that, mainly depending on the sequence context of the lesion, the (HhH)2 domain can be important for 3' and/or 5' incision. We propose that the (HhH)2 domain stabilises specific DNA structures required for the two incisions, thereby contributing to the flexibility of the UvrABC repair system.

Adenosine Triphosphatases↗
PubMed2002

Site-specific interactions of JBP with base and sugar moieties in duplex J-DNA. Evidence for both major and minor groove contacts.

Beta-D-Glucosyl-hydroxymethyluracil, also called base J, is an unusually modified DNA base conserved among Kinetoplastida. Base J is found predominantly in repetitive DNA and correlates with epigenetic silencing of telomeric variant surface glycoprotein genes. We have previously identified a J-binding protein (JBP) in Trypanosoma, Leishmania, and Crithidia, and we have shown that it is a structure-specific binding protein. Here we examine the molecular interactions that contribute to recognition of the glycosylated base in synthetic DNA substrates using modification interference, modification protection, DNA footprinting, and photocross-linking techniques. We find that the two primary requirements for J-DNA recognition include contacts at base J and a base immediately 5' of J (J-1). Methylation interference analysis indicates that the requirement of the base at position J-1 is due to a major groove contact independent of the sequence. DNA footprinting of the JBP.J-DNA complex with 1,10-phenanthroline-copper demonstrates that JBP contacts the minor groove at base J. Substitution of the thymine moiety of J with cytosine reduces the affinity for JBP approximately 15-fold. These data indicate that the sole sequence dependence for JBP binding may lie in the thymine moiety of base J and that recognition requires only two specific base contacts, base J and J-1, within both the major and minor groove of the J-DNA duplex.

Animals↗
PubMed2002

Peptidomimetic glutathione analogues as novel gammaGT stable GST inhibitors.

Elevated levels of glutathione-S-transferase (GST) isoenzymes are found in many tumor cells and are thought to play a role in the onset of multidrug resistance (MDR). To evaluate the contribution of GST to this process, inhibitors are needed. Glutathione (GSH) conjugates, although good GST inhibitors, cannot be used in vivo, because they are eliminated rapidly. In this paper, we describe the synthesis of a series of novel peptidomimetic glutathione analogues that are stabilized against peptidase mediated breakdown. The peptide bonds in GSH were replaced by isosteres, such as the 'reduced' amide (which was prepared using a novel method), N-methylamide, urethane, and methylene linkages. The in vitro evaluation of the compounds focuses on GST inhibition and stability towards gamma-glutamyl-transpeptidase (gammaGT), the main enzyme involved in GSH breakdown. The compounds were conjugated to the model electrophile ethacrynic acid (EA) to resemble GS-EA, an efficient GST inhibitor. All novel GSH-analogues were shown to inhibit rat liver cytosolic GSTs. Furthermore, peptidomimetic changes of the gamma-glutamyl-cysteine amide bond greatly improved stability towards gammaGT. These compounds may therefore be useful in the design of novel in vivo applicable GST inhibitors.

Animals↗
PubMed2001

Recognition of base J in duplex DNA by J-binding protein.

beta-d-Glucosylhydroxymethyluracil, also called base J, is an unusual modified DNA base conserved among Kinetoplastida. Base J is found predominantly in repetitive DNA and correlates with epigenetic silencing of telomeric variant surface glycoprotein genes. We have previously found a J-binding protein (JBP) in Trypanosoma, Leishmania, and Crithidia. We have now characterized the binding properties of recombinant JBP from Crithidia using synthetic J-DNA substrates that contain the glycosylated base in various DNA sequences. We find that JBP recognizes base J only when presented in double-stranded DNA but not in single-stranded DNA or in an RNA:DNA duplex. It also fails to interact with free glucose or free base J. JBP is unable to recognize nonmodified DNA or intermediates of J synthesis, suggesting that JBP is not directly involved in J biosynthesis. JBP binds J-DNA with high affinity (K(d) = 40-140 nm) but requires at least 5 bp flanking the glycosylated base for optimal binding. The nature of the flanking sequence affects binding because J in a telomeric sequence binds JBP with higher affinity than J in another sequence known to contain J in trypanosome DNA. We conclude that JBP is a structure-specific DNA-binding protein. The significance of these results in relation to the biological role and mechanism of action of J modification in kinetoplastids is discussed.

Animals↗
PubMedDate not supplied

A targeted peptide nucleic acid to down-regulate mouse microsomal triglyceride transfer protein expression in hepatocytes.

Peptide nucleic acids (PNA's) have shown to hold potential as antisense drugs. In this study we have designed PNA drugs for the microsomal triglyceride transfer protein (MTP), which is known to play a critical role in the assembly of atherogenic lipoproteins, and have converted the most potent drug into a liver-targeted prodrug. First, we have synthesized three PNA sequences targeting domains on the mouse MTP mRNA, which were not involved in intrastrand base-pairing interactions as jugded from its secondary structure. Only one of the PNA's, PNA569, showed dose-dependent inhibition of MTP expression in a cell-free system for coupled transcription/translation of MTP. Second, to improve the cellular uptake of this PNA drug, we have conjugated PNA569 to a high affinity ligand for the asialoglycoprotein receptor, K(GalNAc)(2). As compared to the parent PNA, the prodrug PNA-K(GalNAc)(2) was found to display to a markedly improved capacity to inhibit MTP mRNA expression in parenchymal liver cells. A glycoconjugated nonsense control appeared to be ineffective. In conclusion, the design of a targeted PNA is described to reduce MTP expression in parenchymal liver cells by 70%. The presented approach for targeted tissue-specific down-regulation of genes by PNA's may be valid for other genes as well.

Animals↗
PubMedDate not supplied

Synthesis and in vitro evaluation of PNA-peptide-DETA conjugates as potential cell penetrating artificial ribonucleases.

We report the synthesis of novel artificial ribonucleases with potentially improved cellular uptake. The design of trifunctional conjugates 1a and 1b is based on the specific RNA-recognizing properties of PNA, the RNA-cleaving abilities of diethylenetriamine (DETA), and the peptide (KFF)(3)K for potential uptake into E. coli. The conjugates were assembled in a convergent synthetic route involving native chemical ligation of a PNA, containing an N-terminal cysteine, with the C-terminal thioester of the cell-penetrating (KFF)(3)K peptide to give 12a and 12b. These hybrids contained a free cysteine side-chain, which was further functionalized with an RNA-hydrolyzing diethylenetriamine (DETA) moiety. The trifunctional conjugates (1a, 1b) were evaluated for RNA-cleaving properties in vitro and showed efficient degradation of the target RNA at two major cleavage sites. It was also established that the cleavage efficiency strongly depended on the type of spacer connecting the PNA and the peptide.

Escherichia coli↗