Metallo-phthalocyanine near-IR fluorophores: oligonucleotide conjugates and their applications in PCR assays

Water soluble, metallo-pthalocyanine (MPc) near-IR fluorophores were designed, synthesized, and evaluated as highly stable and sensitive reporters for fluorescence assays. Their conjugation to oligonucleotides was achieved via succinimidyl ester-amino coupling chemistry with the conditions for conjugation extensively examined and optimized. In addition, various conjugate purification and isolation techniques were evaluated as well. Results showed that under proper conditions and following purification using reverse-phase ion-pair chromatography, labeling efficiencies near 80% could be achieved using ZnPc (Zn phthalocyanine) as the labeling fluorophore. Absorption and fluorescence spectra accumulated for the conjugates indicated that the intrinsic fluorescence properties of the MPc's were not significantly altered by covalent attachment to oligonucleotides. As an example of the utility of MPc reporters, we used the MPc-oligonucleotide conjugates as primers for PCR (polymerase chain reaction) amplifications with the products sorted via electrophoresis and detected using near-IR fluorescence (lambda ex = 680 nm). The MPc dyes were found to be more chemically stable under typical thermal cycling conditions used for PCR compared to the carbocyanine-based near-IR reporter systems typically used and produced single and narrow bands in the electrophoretic traces, indicative of producing a single PCR product during amplification.     

Thermostable trypsin conjugates for high-throughput proteomics: synthesis and performance evaluation

Conjugating bovine trypsin with oligosaccharides maltotriose, raffinose and stachyose increased its thermostability and suppressed autolysis, without affecting its cleavage specificity. These conjugates accelerated the digestion of protein substrates both in solution and in gel, compared to commonly used unmodified and methylated trypsins.     

The use of (oligonucleotide-maleic anhydride copolymer) conjugates in nucleic acid diagnostic assays: effect of the number of oligonucleotides per polymer on test sensitivity improvement

(Polymer-oligonucleotide) conjugates were obtained via direct ON synthesis from the poly(ethylene-alt-maleic anhydride: PEMA) grafted onto glass bead surfaces. The effect of the ON number per polymer chain on binding was evaluated through Tm experiments. Results were correlated with ELOSA (Enzyme Linked Oligosorbent Assay) tests run with conjugates in the capture step.     

Studies on the synthesis of neamine-dinucleosides and neamine-PNA conjugates and their interaction with RNA

Two types of neamine derivatives, neamine-dinucleotide conjugates 8a-g and neamine-PNA conjugates 12a-c and 14a-d, were synthesized. Compound 8a-g were synthesized by the condensation of azido-neamine with dinucleotide-5'-carboxylic acids, followed by reduction and deprotection. Compound 12a-c and 14a-d were synthesized by the similar strategy. The binding affinities of conjugates 8a-g, 12a-c, and 14a-d towards 16S RNA, 18S RNA, and TAR RNA were evaluated by SPR. It indicates that conjugates 12a-c and 14a-d interact with 16S, 18S RNA at the same level as that of neamine, 14a and 14d show about twofold binding affinities to TAR RNA compared to that of neamine. However, the neamine-dinucleotide conjugates 8a-g exhibit very weak binding affinities to 16S, 18S, and TAR RNA, computer modelling results that negative-negative electrostatic repulsion of phosphate group in compound 8a-g and RNA leads to a sharp decrease of the binding affinities compared with that of neamine, neamine-nucleoside and neamine-PNA conjugates.     

The synthesis of α-isomalto-oligosaccharide derivatives and their protein conjugates

2-[4-(p-Toluenesulfonamido)phenyl]ethyl 2,3,4-tri-O-benzyl-α-D-glucopyranoside was condensed with 2,3,4-tri-O-benzyl-6-O-(N-phenylcarbamoyl)-1-O-tosyl-D-glucopyranose to give 2-[4-(p-toluenesulfonamido)phenyl]ethyl 2,3,4,2′,3′,4′-hexa-O-benzyl-6′-O-(N-phenylcarbamoyl)α-isomaltoside. The disaccharide was decarbanilated in ethanol with sodium ethoxide. The sequence of coupling with the 1-O-tosyl-glucose derivative followed by decarbanilation was repeated to form the tri- and tetra-saccharide derivatives. The di-, tri-, and tetra-oligo-saccharides, were deblocked with sodium in liquid ammonia to give the 2-(4-aminophenyl)ethyl α-isomalto-oligosaccharides, which were diazotized with sodium nitrite in acid, and then coupled to bovine serum albumin and edestin to give the protein conjugates.     

New photoreactive oligoribonucleotide conjugates: hybridization and modification assays

An evaluation of hybridization and modification abilities of new types of photoactivatable oligoribonucleotide conjugates bearing p-azidotetrafluorobenzamide group at the N4 of cytosine is presented.     

Dipentafluorophenyl carbonate--a reagent for the synthesis of oligonucleotides and their conjugates.

Dipentafluorophenyl carbonate has been successfully used as condensing agent for the internucleotide bond formation in the synthesis of oligonucleotides via H-phosphonate approach. The mechanism of a nucleotide component activation with this reagent has been investigated with the help of 31P NMR spectroscopy. It was shown that preactivation of deoxynucleoside H-phosphonate with dipentafluorophenyl carbonate has no influence on the efficiency of the synthesis. This reagent is highly reactive, nonhygroscopic and stable on storage at room temperature. The effectiveness of dipentafluorophenyl carbonate in the oligonucleotide chemistry has been demonstrated in the solid-phase synthesis of 10-50-mers on 0.2, 1 and 10 mumol scales. The use of this reagent for the derivatisation of polymer supports as well as for the synthesis of oligonucleotide conjugates with polyethylene glycol and a lipid is described.     

A convenient method for the synthesis of oligonucleotide-cationic peptide conjugates

A method was developed for the synthesis of oligonucleotide-cationic peptide conjugates in solution phase by disulfide bond formation. Precipitation was avoided by the easily removable triethylammonium trifluoroacetate (TEATFAc) salt which served at the same time as a buffer of the reaction mixture. The fast and high yielding disulfide bond formation was due to the Npys thio protecting and activating group of Cys. A solution of the free 5-thiol modified oligonucleotide obtained from Poly-Pak purification was used for conjugation.     

A synthetic method for peptide-PEG-lipid conjugates: application of octreotide-PEG-DSPE synthesis

A solid phase synthesis method was established for the synthesis of peptide-poly(ethylene glycol)-lipid (peptide-PEG-lipid) conjugates. Octreotide-PEG(2000)-DSPE (OPD(2000)) was used as an example to demonstrate the synthetic approach. The OPD(2000) obtained had confirmed structure, activity, and purity providing a targeting molecule for preparation of well-defined drug delivery systems, such as targeted liposomes, for further studies.     

A convenient solid-phase method for the synthesis of novel oligonucleotide-folate conjugates

We describe the preparation of two batches of a polymer support for the incorporation of folic acid into oligonucleotides. The method permits the regioselective attachment of a target nucleic acid sequence through its 3'-end to either the alpha-or gamma-carboxyl group of L-glutamic acid, respectively. The supports have been tested in solid-phase synthesis of oligonucleotide-folate conjugates for cell delivery studies.     

Acridine conjugates of 3-clip-phen: influence of the linker on the synthesis and the DNA cleavage activity of their copper complexes

To increase the DNA cleavage activity and the cell delivery of the bis(phenanthroline) DNA cleaver "3-Clip-Phen", conjugates between 3-Clip-Phen and the intercalators acridine and 6-chloro-2-methoxyacridine, through amino acid linkers of various length, were prepared. After complexation with CuCl(2), the ability of these conjugates to cleave phiX 174 DNA in the presence of a reductant and air was compared. The results indicated that (i) the coupling of 3-Clip-Phen to an acridine derivative increased the DNA cleavage efficiency of the copper complexes, (ii) the acridine derivatives were more active than 6-chloro-2-methoxyacridine derivatives, (iii) the linker length influenced cleavage efficiency, the highest DNA cleavage activity being obtained for an aminocaproic spacer.     

Preparation of hydrazino-modified proteins and their use for the synthesis of 99mTc-protein conjugates.

The syntheses and protein linking properties of succinimidyl 4-hydrazinobenzoate hydrochloride (SHBH) and succinimidyl 6-hydrazinonicotinate hydrochloride (SHNH), two new heterobifunctional linkers which lead to hydrazino-modified proteins, are described. SHBH-modified proteins are unstable due to the presence of the phenylhydrazine moiety. This problem was overcome by synthesizing the hydrazinopyridine analogue SHNH, and the conjugates derived from this linker are stable. Tc(V) oxo precursors readily add to hydrazinopyridine-modified proteins to yield the desired 99mTc-radiolabeled protein. 99mTc-hydrazinopyridine-polyclonal IgG conjugates are useful agents for the imaging of focal sites of infection.     

Enzyme-assisted synthesis and structure characterization of glucuronide conjugates of eleven anabolic steroid metabolites

Enzyme-assisted in vitro synthesis of eleven glucuronide-conjugated anabolic androgenic steroid (AAS) metabolites was performed using biphenyl-induced rat liver microsomal enzymes. The substrates within the study were the main compounds and metabolites detected in human urine after dosing of, e.g. metandienone, metenolone, methyltestosterone, nandrolone, and testosterone. Yields of glucuronidation reactions were 13-28% for most compounds, but significantly higher (77-78%) for the substrates with 4-ene-3-one double bond system of the steroid A-ring. Characterization of glucuronide-conjugated AAS structures was based on nuclear magnetic resonance spectroscopy ((1)H NMR) and on liquid chromatographic-mass spectrometric (LC-MS) and tandem mass spectrometric (LC-MS/MS) analyses in positive and negative ion mode electrospray ionization (ESI). Only minor differences were observed in optimal synthesis conditions between various substrates, which offer a potential to apply this in vitro assay as a default method for glucuronidation of new AAS substrates. The method allowed for a rapid production pathway of stereochemically pure AAS glucuronides in milligram amount, such as needed, e.g. in the development of analytical methods in forensic or pharmaceutical sciences, as well as in doping control.     

New ferrocene containing peptide conjugates: synthesis and effect on human leukemia (HL-60) cells

Data reported in this article describe the synthesis of Arg-rich oligopeptide conjugates of ferrocenecarboxylic acid on solid support with two different strategies and for the first time, the successful preparation of peptide conjugates of ferrocenylacrylic acid in solution. The antitumor effect of conjugates was analyzed by MTT assay in vitro. We demonstrated that ferrocenylacrylic acid possessing an enone (--CH==CH--CO--) moiety exhibited remarkable antiproliferative effect against human leukemia cells (HL-60) in vitro, but its effect was not improved by conjugation with hexa- or octaarginines. However, we observed highly increased water-solubility. In contrast, the results provide evidence that conjugation of ferrocenecarboxylic acid to Arg(n) (n = 6, 8) improved not only its water-solubility, but also antitumor effect on human leukemia cells in vitro.     

Design and synthesis of enediyne–peptide conjugates and their inhibiting activity against chymotrypsin

Novel enediyne–amino acid conjugates 1–4 have been synthesized. All of these effectively target the enzyme chymotrypsin inhibiting its proteolytic activity. The conjugate with a directly linked phenyl alanine is the most effective inhibitor with a K_i of 3 μM. The mode of inhibition is mostly competitive or of a mixed type depending on the nature of the inhibitor.     

Design, synthesis, and characterization of pH-sensitive PEG-PE conjugates for stimuli-sensitive pharmaceutical nanocarriers: the effect of substitutes at the hydrazone linkage on the ph stability of PEG-PE conjugates

A set of aliphatic and aromatic aldehyde-derived hydrazone (HZ)-based acid-sensitive polyethylene glycol-phosphatidylethanolamine (PEG-PE) conjugates was synthesized and evaluated for their hydrolytic stability at neutral and slightly acidic pH values. The micelles formed by aliphatic aldehyde-based PEG-HZ-PE conjugates were found to be highly sensitive to mildly acidic pH and reasonably stable at physiologic pH, while those derived from aromatic aldehydes were highly stable at both pH values. The pH-sensitive PEG-PE conjugates with controlled pH sensitivity may find applications in biological stimuli-mediated drug targeting for building pharmaceutical nanocarriers capable of specific release of their cargo at certain pathological sites in the body (tumors, infarcts) or intracellular compartments (endosomes, cytoplasm) demonstrating decreased pH.     

Glycosyl bis-porphyrin conjugates: synthesis and potential application in PDT

Syntheses of new glycosylated neutral and cationic porphyrin dimers linked at the meso-position via a flexible hydrocarbon chain are described. A detailed 1H and 13C NMR study allows their complete structural elucidation. The UV-visible, fluorescence and MALDI mass spectra are also presented. Photocytotoxicities of these compounds against K562 leukaemia cell line are compared to those of Photofrin II.     

Bile acid-oligodeoxynucleotide conjugates: synthesis and liver excretion in rats

The synthesis of bile acid oligodeoxynucleotide conjugates via the 3-OH group of the bile acids is described. When used in vivo in rats, covalent conjugation of an oligodeoxynucleotide via a linker to cholic acid resulted in an increased biliary excretion of bile acid-oligodeoxynucleotide conjugates compared to unconjugated oligodeoxynucleotides.