Absolute configurations of spiroiminodihydantoin and allantoin stereoisomers: comparison of computed and measured electronic circular dichroism spectra

Enantioselective Degradation and Bioactivity Mechanism of a New Chiral Fungicide Fluindapyr in Paddy Ecosystems

Fluindapyr is a novel chiral succinate dehydrogenase inhibitor used to control fungal diseases. The enantioselective effects of fluindapyr in paddy ecosystems are unknown. We developed a new chiral determination method of fluindapyr using ultrahigh performance liquid chromatography tandem mass spectrometry. The absolute configuration of the fluindapyr enantiomers was identified by an electron circular dichroism model. A new husk-based biochar material was used to optimize and establish a QuEchERs method for paddy soil determination. Under anaerobic conditions, the half-lives of R-fluindapyr and S-fluindapyr in paddy soil were 69.6 and 101.8 days, respectively. R-fluindapyr degraded more rapidly than S-fluindapyr. S-fluindapyr was 87.8 times more active against Rhizoctonia solani than R-fluindapyr. The enantioselective bioactivity mechanism was illustrated by molecular docking between the fluindapyr enantiomers and SDH of R. solani. The binding powers of R-fluindapyr and S-fluindapyr to proteins were -32.12 and - 42.91 kcal/mol, respectively. This study reports the stereoselectivity of fluindapyr about determination, degradation, bioactivity, and its mechanism. It provides a foundation for an in-depth study of fluindapyr at the enantiomer level.

Reactivity of Singlet Oxygen with DNA, an Update

The reactivity of singlet oxygen with DNA constituents and in particular with the guanine base has been studied during more than four decades but the exact mechanisms by which such a reactive oxygen species reacts with DNA is still a matter of debate. In this review article, a summary of the data that were obtained from several laboratories and using complementary experimental and theoretical approaches are presented. Reaction mechanisms of ¹ O₂ with guanine and its oxidation product 8-oxo7,8-dihydroguanine are presented both at the nucleoside level and when the base is inserted into DNA since significant differences have been observed. Efforts have been made to propose tentative mechanisms to explain the conflicting results that were sometimes reported and hypotheses have been put forward to tentatively explain still contradictory observations.

Development of RS-pyrisoxazole for reduction of pesticide inputs: A new insight from systemic evaluation of pyrisoxazole at the stereoisomeric level

Pyrisoxazole is a chiral fungicide that is routinely applied to agricultural plant protection, but the potential environmental risk may be under- or over-estimated because the risk induced by stereoisomers have never been evaluated individually. Thus, we carried out a systemic evaluation of pyrisoxazole at the stereoisomeric level, including absolute configuration, stereoselective bioactivity, acute toxicity, and stereoselective dissipation behavior. There were 99.0-3545.3 fold difference in bioactivity toward six target pathogens (e.g., Alternaria solani) and 1.3-4.0 times difference in toxicity against aquatic organisms (Selenastrum capricornutum and Daphnia magna) between the best and worst stereoisomer. There appeared to be no significant stereoselective dissipation in all three kinds of soil under aerobic and anaerobic conditions. Stereoselective dissipation in buffer solution and river water only observed between diastereomers rather than between enantiomers. In addition, photolysis played a central role in the dissipation of pyrisoxazole in river water. RS-pyrisoxazole was 2.2- to 6.9-times more bioactive and 1.2- to 2.1-times more toxic than Rac-pyrisoxazole, and what is more, RS-pyrisoxazole degraded faster than other stereoisomers in river water. The result implicated that developing pure RS-pyrisoxazole as commercial product could reduce the input of inactive isomer on the basis of guaranteeing the efficacy against the target pathogens.

Products of Oxidative Guanine Damage Form Base Pairs with Guanine

Among the natural bases, guanine is the most oxidizable base. The damage caused by oxidation of guanine, commonly referred to as oxidative guanine damage, results in the formation of several products, including 2,5-diamino-4H-imidazol-4-one (Iz), 2,2,4-triamino-5(2H)-oxazolone (Oz), guanidinoformimine (Gf), guanidinohydantoin/iminoallantoin (Gh/Ia), spiroiminodihydantoin (Sp), 5-carboxamido-5-formamido-2-iminohydantoin (2Ih), urea (Ua), 5-guanidino-4-nitroimidazole (NI), spirodi(iminohydantoin) (5-Si and 8-Si), triazine, the M+7 product, other products by peroxynitrite, alkylated guanines, and 8,5'-cyclo-2'-deoxyguanosine (cG). Herein, we summarize the present knowledge about base pairs containing the products of oxidative guanine damage and guanine. Of these products, Iz is involved in G-C transversions. Oz, Gh/Ia, and Sp form preferably Oz:G, Gh/Ia:G, and Sp:G base pairs in some cases. An involvement of Gf, 2Ih, Ua, 5-Si, 8-Si, triazine, the M+7 product, and 4-hydroxy-2,5-dioxo-imidazolidine-4-carboxylic acid (HICA) in G-C transversions requires further experiments. In addition, we describe base pairs that target the RNA-dependent RNA polymerase (RdRp) of RNA viruses and describe implications for the 2019 novel coronavirus (SARS-CoV-2): When products of oxidative guanine damage are adapted for the ribonucleoside analogs, mimics of oxidative guanine damages, which can form base pairs, may become antiviral agents for SARS-CoV-2.

Photo-induced synthesis, structure and in vitro bioactivity of a natural cyclic peptide Yunnanin A analog

A cyclic analog of natural peptide Yunnanin A was synthesized via photoinduced single electron transfer reaction (SET) in the paper. The resulting compound exhibited potent bioactivity (with IC₅₀ values 29.25 μg mL⁻¹ against HepG-2 cell lines and 65.01 μg mL⁻¹ against HeLa cell lines), but almost have no toxicity to normal cells (with IC₅₀ values 203.25 μg mL⁻¹ against L929 cell lines), which may be served as a potential antitumor drug for medical treatment. The spatial structure was examined by experimental electronic circular dichroism (ECD) and quantum chemistry calculations. Moreover, the theoretical study suggested that special intramolecular hydrogen bonds and γ, β-turn secondary structures may be possible sources affecting cyclic peptide's bioactivity.

The photo-induced synthesis, structure and in vitro bioactivity study of a Yunnanin A cyclopeptide analog was presented.

Development of S-Fluxametamide for Bioactivity Improvement and Risk Reduction: Systemic Evaluation of the Novel Insecticide Fluxametamide at the Enantiomeric Level

Increasing numbers of novel pesticides have been applied in agriculture. However, traditional evaluation of pesticides does not distinguish between their enantiomers, which may lead to inaccurate results. In this study, systematic research on the chiral insecticide fluxametamide was conducted at the enantiomeric level. The methods for enantioseparation and semipreparative separation of fluxametamide enantiomers were developed. The optical rotation and absolute configuration of two enantiomers were determined, and their stability was verified in solvents and soils. Enantioselective bioactivities against four target pests (Plutella xylostella, Spodoptera exigua, Aphis gossypii, and Tetranychus cinnabarinus) were tested. Acute toxicities of fluxametamide enantiomers toward honeybees were also evaluated. S-(+)-Isomer exhibited 52.1-304.4 times and 2.5-3.7 times higher bioactivity than R-(-)-isomer and rac-fluxametamide, respectively. Meanwhile, rac-fluxametamide was more toxic than S/R-isomer, and S-(+)-isomer showed >30-fold higher acute toxicity than R-(-)-isomer. Molecular docking studies were performed with γ-aminobutyric acid receptor (GABAR) to monitor the mechanism of stereoselective bioactivity. The better Grid score of S-(+)-fluxametamide (-60.12 kcal/mol) than R-(-)-enantiomer (-56.59 kcal/mol) indicated higher bioactivity of S-(+)-isomer than of R-(-)-isomer. The dissipation of fluxametamide in cabbage, Chinese cabbage, and soil was nonenantioselective under field conditions. Development of S-(+)-fluxametamide could maintain the high-efficacy and low-risk properties, which should attract attention of producers, applicators, and managers of pesticides.

Photo-induced synthesis of Axinastatin 3 analogs, the secondary structures and their in vitro antitumor activities

Cyclic peptides combine several favorable properties such as good binding affinity, target selectivity and low toxicity that make them an attractive modality for drug development. In an effort to identify what conformation could be accounting for the bioactive disparity of natural and synthetic cyclic peptides, some structurally-constrained analogs of cyclopeptide Axinastatin 3 were prepared by photo-induced single electron transfer (SET) reaction. Detailed stereochemistry study was performed by experimental electronic circular dichroism combined with theoretical calculations. Our study suggested that the cyclopeptide 1 with βI-turn presented stronger antitumor activity comparing with those without such secondary structures. Moreover, a rare 'π helix unit' (compound 3) was realized because of the constrained cyclic structure, which could be considered an important research object for future study of unique helix secondary structures.

Enantioselective effects of the chiral fungicide tetraconazole in wheat: Fungicidal activity and degradation behavior

Tetraconazole, a chiral triazole fungicide, is widely used for the prevention of plant disease in wheat fields. However, the chirality of pesticides like tetraconazole can cause diverse biological responses. Therefore, it is important that research is conducted to investigate the enantioselective effects of chiral enantiomers in this regard. The absolute configurations of two tetraconazole enantiomers were initially confirmed by ECD (Electrostatic circular dichroism). The bioassay test showed that the fungicidal activity of (R)-(+)-tetraconazole against two pathogens (R. cerealis and F. graminearum) was approximately 1.49-1.98 times greater than that for (S)-(-)- tetraconazole. Following recovery experiments, a modified QuEchERS (Quick, easy, cheap, effective, rugged, safe) method was established using UPLC-MS/MS (ultra-performance liquid chromatography tandem mass spectrometry). The mean recoveries from plant and soil sample ranged from 78.9% to 100.5% with intraday relative standard (RSD_r) values of 0.8%-6.9% and interday relative standard (RSD_R) values of 3.0%-5.2% respectively. The stereoselective degradation of tetraconazole in wheat meant that (S)-(-)-tetraconazole was more rapidly degraded than (R)-(+)-tetraconazole. Conversely, (R)-(+)-tetraconazole was preferentially degraded in wheat soil. These results will provide us with a greater understanding when assessing future environmental risk assessments and strategies that invoke pesticide reduction.

Synthesis of novel isoindole-containing phakellistatin 2 analogs and the conformation features affecting their antitumor activities

Two novel phakellistatin 2 analogs were synthesized and the conformational features affecting their antitumor activities were studied.

In situ monitoring of molecular aggregation using circular dichroism

The aggregation of molecules plays an important role in determining their function. Electron microscopy and other methods can only characterize the variation of microstructure, but are not capable of monitoring conformational changes. These techniques are also complicated, expensive and time-consuming. Here, we demonstrate a simple method to monitor in-situ and in real-time the conformational change of (R)-1,1'-binaphthyl-based polymers during the aggregation process using circular dichroism. Based on results from molecular dynamics simulations and experimental circular dichroism measurements, polymers with "open" binaphthyl rings are found to show stronger aggregation-annihilated circular dichroism effects, with more negative torsion angles between the two naphthalene rings. In contrast, the polymers with "locked" rings show a more restrained aggregation-annihilated circular dichroism effect, with only a slight change of torsion angle. This work provides an approach to monitor molecular aggregation in a simple, accurate, and efficient way.

Simultaneous Enantioselective Determination of the Chiral Fungicide Prothioconazole and Its Major Chiral Metabolite Prothioconazole-Desthio in Food and Environmental Samples by Ultraperformance Liquid Chromatography-Tandem Mass Spectrometry

An efficient and sensitive chiral analytical method was established for the determination of the chiral fungicide prothioconazole and its major chiral metabolite prothioconazole-desthio in agricultural and environmental samples using ultraperformance liquid chromatography-tandem mass spectrometry. The optical rotation and absolute configuration of enantiomers were identified by optical rotation detector and electronic circular dichroism spectra. The elution order of prothioconazole and its chiral metabolite enantiomers was R-(+)-prothioconazole-desthio, S-(-)-prothioconazole-desthio, R-(-)-prothioconazole, and S-(+)-prothioconazole. The mean recoveries from the samples was 71.8-102.0% with intraday relative standard deviations (RSDs) of 0.3-11.9% and interday RSDs of 0.9-10.6%. The formation of prothioconazole-desthio was studied in soil under field conditions and enantioselective degradation was observed for chiral prothioconazole. Remarkable enantioselective degradation was observed: R-prothioconazole degraded preferentially with EF values from 0.48 to 0.37. Although prothioconazole-desthio is the most remarkably bioactive metabolite, no obvious enantioselective behavior was observed in soil. These results may help to systematically evaluate prothioconazole and its metabolites in food and environmental safety.

Formation and processing of DNA damage substrates for the hNEIL enzymes

Reactive oxygen species (ROS) are harnessed by the cell for signaling at the same time as being detrimental to cellular components such as DNA. The genome and transcriptome contain instructions that can alter cellular processes when oxidized. The guanine (G) heterocycle in the nucleotide pool, DNA, or RNA is the base most prone to oxidation. The oxidatively-derived products of G consistently observed in high yields from hydroxyl radical, carbonate radical, or singlet oxygen oxidations under conditions modeling the cellular reducing environment are discussed. The major G base oxidation products are 8-oxo-7,8-dihydroguanine (OG), 5-carboxamido-5-formamido-2-iminohydantoin (2Ih), spiroiminodihydantoin (Sp), and 5-guanidinohydantoin (Gh). The yields of these products show dependency on the oxidant and the reaction context that includes nucleoside, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA), and G-quadruplex DNA (G4-DNA) structures. Upon formation of these products in cells, they are recognized by the DNA glycosylases in the base excision repair (BER) pathway. This review focuses on initiation of BER by the mammalian Nei-like1-3 (NEIL1-3) glycosylases for removal of 2Ih, Sp, and Gh. The unique ability of the human NEILs to initiate removal of the hydantoins in ssDNA, bulge-DNA, bubble-DNA, dsDNA, and G4-DNA is outlined. Additionally, when Gh exists in a G4 DNA found in a gene promoter, NEIL-mediated repair is modulated by the plasticity of the G4-DNA structure provided by additional G-runs flanking the sequence. On the basis of these observations and cellular studies from the literature, the interplay between DNA oxidation and BER to alter gene expression is discussed.

Validation of a Chiral Liquid Chromatographic Method for the Degradation Behavior of Flumequine Enantiomers in Mariculture Pond Water

In this work, flumequine (FLU) enantiomers were separated using a Chiralpak OD-H column, with n-hexane-ethanol (20:80, v/v) as the mobile phase at a flow rate of 0.6 mL/min. Solid phase extraction (SPE) was used for cleanup and enrichment. The limit of detection, limit of quantitation, linearity, precision, and intra/interday variation of the chiral high-performance liquid chromatography (HPLC) method were determined. The developed method was then applied to investigate the degradation behavior of FLU enantiomers in mariculture pond water samples. The results showed that the degradation of FLU enantiomers under natural, sterile, or dark conditions was not enantioselective. Chirality 28:649-655, 2016. © 2016 Wiley Periodicals, Inc.

A new phenylpropanoid glucoside and a chain compound from the roots of Allium tuberosum

A new phenylpropanoid glucoside tuberosinine D (1) and a chain compound (Z)-11R,12S,13S-trihydroxy-9-octadecenoate (2) were isolated from the roots of Allium tuberosum. The absolute configuration of 1 was established by comparing of experimental and calculated electronic circular dichroism. The absolute configuration of 2 was determined using the modified Mosher's method for the first time.

Effect of Base-Pairing Partner on the Thermodynamic Stability of the Diastereomeric Spiroiminodihydantoin Lesion

Oxidation of guanine by reactive oxygen species and high valent metals produces damaging DNA base lesions like 8-oxo-7,8-dihydroguanine (8-oxoG). 8-oxoG can be further oxidized to form the spiroiminodihydantoin (Sp) lesion, which is even more mutagenic. DNA polymerases preferentially incorporate purines opposite the Sp lesion, and DNA glycosylases excise the Sp lesion from the duplex, although the rate of repair is different for the two Sp diastereomers. To further understand the biological processing of the Sp lesion, differential scanning calorimetry studies were performed on a series of 15-mer DNA duplexes. The thermal and thermodynamic stabilities of each of the Sp diastereomers paired to the four standard DNA bases were investigated. It was found that, regardless of the base-pairing partner, the Sp lesion was always highly destabilizing in terms of DNA melting temperature, enthalpic stability, and overall duplex free energy. We found no significant differences between the two Sp diastereomers, but changing the base-pairing partner of the Sp lesion produced slight differences in stability. Specifically, duplexes with Sp:C pairings were always the most destabilized, whereas pairing the Sp lesion with a purine base modestly increased stability. Overall, these results suggest that, although the stability of the Sp diastereomers cannot explain the differences in the rates of repair by DNA glycosylases, the most stable base-pairing partners do correspond with the nucleotide preference of DNA polymerases.

A new flavone C-glycoside and a new bibenzyl from Bulbophyllum retusiusculum

A new flavone C-glycoside, apigenin 6-C-α-arabinofuranosyl 8-C-α-arabinopyranoside (1) and a new bibenzyl, bulbotetusine (2), were isolated from the tubers of Bulbophyllum retusiusculum. Their structures were established on the basis of extensive spectroscopic analyses. The absolute configuration of 2 was determined by the comparison of experimental and calculated electronic circular dichroism. Compounds 1 and 2 showed no obvious cytotoxic activity against any five human tumour cell lines with IC50 values >40 μM.

Conformational stabilities of iminoallantoin and its base pairs in DNA: implications for mutagenicity

Under acidic conditions, insertion of G opposite Ia may lead to G to C mutations in DNA.

Normal and reverse base pairing of Iz and Oz lesions in DNA: structural implications for mutagenesis

During replication, incorporation of G opposite Oz lesion is mainly responsible for G to C mutations in DNA.

Investigation into the enantiospecific behavior of trichlorfon enantiomers during microorganism degradation

Degradation of TF enantiomers and generation of dichlorvos in fish at different storage temperatures. (a) Fish was stored at 18 °C, and (b) fish was stored at 25 °C.

Computational studies of electronic circular dichroism spectra predict absolute configuration assignments for the guanine oxidation product 5-carboxamido-5-formamido-2-iminohydantoin

Oxidation of the guanine heterocycle by two electrons can yield the chiral product 5-carboxamido-5-formamido-2-iminohydantoin (2Ih). The 2Ih free base enantiomers were synthesized from 2'-deoxyguanosine oxidized with a Cu(II)/H₂O₂ oxidant system followed by hydrolysis of the N-glycosidic bond. These isomers were each studied by electronic circular dichroism spectroscopy for determination of their absolute configurations. Time-dependent density functional theory calculations of the expected spectra were completed in both the gas phase and with solvent modeling in order to interpret the experimental spectra and provide the absolute configuration assignments.

Proaporphine and aporphine alkaloids with acetylcholinesterase inhibitory activity from Stephania epigaea

An unusual proaporphine alkaloid bearing an isopropanenitrile group at isoquinoline nitrogen, named epiganine A (1) and a new aporphine alkaloid, epiganine B (2), together with eight known alkaloids, pronuciferine (3), dehydrodicentrine (4), romerine (5), romeline (6), N-methylcalycinine (7), phanostenine (8), dicentrine (9), and N-methyllaurotetanine (10), were isolated from the roots of Stephania epigaea. The absolute configuration of 1 was determined by calculating electronic circular dichroism (ECD) and comparing with experimental data. Compounds 2 and 4 showed strong acetylcholinesterase (AChE) inhibitory effects with the IC50 values of 4.36 and 2.98μM, respectively. Compounds 5-9 also exhibited potent AChE inhibitory activities.

Spirodi(iminohydantoin) products from oxidation of 2'-deoxyguanosine in the presence of NH4Cl in nucleoside and oligodeoxynucleotide contexts

Upon oxidation of the heterocyclic ring in 2'-deoxyguanosine (dG), the initial electrophilic intermediate displays a wide range of reactivities with nucleophiles leading to many downstream products. In the present study, the product profiles were mapped when aqueous solutions of dG were allowed to react with NH4Cl in the presence of the photooxidants riboflavin and Rose Bengal as well as the diffusible one-electron oxidant Na2IrCl6. Product characterization identified the 2'-deoxyribonucleosides of spiroiminodihydantoin, 5-guanidinohydantoin, and oxazolone resulting from H2O as the nucleophile. When NH3 was the nucleophile, a set of constitutional isomers that are diastereotopic were also observed, giving characteristic masses of dG + 31. ESI(+)-MS/MS of these NH3 adducts identified them to be spirocycles with substitution of either the C5 or C8 carbonyl with an amine. The NH3 adducts exhibit acid-catalyzed hydrolysis to spiroiminodihydantoin. Quantification of the NH3 and H2O adducts resulting from oxidation of dG in the nucleoside, single-stranded, and duplex oligodeoxynucleotide contexts were monitored allowing mechanisms for product formation to be proposed. These data also provide a cautionary note to those who purify their oligonucleotide samples with ammonium salts before oxidation because this will lead to unwanted side reactions in which ammonia participates in product formation.

The R- and S-diastereoisomeric effects on the guanidinohydantoin-induced mutations in DNA

Although, Gh (Gh1 or Gh2) in DNA would induce mainly G to C mutations, other mutations cannot be ignored.

A short designed semi-aromatic organic nanotube--synthesis, chiroptical characterization, and host properties

The first generation of an organic nanotube based on the enantiomerically pure bicyclo[3.3.1]nonane framework is presented. The helical tube synthesised is the longest to date having its aromatic systems oriented parallel to the axis of propagation (length ∼26 Å and inner diameter ∼11 Å according to molecular dynamics simulations in chloroform). The synthesis of the tube, a heptamer, is based on a series of Friedländer condensations and the use of pyrido[3,2-d]pyrimidine units as masked 2-amino aldehydes, as a general means to propagate organic tubular structures and the introduction of a methoxy group for modification toward solubility and functionalization are described. The electronic CD spectra of the tube and molecular intermediates are correlated with theoretical spectra calculated with time-dependent density functional theory to characterize the chirality of the tube. Both experimental (NMR-titrations) and theoretical (molecular dynamics simulations) techniques are used to investigate the use of the tube as a receptor for the acetylcholine and guanidinium cations, respectively.

Simultaneous enantioselective determination of triazole fungicide flutriafol in vegetables, fruits, wheat, soil, and water by reversed-phase high-performance liquid chromatography

A novel and effective method for enantioselective determination of flutriafol enantiomers in food and environmental matrices (cucumber, tomato, grape, pear, wheat, soil, and water) has been developed. The (R)-(-)-flutriafol was first eluted and measured from electronic circular dichroism spectra using a cellulose tris(3-chloro-4-methyl phenyl carbamate) chiral column. The mean recoveries from the samples ranged from 82.9% to 103.4%, with intraday relative standard deviations (RSD) of 2.2-8.3% and interday RSD of 3.4-7.9%. Good linearity (R(2) ≥ 0.9989) was obtained for all analytes matrix calibration curves within the range of 0.1-10 mg/kg. The limits of detection for two enantiomers in the seven matrices were all below 0.015 mg/kg. The results show that the proposed method is convenient and reliable for the enantioselective detection of the flutriafol in the real samples and is applicable to the environmental stereochemistry of flutriafol in food and environmental matrices.

Crystal structure of DNA polymerase β with DNA containing the base lesion spiroiminodihydantoin in a templating position

The first high-resolution crystal structure of spiroiminodihydantoin (dSp1) was obtained in the context of the DNA polymerase β active site and reveals two areas of significance. First, the structure verifies the recently determined S configuration at the spirocyclic carbon. Second, the distortion of the DNA duplex is similar to that of the single-oxidation product 8-oxoguanine. For both oxidized lesions, adaptation of the syn conformation results in similar backbone distortions in the DNA duplex. The resulting conformation positions the dSp1 A-ring as the base-pairing face whereas the B-ring of dSp1 protrudes into the major groove.

Enantioselective degradation of dufulin in four types of soil

In this study, enantioselective degradation of dufulin in four types of soil (Guiyang silty loam, Nanning silty clay, Hefei silty clay, and Harbin silty clay) was investigated under sterile and nonsterile conditions. Pesticide residues in soil samples were extracted with acetonitrile. S-(+)-Dufulin and R-(-)-dufulin were separated and determined on an amylose tris(3,5-dimethylphenylcarbamate) (Chiralpak IA) chiral column by normal phase high-performance liquid chromatography (HPLC). The absolute configurations of dufulin enantiomers were determined by obtaining experimental and computed circular dichroism spectra. Dufulin enantiomers were found to be configurationally stable in the selected soils, and no interconversion was observed during the incubation of enantiopure S-(+)- or R-(-)-dufulin under nonsterile conditions. Compared to the half-life (t1/2) of dufulin in sterile soils, the degradation rate was higher in nonsterile soils, which suggests that dufulin degradation can be attributed primarily to microbial activity in soils used for agricultural cultivation. Furthermore, enantiopure S-(+)-dufulin degraded more rapidly than its antipode. This suggests that use of enantiopure S-(+)-dufulin could exert less disturbance to soil bioactivity and contribute less to environmental pollution.

Reconciliation of chemical, enzymatic, spectroscopic and computational data to assign the absolute configuration of the DNA base lesion spiroiminodihydantoin

The diastereomeric spiroiminodihydantoin-2'-deoxyribonucleoside (dSp) lesions resulting from 2'-deoxyguanosine (dG) or 8-oxo-7,8-dihydro-2'-deoxyguanosine (dOG) oxidation have generated much attention due to their highly mutagenic nature. Their propeller-like shape leads these molecules to display mutational profiles in vivo that are stereochemically dependent. However, there exist conflicting absolute configuration assignments arising from electronic circular dichroism (ECD) and NOESY-NMR experiments; thus, providing definitive assignments of the 3D structure of these molecules is of great interest. In the present body of work, we present data inconsistent with the reported ECD assignments for the dSp diastereomers in the nucleoside context, in which the first eluting isomer from a Hypercarb HPLC column was assigned to be the S configuration, and the second was assigned the R configuration. The following experiments were conducted: (1) determination of the diastereomer ratio of dSp products upon one-electron oxidation of dG in chiral hybrid or propeller G-quadruplexes that expose the re or si face to solvent, respectively; (2) absolute configuration analysis using vibrational circular dichroism (VCD) spectroscopy; (3) reinterpretation of the ECD experimental spectra using time-dependent density functional theory (TDDFT) with the inclusion of 12 explicit H-bonding waters around the Sp free bases; and (4) reevaluation of calculated specific rotations for the Sp enantiomers using the hydration model in the TDDFT calculations. These new insights provide a fresh look at the absolute configuration assignments of the dSp diastereomers in which the first eluting from a Hypercarb-HPLC column is (-)-(R)-dSp and the second is (+)-(S)-dSp. These assignments now provide the basis for understanding the biological significance of the stereochemical dependence of enzymes that process this form of DNA damage.

Endonuclease and Exonuclease Activities on Oligodeoxynucleotides Containing Spiroiminodihydantoin Depend on the Sequence Context and the Lesion Stereochemistry

8-Oxo-7,8-dihydro-2'-deoxyguanosine (dOG), a well-studied oxidation product of 2'-deoxyguanosine (dG), is prone to facile further oxidation forming spiroiminodihydantoin 2'-deoxyribonucleoside (dSp) in the nucleotide pool and in single-stranded oligodeoxynucleotides (ODNs). Many methods for quantification of damaged lesions in the genome rely on digestion of DNA with exonucleases or endonucleases and dephosphorylation followed by LC-MS analysis of the resulting nucleosides. In this study, enzymatic hydrolysis of dSp-containing ODNs was investigated with snake venom phosphodiesterase (SVPD), spleen phosphodiesterase (SPD) and nuclease P1. SVPD led to formation of a dinucleotide, 5'-d(Np[Sp])-3' (N = any nucleotide) that included the undamaged nucleotide on the 5' side of dSp as the final product. This dinucleotide was a substrate for both SPD and nuclease P1. A kinetic study of the activity of SPD and nuclease P1 showed a sequence dependence on the nucleotide 5' to the lesion with rates in the order dG>dA>dT>dC. In addition, the two diastereomers of dSp underwent digestion at significantly different rates with dSp1>dSp2; nuclease P1 hydrolyzed the 5'-d(Np[Sp1])-3' dinucleotide two- to six-fold faster than the corresponding 5'-d(Np[Sp2])-3', while for SPD the difference was two-fold. These rates are chemically reasoned based on dSp diastereomer differences in the syn vs. anti glycosidic bond orientation. A method for the complete digestion of dSp-containing ODNs is also outlined based on treatment with nuclease P1 and SVPD. These findings have significant impact on the development of methods to detect dSp levels in cellular DNA.

Thermodynamic profiles and nuclear magnetic resonance studies of oligonucleotide duplexes containing single diastereomeric spiroiminodihydantoin lesions

The spiroiminodihydantoins (Sp) are highly mutagenic oxidation products of guanine and 8-oxo-7,8-dihydroguanine in DNA. The Sp lesions have recently been detected in the liver and colon of mice infected with Helicobacter hepaticus that induces inflammation and the development of liver and colon cancers in murine model systems [Mangerich, A., et al. (2012) Proc. Natl. Acad. Sci. U.S.A. 109, E1820-E1829]. The impact of Sp lesions on the thermodynamic characteristics and the effects of the diastereomeric Sp-R and Sp-S lesions on the conformational features of double-stranded 11-mer oligonucleotide duplexes have been studied by a combination of microcalorimetric methods, analysis of DNA melting curves, and two-dimensional nuclear magnetic resonance methods. The nonplanar, propeller-like shapes of the Sp residues strongly diminish the extent of local base stacking interactions that destabilize the DNA duplexes characterized by unfavorable enthalpy contributions. Relative to that of an unmodified duplex, the thermally induced unfolding of the duplexes with centrally positioned Sp-R and Sp-S lesions into single strands is accompanied by a smaller release of cationic counterions (Δn(Na⁺) = 0.6 mol of Na⁺/mol of duplex) and water molecules (Δn(w) = 17 mol of H₂O/mol of duplex). The unfolding parameters are similar for the Sp-R and Sp-S lesions, although their orientations in the duplexes are different. The structural disturbances radiate one base pair beyond the flanking C:G pair, although Watson-Crick hydrogen bonding is maintained at all flanking base pairs. The observed relatively strong destabilization of B-form DNA by the physically small Sp lesions is expected to have a significant impact on the processing of these lesions in biological environments.

Enantioselective analysis and degradation studies of isocarbophos in soils by chiral liquid chromatography-tandem mass spectrometry

An enantioselective method is presented for the determination of isocarbophos in soil by liquid chromatography coupled with tandem mass spectrometry. The pesticide residues in soil samples were extracted with acetonitrile, and complete enantioseparation was obtained on an amylose tris(3,5-dimethylphenylcarbamate) chiral column using acetonitrile/2 mM ammonium acetate solution containing 0.1% formic acid (60:40, v/v) as the mobile phase. The absolute configuration of isocarbophos enantiomers was determined by the combination of experimental and calculated electronic circular dichroism spectra. The method was utilized to investigate the degradation of isocarbophos in soils (Changchun, Hangzhou, and Zhengzhou) under sterilized or native conditions. Isocarbophos enantiomers were configurationally stable in the selected soils, and the pesticide degradation was not enantioselective in the sterilized condition. The degradation behavior of rac-isocarbophos was different under native conditions, with no enantioselectivity in the Changchun soil and with the S-(+)-isocarbophos enriched in the Hangzhou and Zhengzhou soils.

Calculation of the stabilization energies of oxidatively damaged guanine base pairs with guanine

DNA is constantly exposed to endogenous and exogenous oxidative stresses. Damaged DNA can cause mutations, which may increase the risk of developing cancer and other diseases. G:C-C:G transversions are caused by various oxidative stresses. 2,2,4-Triamino-5(2H)-oxazolone (Oz), guanidinohydantoin (Gh)/iminoallantoin (Ia) and spiro-imino-dihydantoin (Sp) are known products of oxidative guanine damage. These damaged bases can base pair with guanine and cause G:C-C:G transversions. In this study, the stabilization energies of these bases paired with guanine were calculated in vacuo and in water. The calculated stabilization energies of the Ia:G base pairs were similar to that of the native C:G base pair, and both bases pairs have three hydrogen bonds. By contrast, the calculated stabilization energies of Gh:G, which form two hydrogen bonds, were lower than the Ia:G base pairs, suggesting that the stabilization energy depends on the number of hydrogen bonds. In addition, the Sp:G base pairs were less stable than the Ia:G base pairs. Furthermore, calculations showed that the Oz:G base pairs were less stable than the Ia:G, Gh:G and Sp:G base pairs, even though experimental results showed that incorporation of guanine opposite Oz is more efficient than that opposite Gh/Ia and Sp.

Different enantioselective degradation of pyraclofos in soils

This study investigated the enantioselective degradation behavior of pyraclofos in three soils (NC, HZ, and ZZ) under native and sterilized conditions. The absolute configuration of pyraclofos enantiomers has been determined by the combination of experimental and calculated electronic circular dichroism spectra. S-(+)- and R-(-)-Pyraclofos were separated and determined on a cellulose tri-(4-chloro-3-methylphenylcarbamate) (Lux Cellulose-4) chiral column by reversed-phase high-performance liquid chromatography-tandem mass spectrometry. Pyraclofos enantiomers were configurationally stable in three soils and no interconversion was observed during the incubation of enantiopure S-(+)- or R-(-)-pyraclofos under native conditions. The enantioselective degradation behavior of chiral pyraclofos was dramatically different in three soils under native conditions, with half-lives (t(1/2)) of pyraclofos in NC, HZ, and ZZ soils of 2.6, 13.4, and 7.8 days for S-(+)-pyraclofos and 9.2, 9.3, and 8.2 days for R-(-)-pyraclofos. Compared to the half-lives (t(1/2)) of rac-pyraclofos of 21.5, 55.9, and 14.4 days in sterilized NC, HZ and ZZ soils, the degradation velocity was greatly improved in native soils, indicating that degradation was greatly attributed to microbially mediated processes in agricultural cultivating soils.

Characterization of 2'-deoxyguanosine oxidation products observed in the Fenton-like system Cu(II)/H2O2/reductant in nucleoside and oligodeoxynucleotide contexts

Reactive oxygen species attack both base and sugar moieties in DNA with a preference among the bases for reaction at guanine. In the present study, 2'-deoxyguanosine (dG) was oxidized by a copper-mediated Fenton reaction with the reductants ascorbate or N-acetyl-cysteine, yielding oxidation on both the base and the sugar. The primary oxidized lesions observed in these studies include the 2'-deoxyribonucleosides of 8-oxo-7,8-dihydroguanosine (dOG), spiroiminodihydantoin (dSp), guanidinohydantoin (dGh), oxazolone (dZ), and 5-carboxamido-5-formamido-2-iminohydantoin (d2Ih), as well as the free base guanine. d2Ih was the major product observed in the nucleoside, single- and double-stranded oligodeoxynucleotide contexts and is proposed to arise from oxidation at C5 of guanine. Product distribution studies provide insight into the role of the reductant in partitioning of dG base oxidation along the C5 and C8 pathways.

Determination of Absolute Configuration of Natural Products: Theoretical Calculation of Electronic Circular Dichroism as a Tool

Determination of absolute configuration (AC) is one of the most challenging features in the structure elucidation of chiral natural products, especially those with complex structures. With revolutionary advancements in the area of quantum chemical calculations of chiroptical spectroscopy over the past decade, the time dependent density functional theory (TDDFT) calculation of electronic circular dichroism (ECD) spectra has emerged as a very promising tool. The principle is simply based on the comparison of the calculated and experimental ECD spectra: the more closely they match, the more reliable conclusion for the AC assignment can be drawn. This review attempts to use several examples representing monomeric flavonoids, rotationally restricted biflavonoids, complex hexahydroxydiphenoyl-containing flavonoids, conformationally flexible and restrained sesquiterpenoids, cembrane-africanene terpenoids, dihydropyranocoumarins, alkaloids, and dihydroxanthones to illustrate the applicability of this approach in determining the AC of structurally diverse natural products. The findings clearly indicate that the TDDFT calculation of ECD spectra can quantify the contribution of individual conformers and the interaction of multiple chromophores, making it possible to determine the AC of complex chiral molecules. The calculated electronic transitions and molecular orbitals provide new insight into the interpretation of ECD spectra at the molecular level.

Absolute configurations of DNA lesions determined by comparisons of experimental ECD and ORD spectra with DFT calculations

The usefulness of modern density functional theory (DFT) methods is considered for establishing the absolute configurations of DNA lesions by comparisons of computed and experimentally measured optical rotatory dispersion (ORD) and electronic circular dichroism (ECD) spectra. Two rigid, structurally different DNA lesions (two spiroiminodihydantoin stereoisomers and four equine estrogen 4-hydoxyequilenin-DNA stereoisomeric adducts) have been investigated. In all cases, the signs and shapes of the computed ORD spectra reproduced the experimentally measured ORD spectra, although the magnitudes of the computed and experimental ORD values do not coincide exactly. The computed ECD spectra also reproduced the shapes of the experimental ECD spectra rather well, but are blue-shifted by 10-20 nm. Since the assignments of the absolute configurations of the DNA lesions studied based on computed and experimental ORD and ECD spectra are fully consistent with one another, the computational DFT method shows significant promise for determining the absolute configurations of DNA lesions. Establishing the stereochemistry of DNA lesions is highly useful for understanding their biological impact, especially when sufficient amounts of material are not available for other methods of structural characterization.

Influence of substrate complexity on the diastereoselective formation of spiroiminodihydantoin and guanidinohydantoin from chromate oxidation

Chromate is a human carcinogen with a poorly defined mechanism of DNA damage. In vitro and prokaryotic studies have shown that DNA damage may occur via the formation of the hydantoin lesions guanidinohydantoin (Gh) and spiroiminodihydantoin (Sp) from further oxidation of 8-oxo-7,8-dihydroguanine (8oxoG). The unusual structure of these lesions coupled with their enhanced mutagenicity make them attractive for study with regard to their role in chromate-induced cancer. We have studied the formation of Gh versus Sp and their associated diastereomers following oxidation by model Cr(V) complexes and from in situ chromate reduction by ascorbate and glutathione. Identification of the two optically assigned diastereomers of Sp (R-Sp and S-Sp) as well as the two diastereomers of Gh (Gh1 and Gh2, not yet optically assigned) was carried out using increasingly sterically hindered substrates (nucleoside --> ssDNA --> dsDNA). Lesion formation and diastereomeric preference were found to be highly oxidant- and substrate-dependent. The Ir(IV)-positive control showed a shift from near equal levels of Gh and Sp and near equal levels of all four diastereomers in the nucleoside to all Gh formation in dsDNA, with a 5-fold enhancement in Gh2 over Gh1. The two model Cr(V) complexes used in this study, Cr(V)-salen and Cr(V)-ehba, showed opposite trends going from nucleoside to dsDNA with Cr(V)-salen giving enhanced Sp formation (with mainly R-Sp formed) and the Cr(V)-ehba having an oxidation profile nearly identical to that of Ir(IV). The two chromate reduction systems, Cr(6+)/ascorbate and Cr(6+)/glutathione, designed to model the intracellular reduction of chromate, showed lower levels of oxidation in all substrates. Notable in this group was the shift in the formation of the lesions to essentially all Sp for the Cr(6+)/ascorbate system with the most sterically hindered substrate, dsDNA. These results, when coupled with the known diastereomeric preference for excision of hydantoin lesions by the hNEIL1 enzyme, show the importance of defining both levels of lesion formation and diastereomeric preference of formation with regard to their potential impact on chromate carcinogenesis.