1,2-Diol and Hydrazide Phosphoramidites for Solid-Phase Synthesis and Chemoselective Ligation of 2′-Modified Oligonucleotides

Abstract

The preparation of two novel 2′-O-alkyl phosphoramidites bearing 1,2-diol and hydrazide functions for a chemoselective ligation is described. The former amidite was used to obtain 2′-modified oligodeoxyribonucleotides, which can be later oxidised by NaIO₄ to generate 2′-aldehyde oligonucleotides. These were successfully conjugated to acceptor molecules. The latter amidite also showed good coupling yields, but the hydrazide function was demonstrated to be labile under basic deprotection conditions.     

Solution stability and degradation pathway of deoxyribonucleoside phosphoramidites in acetonitrile

The impuritiy profiles of acetonitrile solutions of the four standard O-cyanoethyl-N,N-diisopropyl-phosphoramidites of 5'-O-dimethoxytrityl (DMT) protected deoxyribonucleosides (dG(ib), dA(bz), dC(bz), T) were analyzed by HPLC-MS. The solution stability of the phosphoramidites decreases in the order T, dC>dA>dG. After five weeks storage under inert gas atmosphere the amidite purity was reduced by 2% (T, dC), 6% (dA), and 39% (dG), respectively. The main degradation pathways involve hydrolysis, elimination of acrylonitrile and autocatalytic acrylonitrile-induced formation of cyanoethyl phosphonoamidates. Consequently, the rate of degradation is reduced by reducing the water concentration in solution with molecular sieves and by lowering the amidite concentration. Acid-catalyzed hydrolysis could also be reduced by addition of small amounts of base.     

Synthesis of Oligodeoxynucleotides Containing 5-Bromouracil and N6-Methyladenine

Abstract

Oligodeoxynucleotides containing uracil, 5-bromouracil and N6-methyladenine were prepared by phosphotriester or amidite approaches and by a hybrid phosphotriester-phosphoramidite method.     

Solution Stability and Degradation Pathway of Deoxyribonucleoside Phosphoramidites in Acetonitrile

The impuritiy profiles of acetonitrile solutions of the four standard O‐cyanoethyl‐N,N‐diisopropyl‐phosphoramidites of 5′‐O‐dimethoxytrityl (DMT) protected deoxyribonucleosides (dG^ib, dA^bz, dC^bz, T) were analyzed by HPLC‐MS. The solution stability of the phosphoramidites decreases in the order T, dC>dA>dG. After five weeks storage under inert gas atmosphere the amidite purity was reduced by 2% (T, dC), 6% (dA), and 39% (dG), respectively. The main degradation pathways involve hydrolysis, elimination of acrylonitrile and autocatalytic acrylonitrile‐induced formation of cyanoethyl phosphonoamidates. Consequently, the rate of degradation is reduced by reducing the water concentration in solution with molecular sieves and by lowering the amidite concentration. Acid‐catalyzed hydrolysis could also be reduced by addition of small amounts of base.     

Microbial transformation of isonicotinic acid hydrazide and isonicotinic acid bySarcina sp

Metabolism of isonicotinic acid and isoniazid bySarcina sp. led to the formation of two metabolites which were characterised as 2-hydroxyisonicotinic acid and citrazinic acid. The blue pigment formed during fermentation was shown to be derived from the auto-oxidation of citrazinic acid. 2-Oxo-glutarate accumulated as the major keto acid when isonicotinic acid or isonicotinic acid hydrazide metabolism was inhibited by 1 mM sodium arsenite. Isonicotinic acid, 2-hydroxy-isonicotinic acid and 2-oxo-glutarate were oxidised by isonicotinic acid hydrazide or isonicotinic acid-grown cells; citrazinic acid was, however, not oxidised. Isoniazid hydrazine hydrolase, isonicotinic acid and 2-hydroxyisonicotinic acid hydroxylases were detected in the cell-free extract ofSarcina sp. grown on isonicotinic acid hydrazide or isonicotinic acid. Communication no. 2427from Central Drug Research Institute, Lucknow.     

Evaluation of new linkers and synthetic methods for internal modified oligonucleotides

Several fluorescence resonance energy transfer (FRET) oligonucleotide probes were made with different internal linkages between the DNA and the quencher dye. In one example, a 5'-fluorescein beta-actin-based 26-mer DNA sequence was synthesized bearing an internal Tamra quencher. Two different versions were prepared using either conventional C5 [N-(6-aminohexyl)-3-acrylamido]pyrimidine-modified uridine and solution-phase Tamra active ester coupling or solid-phase addition of a Tamra amidite to a C5 [N-(6-hydroxyhexyl)-3-acrylamido]pyrimidine-modified uridine. The products were compared in functional assays. They performed very similarly both in a fluorescence-based melting point assay as well as in quantitative PCR. Another set of beta-actin probes were synthesized utilizing N4 [N-2-(ethylene glycol ethyl)-5-methyl]cytidine and solid-phase Tamra amidite addition at positions flanking those of the uridine. These versions gave lower T(m)s than either uridine-labeled probe and did not work as well in quantitative PCR. A control experiment using oligonucleotides with the same modified residues but without fluorophores attached revealed the same trend as the T(m) study of internal Tamra-labeled probes. Experimental details for the synthesis, purification, and testing are presented.     

Morphological and Physiological Effects of Maleic Hydrazide on Tobacco

Tobacco plants (Nicotiana tabacum cv. Burley 21) were cultured in the greenhouse to the 18-leaf stage. The apical meristem was removed and subsequent axillary bud growth was removed by hand (controls) or axillary bud development was inhibited by application of maleic hydrazide. Compared with the controls, maleic hydrazide treated plants had a decreased stem diameter and stem weight, but an increased leaf weight and leaf weight/area. Plant height and leaf area were the same for both treatments. Maleic hydrazide inhibited translocation of ¹⁴C from a single leaf exposed to ¹⁴CO₂. Respiration was greater than in the controls three days after application of maleic hydrazide, but 9 and 14 days after application there were no differences in respiration between the two treatments. Maleic hydrazide did not affect photosynthetic activity.     

Synthesis and DNA binding properties of a new benzo[f]imidazo[1,5b]-isoquinoline-butan-1,2-diol derivative

A benzo[f]imidazo[1,5b]-isoquinoline derivative 4 with a 1,2-butandiol linker was prepared by reaction of a trimethylsilylated 5-naphthylidenehydantoin 3 with a 2,3-dideoxy-D-glycero-pentafuranoside 2 in 22% yield. After deprotection, the resulting compound 5 was converted to a DMT protected phosphoramidite building block 7 for standard DNA synthesis. DNA/DNA, DNA/RNA duplexes with 5 inserted as bulges were destabilized, except when the new amidite was used for the synthesis of a zipping duplex.     

Genotoxicity of maleic hydrazide,acridine and DEHP in Allium cepa root cells performed by two different laboratories

The purpose of this paper was to compare the results of the Allium cepa chromosome aberration assay between two laboratories under the same test protocol and at the same time, use chemicals and onions obtained in their own homeland. For this study three chemicals were selected: di(2-ethylhexyl)phthalate (DEHP), maleic hydrazide, and acridine. Both laboratories found genotoxicity with a positive dose-response relationship for maleic hydrazide and acridine. However, for DEHP the results were quite different--one of the laboratories found this compound not genotoxic but the other found a positive response. Although the comparative study was inconclusive for DEHP, it was successful for the maleic hydrazide, acridine and also for the positive control (methyl methanesulfonate). Further studies need to be performed in the case of DEPH.     

Effect of pyridoxal isonicotinoyl hydrazone and other hydrazones on iron release from macrophages, reticulocytes and hepatocytes

A model consisting of 59Fe-labelled macrophages was developed for screening potential iron-chelating drugs. Mouse peritoneal macrophages, induced by previous intraperitoneal injections of 3% thioglycollate, were labelled in vitro by their exposure to immune complexes of 59Fe-transferrin-antitransferrin antibody. Optimal conditions for macrophage labelling and subsequent 59Fe release were established. Sixty-two aromatic hydrazones, the majority of which had iron binding structures similar to pyridoxal isonicotinoyl hydrazone, were synthesized by condensation of aromatic aldehydes (pyridoxal, salicylaldehyde, 2-hydroxy-1-naphthylaldehyde and 2-furaldehyde) with various acid hydrazides prepared by systematic substitutions on the benzene ring. These compounds were examined for their potential to stimulate 59Fe release from 59Fe-labelled macrophages and also from reticulocytes and hepatocytes loaded with non-heme 59Fe. The majority of hydrazones derived from pyridoxal, salicylaldehyde and 2-hydroxy-1-naphthylaldehyde seemed to be equally effective in both the macrophage and reticulocyte testing systems. However, the pyridoxal hydrazones were much more active in hepatocytes than the other groups of hydrazones. Several compounds proved to be very potent in mobilizing 59Fe. These included hydrazones derived from 2-hydroxy-1-naphthylaldehyde and benzoic acid hydrazide, p-hydroxybenzoic acid hydrazide, 2-thiophenecarboxylic acid hydrazide, and also pyridoxal benzoyl hydrazone, pyridoxal m-fluorobenzoyl hydrazone and pyridoxal 2-thiophenecarboxyl hydrazone.     

Thiazolidin-4-one and hydrazone derivatives of capric acid as possible anti-inflammatory, analgesic and hydrogen peroxide-scavenging agents

Starting from capric acid, hydrazone and thiazolidin-4-one derivatives have been synthesized in the present investigation. Decanoic acid hydrazide was reacted appropriately to yield hydrazones, which were then cyclized to yield the corresponding thiazolidin-4-ones. The structures of the newly synthesized compounds were confirmed by analytical and spectral methods. Anti-inflammatory, analgesic, and hydrogen peroxide-scavenging activity of the title compounds were evaluated. Among synthesized compounds, 2-hydroxyphenyl thiazolidinone with 44.90% inhibition of inflammation was the most potent anti-inflammatory agent. Similarly, 4-methoxybenzylidine hydrazide with 64.90% inhibition of writhing was observed to be the most potent analgesic agent of the synthesized compounds. All the synthesized compounds exhibited potent hydrogen peroxide-scavenging activity.     

Thiazolidin-4-one and hydrazone derivatives of capric acid as possible anti-inflammatory,analgesic and hydrogen peroxide-scavenging agents

Starting from capric acid, hydrazone and thiazolidin-4-one derivatives have been synthesized in the present investigation. Decanoic acid hydrazide was reacted appropriately to yield hydrazones, which were then cyclized to yield the corresponding thiazolidin-4-ones. The structures of the newly synthesized compounds were confirmed by analytical and spectral methods. Anti-inflammatory, analgesic, and hydrogen peroxide-scavenging activity of the title compounds were evaluated. Among synthesized compounds, 2-hydroxyphenyl thiazolidinone with 44.90% inhibition of inflammation was the most potent anti-inflammatory agent. Similarly, 4-methoxybenzylidine hydrazide with 64.90% inhibition of writhing was observed to be the most potent analgesic agent of the synthesized compounds. All the synthesized compounds exhibited potent hydrogen peroxide-scavenging activity.     

Evaluation of CNBr, FMP and hydrazide resins for immunoaffinity purification of factor IX.

The American Red Cross has developed an immunoaffinity chromatography method to purify human coagulation Factor IX to high levels of purity for therapeutic treatment of hemophilia B. The resin currently used in this process is Sepharose CL2B, a cross-linked 2% agarose, which is activated with cyanogen bromide to immobilize an anti-Factor IX monoclonal antibody. This study evaluated two alternative resins and coupling chemistries, a synthetic polymer bead activated by 2-fluoro-1-methyl-pyridinium toluene 4-sulfonate (FMP) and a cross-linked 2% agarose bead with free hydrazide groups for site-specific coupling. The cyanogen bromide and FMP chemistries immobilize the monoclonal antibody in a random orientation. In hydrazide coupling, the monoclonal antibody is immobilized by the non-antigen-binding part of the molecule which, theoretically, should increase the amount of immobilized monoclonal antibody able to bind antigen. To examine this, the capacity of the resins to bind Factor IX and the purity and recovery of Factor IX eluted from the resins were measured. The FMP-activated resin exhibited the lowest capacity, binding only 2% of the Factor IX feed. Sepharose CL2B bound 87% of the loaded protein, while the hydrazide resin bound 43%. These results suggest that (a) hydrazide activation may be insufficient to orient monoclonal antibody and (b) other factors such as steric hindrances and diffusional resistances during immobilization may be important. Neither of the other resins tested demonstrated improved performance compared with cyanogen bromide-activated Sepharose CL2B for the immunoaffinity purification of Factor IX.     

凝集素法与酰肼法富集糖肽的方法学比较

蛋白质糖基化(glycosylation)是最常见和最重要的翻译后修饰之一.大规模N-连接糖基化位点鉴定是糖蛋白质组学研究的重要组成部分,而N-连接糖肽富集是高通量N-连接糖基化位点鉴定的关键步骤.凝集素富集法和酰肼化学法是目前被广泛应用的N-连接糖肽富集技术,有报道认为两种方法具有很强的互补性,联合使用能提高糖基化位点的鉴定数目.本文以Hep G2细胞系为模型,系统比较了这两种方法的富集效率和糖蛋白鉴定数目.结果表明,虽然酰肼法的糖肽富集效率为76.6%,远高于凝集素法的54.6%,但是凝集素法却能鉴定到825个糖蛋白和1 959个N-连接糖基化位点,显著多于酰肼法富集到的522个糖蛋白和1 014个糖基化位点.并且,两种方法并未显示出显著的互补性,仅28个糖蛋白和80个糖基化位点未在凝集素法中鉴定到.     

Design of dendritic macromolecules containing folate or methotrexate residues

Polyether dendritic compounds bearing folate residues on their surface were prepared as model drug carriers with potential tumor cell specificity. Starting from ester-terminated polyether dendrimers, hydrazide groups were easily introduced to the surface of the dendrimers by reaction with hydrazine. Folate residues were then conjugated to the hydrazide chain ends of the dendrimers by direct condensation with folic acid in the presence of a condensing agent or by reaction with an active ester derivative of folic acid. Essentially complete functionalization of the terminal hydrazide groups was achieved for both the first and the second generation dendrimers with four and eight hydrazide groups. For the G-2 dendrimer with 16 hydrazide groups, an average number of only 12.6 folate residues were attached to each dendrimer. The conjugates are soluble in aqueous medium above pH 7.4. In addition, a similar conjugation of the antitumor drug methotrexate to the dendrimer was also investigated. Once optimized, these molecules may form the basis for a novel family of multivalent drug carriers.     

A DNA minor groove binder shows high effectiveness as a quencher for FRET probes

A non-fluorescent quencher based on thiazole orange was incorporated into oligonucleotides. Fluorimetry and fluorogenic real-time polymerase chain reaction experiments demonstrated that the quencher is effective for fluorescein amidite dyes. The thiazole orange quencher also increased the melting temperature of DNA duplexes, which may facilitate the design of shorter and more discriminatory probes. The effectiveness of the quencher in TaqMan probes was also demonstrated.     

Diastereomeric process control in the synthesis of 2'-O-(2-methoxyethyl) oligoribonucleotide phosphorothioates as antisense drugs

Coupling of 2'-O-methoxyethylsubstituted nucleoside phosphoramidites to 5'-hydroxyl group of a nucleoside or nucleotide on solid support is under stereochemical process control and is independent of scale, concentration, synthesizer, ratio of amidite diastereomers, solid support etc. However, activators and phosphate protecting groups do play a role in influencing the ratio of phosphorothioate diesters obtained by sulfurization of phosphite triesters.     

Unusual reactivity of cytotoxic cis-dihydrazide Pt(II) complexes in aqueous solution

Complexes of the general structure cis-[PtX(2)(hydrazide)(2)] and cis-[PtX(2)NH(3)(hydrazide)], where X=Cl(-), Br(-) and I(-), and hydrazide=cyclohexylcarboxylic acid hydrazide (chcah), cyclopentylcarboxylic acid hydrazide (cpcah), 3-aminocyclohexanspiro-5-hydantoin (achsh) and 3-aminocyclopentanspiro-5-hydantoin (acpsh), were investigated with respect to aqueous stability, DNA platination rates and cytotoxic activity on a panel of seven human cancer cell lines as well as a cisplatin-resistant cell line. Stabilities in aqueous solution, determined by RP-HPLC and UV-Vis methods, were highly dependent on the type of halide ligand, with stability decreasing in the order I(-)>Cl(-)>Br(-). Added chloride (100 mM) only stabilized the dichloro-Pt(II) complexes containing the hydrazide as part of a hydantoin ring (i.e., achsh). Platination of calf thymus DNA determined by AAS was most rapid with dichloro-Pt(II) complexes containing achsh ligand. The mixed-amine dichloro-Pt(II) complexes with either chcah or cpcah ligands also platinated DNA >80%, but at a slower rate, while dihydrazide dichloro-Pt(II) complexes with either chcah or cpcah ligands resulted in <25% DNA platination at 24 h. cis-[PtX(2)(hydrazide)(2)], where hydrazide=chcah or cpcah, were the most potent compounds (chcah>cpcah), but activity was independent of the halide ligand (I(-)=Cl(-)=Br(-)). These complexes showed no cross-resistance with cisplatin, but they also showed little differentiation in potency over the seven cell lines. Complexes with the hydantoin ligands achsh and acpsh were inactive in all cell lines. Thus, neither stability in aqueous media nor covalent binding to DNA are correlated with biological activity, suggesting that cis-dihydrazide Pt(II) complexes act by a unique mechanism of action.     

Synthesis, and conformational and biological study of 2-D-Ala,5-des-Met-enkephalin hydrazide modified at the carboxylic end by poly-N-vinylimidazole

N, N-bis-2-D -Ala,5-des-Met-enkephalin hydrazide of azo-isobutyric acid was synthesized. This was used to obtain polyvinylimidazole derivatives of an enkephalin analog, modified at the carboxylic end by poly-N-vinylimidazole. The effect of modification of tetrapeptide hydrazide on its conformational properties and biological activity in vivo and in vitro was studied.     

The emitting species formed by the oxidation of hydrazides with hypohalites or N-halosuccinimides.

The chemiluminescence accompanying the oxidation of salicylic hydrazide (2-hydroxybenzoic acid hydrazide) with hypochlorite, hypobromite, N-chlorosuccinimide, N-bromosuccinimide or hydrogen peroxide with cobalt(II) matched the photoluminescence emission of salicylic acid. In a related reaction, the oxidation of a mixture of isoniazid and ammonia, a synergistic effect was observed. The chemiluminescence spectrum for this reaction matches that accompanying the oxidation of the hydrazide, rather than the oxidation of ammonia. These results were used to assess mechanisms proposed by previous authors.