Synthesis, thermal stability and reactivity towards 9-aminoellipticine of double-stranded oligonucleotides containing a true abasic site.

A 13 mers abasic oligonucleotide was synthetized. It was therefore possible to compare thermal stability and reactivity of duplex oligonucleotides either with an apurinic/apyrimidinic site or without any lesion. An important decrease in the melting temperature appeared for duplexes with an abasic site. The chemical reaction of these modified oligonucleotides with the intercalating agent 9-aminoellipticine was studied by gel electrophoresis and by fluorescence. The formation of a Schiff base between 9-aminoellipticine and abasic sites was rapid and complete with duplexes at 11 degrees C. Schiff base related fluorescence and beta-elimination cleavage were more important with the apyrimidinic sites than with the apurinic ones. When compared to previous results obtained with the model d(TprpT) some unexpected behaviours appeared with longer and duplex oligonucleotides. For instance only partial beta-elimination cleavage was observed. It is likely that stacking parameters in the double helix play a great role in the studied reaction.     

9-amino-ellipticine inhibits the apurinic site-dependent base excision-repair pathway.

The aromatic amine 9-amino-ellipticine is a synthetic DNA intercalating compound derived from the antitumor agent ellipticine, which cleaves at very low doses DNA containing apurinic sites by beta-elimination through formation of a Schiff base. This compound has been shown to potentiate the cytotoxic effect of alkylating drugs, such as dimethyl sulfate, in E. coli through a mechanism involving apurinic sites. We have studied the ability of 9-amino-ellipticine to inhibit an enzymatic repair system mimicking base-excision repair, in which E. coli exonuclease III only presents an endonuclease for apurinic/apyrimidinic site activity. 10 microM of 9-amino-ellipticine inhibits 70% of apurinic site repair. Other intercalating agents with similar affinities for DNA do not induce any inhibition. In another system designed for the direct assay of the exonuclease III-induced incisions 5' to AP sites 10 microM of 9-amino-ellipticine inhibits 65% of the endonuclease for apurinic/apyrimidinic site activity of E. coli exonuclease III. The 9-amino-ellipticine-induced formation of a 2',3'-unsaturated deoxyribose and cleavage at the 3' side of the apurinic site, and possible creation of an adduct, as suggested by Bertrand and coworkers (1989), on the 3' position of the deoxyribose seem to strongly inhibit the endonuclease for apurinic/apyrimidinic site activity. 9-Amino-ellipticine appears therefore to be the first small ligand which can inhibit, by an irreversible modification of the substrate, the repair of apurinic sites through the base excision-repair pathway at a pharmacological concentration.     

Spectroscopic and molecular docking studies on interaction of two Schiff base complexes with bovine serum albumin

Abstract

This study was designed to examine interaction of two ternary copper (II) Schiff base complexes with bovine serum albumin (BSA), using spectroscopic and molecular docking techniques. The fluorescence quenching measurements revealed that the quenching mechanism was static and the binding site of both Schiff bases to BSA was singular. Förster energy transfer measurements, synchronous fluorescence spectroscopy, and docking study showed both Schiff bases bind to the Trp residues of BSA in short distances. Docking study showed that both Schiff base molecules bind with BSA by forming several hydrogen and van der Waals bonds. In addition, molecular docking study indicated that Schiff base A and Schiff base B were located within the binding pocket of subdomain IB and subdomain IIA of BSA, respectively. Results of Fourier transform-infrared spectroscopy demonstrated that bovine serum albumin interacts with both Schiff bases and the secondary structure of BSA was changed.

Communicated by Ramaswamy H. Sarma     

Mechanism of cleavage of apurinic sites by 9-aminoellipticine

We have studied the kinetics of breakage of apurinic (AP) sites by the intercalating agent 9-aminoellipticine using fluorimetric methods with single (ss)- and double (ds)-stranded apurinic DNA. In order to understand the chemical process, high performance liquid chromatography was used to follow the reaction kinetics with the apurinic oligonucleotide model T(AP)T. The unstable intermediate, which is responsible for the beta-elimination step, is a Schiff base resulting from the interaction of the amino group of the aromatic amine with the aldehyde function of the deoxyribose moiety (AP site). Fluorescence occurs simultaneously with the breakage of both ss and ds DNA and of the oligonucleotide and arises from the formation of a conjugated double bond on the Schiff base through the beta-elimination reaction. In optimal conditions, the second order rate constant for the fluorescence build up is 15 x 10(3) min-1 M-1 for ds DNA and 0.105 x 10(3) min-1 M-1 for T(AP)T. The ability of 9-aminoellipticine to induce fluorescence and breakage of ss DNA and T(AP)T shows that intercalation is not essential for this reaction to occur. Nevertheless, the greater rate constant with DNA suggests that stacking is an important parameter for the reaction of the aromatic amine with the AP site.     

A computational approach to the synthesis of dirithromycin

Dirithromycin is a macrolide antibiotic derived from erythromycin A. Dirithromycin is synthesized by the condensation of 9(S)-erythromycylamine with 2-(2-methoxyethoxy)-acetaldehyde. To gain insight into the synthesis, the condensation mechanism has been analyzed computationally by the AM1 method in the gas phase. First, the formation of the Schiff bases of dirithromycin and epidirithromycin from 9(S)-erythromycylamine and 2-(2-methoxyethoxy)-acetaldehyde were modeled. Then, the tautomerization of the Schiff bases to dirithromycin and epidirithromycin were considered. Finally, the epimerization of the Schiff base of epidirithromycin to the Schiff base of dirithromycin was investigated. Our results show that, even though carbinolamine forms faster for epidirithromycin than the corresponding structure for dirithromycin, dirithromycin is the major product of the synthesis. Figure Synthesis of dirithromycin     

The active site of the Escherichia coli MutY DNA adenine glycosylase.

Escherichia coli MutY is an adenine DNA glycosylase active on DNA substrates containing A/G, A/C, or A/8-oxoG mismatches. Although MutY can form a covalent intermediate with its DNA substrates, its possession of 3' apurinic lyase activity is controversial. To study the reaction mechanism of MutY, the conserved Asp-138 was mutated to Asn and the reactivity of this mutant MutY protein determined. The glycosylase activity was completely abolished in the D138N MutY mutant. The D138N mutant and wild-type MutY protein also possessed different DNA binding activities with various mismatches. Several lysine residues were identified in the proximity of the active site by analyzing the imino-covalent MutY-DNA intermediate. Mutation of Lys-157 and Lys-158 both individually and combined, had no effect on MutY activities but the K142A mutant protein was unable to form Schiff base intermediates with DNA substrates. However, the MutY K142A mutant could still bind DNA substrates and had adenine glycosylase activity. Surprisingly, the K142A mutant MutY, but not the wild-type enzyme, could promote a beta/delta-elimination on apurinic DNA. Our results suggest that Asp-138 acts as a general base to deprotonate either the epsilon-amine group of Lys-142 or to activate a water molecule and the resulting apurinic DNA then reacts with Lys-142 to form the Schiff base intermediate with DNA. With the K142A mutant, Asp-138 activates a water molecule to attack the C1' of the adenosine; the resulting apurinic DNA is cleaved through beta/delta-elimination without Schiff base formation.     

Occurrence of Δ1(10) Gibberellin A1 Counterpart,GA1, GA4 and GA7 in Somatic Cell Embryo Cultures of Carrot and Anise

Amine oxidase of Aspergillus niger was inactivated by ethylenediamine under aerobic conditions, but not under anaerobic conditions. In the presence of ethylenediamine, the oxidized form of the enzyme did not react with phenylhydrazine under anaerobic conditions, but reacted slowly under aerobic conditions. These findings and previous study [Suzuki et al., J. Biochem. 69, 1065 (1971)] suggest that the oxidized form of the enzyme develops an inactive Schiff base between the carbonyl group of the enzyme and the amino group of ethylenediamine under aerobic conditions. The circular dichroic (CD) spectra in the near-ultraviolet region indicated that the structure around the inactive Schiff base was slightly different from that of the reduced form of the enzyme.     

Antibacterial and antifungal metal based triazole Schiff bases

A new series of four biologically active triazole derived Schiff base ligands (L¹–L⁴) and their cobalt(II), nickel(II), copper(II) and zinc(II) complexes (1–16) have been synthesized and characterized. The ligands were prepared by the condensation reaction of 3-amino-5-methylthio-1H-1,2,4-triazole with chloro-, bromo- and nitro-substituted 2-hydroxybenzaldehyde in an equimolar ratio. The antibacterial and antifungal bioactivity data showed the metal(II) complexes to be more potent antibacterial and antifungal than the parent Schiff bases against one or more bacterial and fungal species.     

The chromophore-binding site of bacteriorhodopsin. Resonance Raman and surface-enhanced resonance Raman spectroscopy and quantum chemical study

Surface-enhanced Raman spectra of membrane protein, located in native mem brane, bacteriorhodopsin, adsorbed by silver electrodes and hydrosols have been obtained for the first time. The distance between the retinal Schiff’s base and the external side of purple membrane of Halobacteriim halobiim was shown to be 6–9 A. The possible distribition of the point charges aroind protonated retinal Schiff’s base has been proposed on the basis of the resonance Raman data and quantim chemical CNDO/S-CI calculations. Such a model contains tyrosine residue located near the retinal Schiff’s base and connected with COO^- groipvia hydrogen bond COO^- group acts as a protonated Schiff’s base counterion. The distance between oxygen atoms of COO^- group and retinal Schiff’s base plane is 2.5–3.0A. The hydrogen bond (O-H. . .O^-) length between oxygen atom of OH-group and oxygen atom of COO^- group has been chosen 2.7±0.1Å Tyrosine hydroxyl group is located at 2.8–3.5 A from retinal Schiff’s base plane. It was shown that in contrast to generally accepted Honig and Nakanishi model the spectral properties of Brh570, K610, L550 and M4Ï2 forms of bacteriorhodopsin photocycle as well as observed tyrosine deprotonation and COO^- group protonation during M412 formation can be explained reasonably well by the suggested charge distribution. Furthermore, such a model of bacteriorhodopsin active site microenvironment allows to explain catalyzing of photo-induced protonated retinal Schiff’s base deprotonation observed in our preliminary experiments.     

Assessment of cytotoxic and genotoxic potentials of a mononuclear Fe(II) Schiff base complex with photocatalytic activity in Trigonella

BackgroundIn recent times, coordination complexes of iron in various oxidation states along with variety of ligand systems have been designed and developed for effective treatment of cancer cells without adversely affecting the normal cell and tissues of various organs.MethodsIn this study, we have evaluated the mechanism of action of a Fe(II) Schiff base complex in the crop plant Trigonella foenum-graecum L. (Fenugreek) as the screening system by using morphological, cytological, biochemical and molecular approaches. Further functional characterization was performed using MCF-7 cell line and solid tumour model for the assessment of anti-tumour activity of the complex.ResultsOur results indicate efficiency of the Fe(II) Schiff base complex in the induction of double strand breaks in DNA. Complex treatment clearly induced cytotoxic and genotoxic damage in Trigonella seedlings. The Fe-complex treatment caused cell cycle arrest via the activation of ATM-ATR kinase mediated DNA damage response pathway with the compromised expression of CDK1, CDK2 and CyclinB1 protein in Trigonella seedlings. In cultured MCF-7 cells, the complex induces cytotoxicity and DNA fragmentation through intracellular ROS generation. Fe-complex treatment inhibited tumour growth in solid tumour model with no additional side effects.ConclusionThe growth inhibitory and cytotoxic effects of the complex result from activation of DNA damage response along with oxidative stress and cell cycle arrest.General significanceOverall, our results have provided comprehensive information on the mechanism of action and efficacy of a Fe(II) Schiff base complex in higher eukaryotic genomes and indicated its future implications as potential therapeutic agent.     

Preparation of a short synthetic apurinic oligonucleotide

The synthesis of the model apurinic oligonucleotide Tp(AP)pT is reported. Furthermore during the course of purification of this compound we have shown that the adduct formed upon reaction with methoxyamine has a Schiff base structure.     

Spectral properties and desmotropy of the Schiff base of diethylaminomalonate and pyridoxal hydrochloride

Evidence is presented indicating that in aqueous solution, the product formed between diethyl aminomalonate and pyridoxal (vitamin B₆)is the Schiff base, and not the 1,4-dihydropyridine tautomer which exists in the solid state. The structure of the Schiff base is established unequivocally by its ¹H and ¹³C NMR spectra. Reflectance spectroscopy shows that the solid dihydropyridine tautomer absorbs at 560 nm.     

Surfactant–copper(II) Schiff base complexes: synthesis,structural investigation,DNA interaction,docking studies,and cytotoxic activity

A series of surfactant–copper(II) Schiff base complexes (1–6) of the general formula, [Cu(sal-R₂)₂] and [Cu(5-OMe-sal-R₂)₂], {where, sal?=?salicylaldehyde, 5-OMe-sal?=?5-methoxy- salicylaldehyde, and R₂?=?dodecylamine (DA), tetradecylamine (TA), or cetylamine (CA)} have been synthesized and characterized by spectroscopic, ESI-MS, and elemental analysis methods. For a special reason, the structure of one of the complexes (2) was resolved by single crystal X-ray diffraction analysis and it indicates the presence of a distorted square-planar geometry in the complex. Analysis of the binding of these complexes with DNA has been carried out adapting UV-visible-, fluorescence-, as well as circular dichroism spectroscopic methods and viscosity experiments. The results indicate that the complexes bind via minor groove mode involving the hydrophobic surfactant chain. Increase in the length of the aliphatic chain of the ligands facilitates the binding. Further, molecular docking calculations have been performed to understand the nature as well as order of binding of these complexes with DNA. This docking analysis also suggested that the complexes interact with DNA through the alkyl chain present in the Schiff base ligands via the minor groove. In addition, the cytotoxic property of the surfactant–copper(II) Schiff base complexes have been studied against a breast cancer cell line. All six complexes reduced the visibility of the cells but complexes 2, 3, 5, and 6 brought about this effect at fairly low concentrations. Analyzed further, but a small percentage of cells succumbed to necrosis. Of these complexes (6) proved to be the most efficient aptotoxic agent.     

Repair pathway for PARP-1 DNA-protein crosslinks

Poly(ADP-ribose) polymerase-1 (PARP-1) is a regulatory enzyme involved in many different processes of DNA and RNA metabolism, including DNA repair. Previously, PARP-1 was found capable of forming a covalent DNA-protein crosslink (DPC) at the apurinic/apyrimidinic (AP) site in double-stranded DNA. The C1´ atom of the AP site participates in Schiff base formation with a lysine side chain in PARP-1, and a covalent bond is formed upon reduction of the Schiff base. The PARP-1 DPC is formed in vivo where DPC formation correlates with AP site induction by a monofunctional alkylating agent. Here, we examined repair of PARP-1 DPCs in mouse fibroblasts and found that a proteasome inhibitor, MG-132, reduces repair resulting in accumulation of PARP-1 DPCs and increased alkylating agent cytotoxicity. Using a model DNA substrate mimicking the PARP-1 DPC after proteasomal degradation, we found that repair is completed by a sub-pathway of base excision repair (BER). Tyrosyl-DNA phosphodiesterase 1 was proficient in removing the ring-open AP site sugar at the phosphodiester linkage, leaving an intermediate for processing by other BER enzymes. The results reveal proteasomal degradation of the PARP-1 DPC is active in mouse fibroblasts and that a model repair intermediate is processed by the BER machinery.     

Proton translocation in hydrogen bonds with large proton polarizability formed between a Schiff base and phenols

OH…N ? O^?…H⁺N hydrogen bonds formed between N-all-transretinylidene butylamine (Schiff base) and phenols (1:1) are studied by IR spectroscopy. It is shown that both proton limiting structures of these hydrogen bonds have the same weight with Δ pK_a (50%) = (pK_a protonated Schiff base minus pK_a phenol) = 5.5. With the largely symmetrical systems, continua demonstrate that these hydrogen bonds show great proton polarizability. In the Schiff base + tyrosine system in a non-polar solvent the residence time of the proton at the tyrosine residue is much larger than that at the Schiff base. In CH₂CCl₂ these hydrogen bonds show, however, still proton polarizability, i.e., the position of the proton transfer equilibrium OH…N ? O^?…H⁺N is shifted to and fro as function of the nature of the environment of this hydrogen bond. Consequences regarding bacteriorhodopsin are discussed.     

Synthesis and antiviral,insecticidal, and fungicidal activities of gossypol derivatives containing alkylimine,oxime or hydrazine moiety

Gossypol is a part of the cotton plant’s defense system against pathogens and herbivorous insects. To discover gossypol analogs with broad spectrum and high activity, a series of gossypol alkylamine Schiff base, oxime and hydrazone derivatives were synthesised and bioassayed. The biological results indicated that most of these derivatives exhibited higher anti-TMV activity than gossypol. Interestingly, the activities of compounds 10, 15, 18, 20, 23 and 26 were much higher than that of ribavirin. Furthermore, compound 26, which was low toxicity to rat, showed better activity than control plant virus inhibitors in the field. Additionally, allyl amine Schiff base (9) displayed remarkable insecticidal activities against Mythimna separata, Helicoverpa armigera and Ostrinia nubilalis, whereas (pyridin-3-yl)methanamine Schiff base (13) showed excellent activity against Culex pipiens pallens. The fungicidal results revealed that all of compounds exhibited good activity against Physalospora piricola.     

Novel palladium(II) and Zinc(II) Schiff base complexes: Synthesis,biophysical studies,and anticancer activity investigation

BackgroundSchiff base metal complexes are considered promising chemotherapeutic agents due to their potential application in cancer therapy.MethodsThe current work sought to synthesize a brand-new Schiff base ligand obtained from 2-hydroxybenzohydrazide and (E)− 1-(2-(p-tolyl)hydrazono)propan-2-one with metal ions which included Pd(II) and Zn(II) ions. Elemental analyses, FT-IR, mass spectra, 1H NMR, UV-Vis spectrometer, and computational analysis characterized the compound's structure. In vitro, the breast cancer cell line (MCF-7) was tested for its sensitivity to Schiff base (HL) and its Pd(II) and Zn(II) complexes. The half-maximal inhibitory concentration IC₅₀ of the compounds was determined and used to perform the comet assay, which was carried out to reveal the photo-induced DNA damaging ability of the compounds of individual cells. Moreover, the compounds' effects on antioxidant defense systems of enzymes in cells: superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GPx) activities and oxidant Malondialdehyde (MDA) were examined in MCF-7 cells.ResultsThe Pd(II) complex displayed approximately the same IC₅₀ as Cisplatin, while Zn(II) complex had better activity than Cisplatin with very low IC₅₀, 1.40 μg/ml. Significant alterations in SOD, CAT, GPx, and MDA production were discovered, inducing oxidative stress, enlarging ROS production, and reducing the antioxidant amount. This change was approximately similar in most compounds. Consequently, it promoted apoptosis, particularly the Zn(II) complex, which demonstrated an improved impact because of its ability to influence the antioxidant defense systems of enzymes, mostly SOD and GPx, besides increasing MDA levels.ConclusionIt can be concluded that Zn(II) complex is the most effective anticancer drug since it induced a very similar genotoxic effect as Cisplatin and has a very low IC₅₀ value.     

Synthesis,antimicrobial and anti-biofilm activities of novel Schiff base analogues derived from methyl-12-aminooctadec-9-enoate

A novel library of Schiff base analogues (5a–q) were synthesized by the condensation of methyl-12-aminooctadec-9-enoate and different substituted aromatic aldehydes. The synthesized compounds were thoroughly characterized by spectroscopic techniques (FT-IR, ¹H NMR, ¹³C NMR, ESI-MS and HRMS). The Schiff base analogues with different substitutions were screened for in vitro antibacterial activity against 7 different bacterial strains. Among these, the compounds with electron withdrawing substituent, namely chlorine (5a) and electron donating substituents, namely hydroxy (5n) and methoxy (5o), were found to exhibit excellent to good antimicrobial activities (MIC value 9–18 μM) against Staphylococcus aureus MTCC 96, Staphylococcus aureus MLS-16 MTCC 2940 and Bacillus subtilis MTCC 121. The products were also screened for anti-biofilm and MBC (Minimum Bactericidal Concentration) activities which exhibited promising activities.     

Specific Recognition and Stabilization of an Abasic Site-Containing DNA Duplex by a Macrocyclic Bisacridine

Abstract

A strong and specific stabilization of a DNA undecamer containing an analog of the abasic site has been induced by the macrocyclic Bisacridine 1 . ¹H NMR analysis and molecular modeling of the structure of the complex showed that the drug was specifically docked into the apurinic pocket.     

DNA Apurinic Sites: Synthesis of a Model Compound and Study of its Reactivity with 3-Aminocarbazole

Abstract

The mechanism of breakage of apurinic DNA with 3-aminocarbazole was determinated on a short oligonucleotide model. The results founded contrast with those reported in the literature.¹