Molecular design and evaluation of quinoxaline-carbohydrate hybrids as novel and efficient photo-induced GG-selective DNA cleaving agents

Quinoxaline, found in antitumor quinoxaline antibiotics, was found to cleave double stranded DNA at the 5' side guanine of 5'-GG-3' site on irradiation with long wavelength UV light without any additive; furthermore, a bis(quinoxaline-carbohydrate) hybrid system was very effective for DNA cleavage.     

Intercalating nucleic acids (INAs) containing insertions of 6H-indolo[2,3-b]quinoxaline

6H-Indolo[2,3-b]quinoxaline was studied as a covalently bound heteroaromatic intercalator. Six monomers were synthesized and incorporated into DNA oligonucleotides. Through a study of linker length dependence it was concluded that the linker between the oligo and the intercalator must consist of at least five C atoms in order to stabilize a DNA duplex. An intercalator with a 2′-deoxy-d-riboside linker to the oligo could also stabilize a DNA/RNA duplex, while (S)-4-(6-methylindolo[2,3-b]quinoxalin-3-ylmethoxy)-butane-1,2-diol was able to stabilize both DNA/DNA, DNA/RNA and a DNA/LNA duplex. Mismatch studies revealed a huge sensitivity to the C-C mismatch at the 5′-site of the intercalator.     

Pyrazolo[2′,3′:3,4][1,3]oxazino[5,6-b]quinoxaline, a novel tetracyclic ring system

Reaction of 2-chloro-3-(3-chloro-1H-pyrazol-5-yl)quinoxaline and aldehydes does not afford the corresponding N-(α-hydroxyalkylated) derivatives but results in a cyclisation reaction to give a derivative bearing the hitherto undescribed pyrazolo[2′,3′:3,4][1,3]oxazino[5,6-b]quinoxaline system.     

Multi-component, 1,3-dipolar cycloaddition reactions for the chemo-, regio- and stereoselective synthesis of novel hybrid spiroheterocycles in ionic liquid

A library of novel 1-methyl-4-arylpyrrolo-(spiro[2.2′]indan-1′,3′-dione)-spiro[3.3″]-1″-methyl/benzyl-5″-(arylmethylidene)piperidin-4″-ones and 1-methyl-4-arylpyrrolo-(spiro[2.11′]-11H-indeno[1,2-b]quinoxaline)-spiro[3.3″]-1″-methyl/benzyl-5″-(arylmethylidene)piperidin-4″-ones have been synthesized via 1,3-dipolar azomethine ylide cycloaddition in the ionic liquid, 1-butyl-3-methylimidazolium bromide ([BMIm]Br), in excellent yields.     

Design, synthesis, and evaluation of a novel bridged nucleic acid, 2′,5′-BNA, with S-type sugar conformation fixed by N-O linkage

We designed a novel 2′-O,5′-N bridged nucleic acid, 2′,5′-BNA^ON, whose sugar puckering was fixed to S-type conformation by an N-O linkage. A dimer unit formed from 2′,5′-BNA^ON-U and thymidine was synthesized via a coupling reaction between a protected 2′,5′-BNA^ON-U monomer and a thymidine derivative. Introduction of 2′,5′-BNA^ON-U into DNA was carried out using conventional phosphoramidite chemistry with a DNA synthesizer. The hybridization abilities of 2′,5′-BNA^ON-U-modified oligonucleotides against DNA or RNA complement were evaluated.     

Synthesis,structure, and biological properties of N-oxides of some 2-substituted quinoxalines and pyrazines

2-Methoxy- and 2-hydroxy-substituted quinoxaline and pyrazine N,N-dioxides and N-oxides of a number of quinoxaline-2-carboxylic acid derivatives were synthesized in order to study their biological activity. It is shown that the N-monoxides and N,N-dioxides of 2-hydroxy derivatives of quinoxaline exist primarily in the oxo form. Strong intramolecular hydrogen bonds were detected in the case of 1-N-oxides of 2-hydroxy and 2-carboxamido derivatives of quinoxaline. Substances with antibacterial and antituberculous activity were found among the synthesized compounds.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 2, pp. 278–283, February, 1976.     

A new mechanism for oxidation of epigallocatechin and production of benzotropolone pigments

Enzymatic oxidation of (−)-epigallocatechin gave two new quinone dimers, dehydrotheasinensin C and proepitheaflagallin. Dehydrotheasinensin C has a hydrated cyclohexenetrione structure and its oxidation-reduction dismutation reaction yielded black tea polyphenols, theasinensins C and E, and desgalloyl oolongtheanin. The structure of proepitheaflagallin was determined based on spectroscopic data of its quinoxaline derivatives prepared by condensation with o-phenylenediamine. Proepitheaflagallin was decomposed on heating to give epitheaflagallin and hydroxytheaflavin. The former is a known black tea pigment and the latter is a new pigment with 1′,2′,3′-trihydroxy-3,4-benzotropolone moiety. The results revealed a new mechanism for the production of these pigments from epigallocatechin.     

Imidazo[1,2-a]quinoxaline and its transformations. I

The transformations that occur during the reduction of 1-(o-nitrophenyl)-2-formylimidazole with sodium hydrosulfite in the presence of ammonia were studied. The 4-amino derivatives of imidazo[1,2-a]quinoxaline and the bisulfite derivatives of 1-(o-aminophenyl)-2-formylimidazole are formed along with the previously described imidazo[1,2-a]quinoxaline. 4-Aminoimidazo[1,2-a]quinoxaline was also obtained by alternative synthesis by amination of imidazo-[1,2-a]quinoxaline with sodium amide in dimethylaniline. The major product of the transformation is 4,4-bisimidazo[1,2-a]quinoxalyl when the reaction is carried out in xylene.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 3, pp. 416–418, March, 1972.     

New junction models for alternate-strand triple-helix formation

Background: Oligonucleotide-directed triple-helix (triplex) formation can interfere with gene expression but only long tracts of oligopyrimidine·oligopurine sequences can be targeted. Attempts have been made to recognize short oligopurine sequences alternating on the two strands of double-stranded DNA by the covalent linkage of two triplex-forming oligonucleotides. Here we focus on the rational optimization of such an alternate-strand triplex formation on a DNA duplex containing a 5′-GpT-3′/3′-CpA-5′ or a 5′-TpG-3′/3′-ApC-5′ step by combination of (G,T)- and (G,A)-contain ing oligonucleotides that bind to the oligopurine strands in opposite orientations.Results: The deletion of one nucleotide in the reverse Hoogsteen region of the oligonucleotide provides the best binding at the 5′-GpT-3′/3′-CpA-5′ step, whereas the addition of two cytosines as a linker between the two oligonucleotides is the best strategy to cross a 5′-TpG-3′/3′-ApC-5′ step. Energy minimization and experimental data suggest that these two cytosines are involved in the formation of two novel base quadruplets.Conclusions: These data provide a rational basis for the design of oligonucleotides capable of binding to oligopurine sequences that alternate on the two strands of double-stranded DNA with a 5′-GpT-3′/3′-CpA-5′ or a 5′-TpG-3′/3′-ApC-5' step at the junction.     

Reactivity between acetone and single-stranded DNA containing a 5′-capped 2′-fluoro-N7-methyl guanine

DNA-mediated catalysis is an emerging field in bioorganic chemistry and chemical biology. However, the functional group diversity and known reactivity of DNA (A, T, C, and G) is relatively limited in scope. This relatively defined reactivity can limit the utility of DNA as a catalyst. In an effort to expand the functional group diversity and chemical reactivity of DNA, we sought to explore reactions involving single-stranded DNA equipped with a stabilized variant of N7-methyl guanine (2′-fluoro-5′-N7-methyl guanine). Here, we show that 5′-capped 2′-fluoro-N7-methyl guanine-labeled single-stranded DNA reacts with a ketone to afford a ketone-labeled DNA. This reaction likely proceeds through a reactive ylide or N-heterocyclic carbene. Taken together, our findings suggest that 2′-fluoro-5′-N7-methyl guanine is a stable adduct that can be selectively incorporated into ssDNA and functionalized with a ketone moiety by reaction with a simple ketone. Incorporation of this nucleoside into ssDNA may be useful for the evolution of novel deoxyribozymes that catalyze new reactions, including those which proceed via a reactive ylide or N-heterocyclic carbene-mediated chemistry.     

N-oxides of imidazo[4,5-b]quinoxalines and imidazo[4,5-b]pyrazines

The N-oxides and N,N-dioxides of methyl derivatives of imidazo[4,5-b]quinoxaline and imidazo[4,5-b]pyrazine were synthesized. The higher reactivity of the 2-methyl group in the N-oxides of 2-methylimidazo[4,5-b]quinoxaline as compared with the corresponding unoxidized derivatives was demonstrated.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 9, pp. 1266–1270, September, 1972.     

Bis-1,2,4-triazolo[4,3-a:3′,4′-c]quinoxalines of pharmaceutical interest from 1,3-dipolar cycloaddition

Various derivatives of the heterocyclic system 1,12,12a,12b-tetrahydrobis-1,2,4-triazolo[4,3-a:3′,4′-c]quinoxaline of pharmaceutical interest have been obtained by double site- and regio-selective 1,3-dipolar cycloaddition of arylnitrilimines to quinoxalines. No evidence for the formation of mono-adducts was obtained, at variance with literature reports. Specific studies to establish the exact stereochemistry of the bis-cycloadducts were undertaken.     

Photocytotoxic and anaerobic DNA cleavage activity of binuclear 3,3′-dithiodipropionic acid cobalt(II) complexes having phenanthroline bases

Dicobalt(II) complexes [{(B)Co^II}₂(μ-dtdp)₂] (1–3) of 3,3′-dithiodipropionic acid (dtdp) and phenanthroline bases (B), viz. 1,10-phenanthroline (phen in 1), dipyrido[3,2-d:2′,3′-f]quinoxaline (dpq in 2) and dipyrido[3,2-a:2′,3′-c]phenazine (dppz in 3), have been prepared, characterized and their photo-induced anaerobic DNA cleavage activity studied. The elemental analysis and mass spectral data suggest binuclear formulation of the complexes. The redox inactive complexes have magnetically non-interacting dicobalt(II) core showing magnetic moment of ∼3.9 μ_B per cobalt(II) center. The complexes show good binding propensity to calf thymus DNA giving K_b values within 4.3 × 10⁵–4.0 × 10⁶ M⁻¹. Thermal melting and viscosity data predict DNA groove binding and/or partial intercalative nature of the complexes. The complexes show significant anaerobic DNA cleavage activity in green light under argon atmosphere possibly involving radical species generated from the disulfide moiety in a type-I pathway. The DNA cleavage reaction under aerobic medium in green light is found to involve hydroxyl radical species. The dppz complex 3 exhibits significant photocytotoxicity in HeLa cervical cancer cells with an IC₅₀ value of 2.3 μM in UV-A light of 365 nm, while it is essentially non-toxic in dark giving an IC₅₀ value of >200 μM. A significant reduction of the dark toxicity of the organic dppz base (IC₅₀ = 8.3 μM in dark) is observed on binding to the cobalt(II) center while essentially retaining its photocytotoxicity in UV-A light (IC₅₀ = 0.4 μM).     

Synthesis of substituted dipyrido[3,2-a:2′,3′-c]phenazines and a new heterocyclic dipyrido[3,2-f:2′,3′-h]quinoxalino[2,3-b]quinoxaline

Three new α,α′-diimine ligands were synthesized based on condensation of 1,10-phenanthroline-5,6-dione with 1,2-phenylenediamine derivatives using different approaches. All compounds were fully characterized by IR, ¹H and ¹³C NMR, UV-visible, and MS spectroscopies. We report the first example of a dipyrido[3,2-f:2′,3′-h]quinoxalino[2,3-b]quinoxaline, which exhibits a strong absorption at 430 nm and an interesting electrochemical behavior. These new molecules may have biological potential and are of synthetic and technological importance.     

Electrochemical detection of DNA 3′-phosphatases based on surface-extended DNA nanotail strategy

Determination of DNA dephosphorylation is of great value due to its vital role in many cellular processes. Here we report a surface-extended DNA nanotail strategy for simple and ultrasensitive detection of DNA 3′-phosphatases by terminal deoxynucleotidyl transferase (TdT) mediated signal amplification. In this work, DNA probes labeled with thiols at their 5′ terminals and phosphoryls at 3′ terminals are immobilized on gold electrode and are used as substrates for DNA 3′-phosphatases, taking T4 polynucleotide kinase phosphatase (T4PNKP) as an example. T4PNKP can catalyze the dephosphorylation reaction of the substrate DNA, followed by the formation of a long DNA strand by TdT on its 3′ terminal hydroxyl, leading to an evident chronocoulometry signal enhancement. The proposal presents a considerable analytical performance with low detection limit and wide linear range, making it promise to be applied in the fields of DNA dephosphorylation related processes, drug discovery, and clinical diagnostics.     

Synthesis and biochemical properties of oligodeoxynucleotides acylated by the chemically stable 2-(trimethylsilyl)benzoyl (TMSBz) group at the 5′ or 3′ terminus

Oligodeoxynucleotides acylated with a 2-(trimethylsilyl)benzoyl (TMSBz) group at the 5′ or 3′ terminus were synthesized according to the general method used for DNA synthesis. The acylated DNA oligomers could be easily purified due to the high lipophilicity of the TMSBz group and showed enhanced hybridization ability and resistance to exonucleases.     

Photoreaction of iodouracil in DNA duplex; C-I bond is cleaved via two different pathways ‘homolysis and heterolysis’

We recently found that a selective photoreaction of 5-iodouracil (^IU) occurs in 5′-(G/C)AA^IU^IU-3′ and 5′-(G/C)A^IU^IU-3′ sequences in ^IU-substituted duplex DNA. In this study, the photoreactivity of the 5′-G(A)_n^IUT-3′ sequence was examined using various ^IU-containing oligonucleotides. HPLC analysis revealed that their photoreactivity largely depends on the number of As between G and ^IU. The most efficient reactivity was observed when the number of As was two and this decreased with increasing numbers from three to five, as observed for the 5′-G(A)_n^IUT-3′ sequence. These results indicate that the G located 5′ from ^IU acts as an electron donor for ^IU, as in the photoreaction of ^BrU. In sharp contrast to the ^BrU photoreaction, ^IU was photoreactive when the number of As was zero or more than five. These results indicate that both homolytic and heterolytic pathways operate in the formation of the uracil-5-yl radical in the photoreaction of ^IU in duplex DNA. In addition, the ratio of these pathways is highly dependent on DNA sequence.     

Synthesis of a formamidine-protected 5-amino-2,5-dideoxyguanosine phosphoramidite and preparation of 5-acylamidooligonucleotides

A 5^′-amino-2^′,5^′-dideoxyguanosine phosphoramidite building block for DNA synthesis was prepared from 2-N-(dibutylformamidino)-2^′-deoxyguanosine in four steps and 68% overall yield. Two of the three steps of the conversion from the 5^′-alcohol to the monomethoxytritylamine were performed in the same flask.     

Synthesis,Biological Evaluation,and In Silico Studies of New Acetylcholinesterase Inhibitors Based on Quinoxaline Scaffold

A quinoxaline scaffold exhibits various bioactivities in pharmacotherapeutic interests. In this research, twelve quinoxaline derivatives were synthesized and evaluated as new acetylcholinesterase inhibitors. We found all compounds showed potent inhibitory activity against acetylcholinesterase (AChE) with IC₅₀ values of 0.077 to 50.080 µM, along with promising predicted drug-likeness and blood–brain barrier (BBB) permeation. In addition, potent butyrylcholinesterase (BChE) inhibitory activity with IC₅₀ values of 14.91 to 60.95 µM was observed in some compounds. Enzyme kinetic study revealed the most potent compound (6c) as a mixed-type AChE inhibitor. No cytotoxicity from the quinoxaline derivatives was noticed in the human neuroblastoma cell line (SHSY5Y). In silico study suggested the compounds preferred the peripheral anionic site (PAS) to the catalytic anionic site (CAS), which was different from AChE inhibitors (tacrine and galanthamine). We had proposed the molecular design guided for quinoxaline derivatives targeting the PAS site. Therefore, the quinoxaline derivatives could offer the lead for the newly developed candidate as potential acetylcholinesterase inhibitors.     

Chirality at phosphorus: hybrid duplexes of chimeric oligonucleotides containing methylphosphonothioate linkages with complementary DNA and RNA

Chimeric oligonucleotides with incorporated diastereomerically pure dinucleoside(3′,5′)-methylphosphonothioates and their oxo- and seleno- congeners of known absolute configuration are reported. The relation between stability of the hybrid duplexes with complementary DNA and RNA and their structure is analyzed in context of absolute configuration of the P-chiral internucleotide bonds.