Mechanism for ribonucleotide reductase inactivation by the anticancer drug gemcitabine

Gemcitabine (2',2'-difluoro-2'-deoxycytidine, dFdC) is a very promising anticancer drug, already approved for clinical use in three therapeutic indications. It is metabolized intracellularly to 5'-diphosphate (dFdCDP), which is known to be a potent inhibitor of ribonucleotide reductase (RNR). Although several nucleotide analogs show in vitro capacity of RNR inactivation, none has shown the in vivo efficacy of dFdCDP. Accordingly, the experimental data suggests that its mechanism of inhibition is different from the other known RNR suicide inhibitors. Enzyme inhibition in the absence of reductive species leads to complete loss of the essential radical in subunit R2, and formation of a new nucleotide-based radical. Interestingly, however, the presence of the reductants does not prevent inhibition--the radical is not lost but the targeted subunit of RNR becomes R1, which is inactivated possibly by alkylation. We have conducted a theoretical study, which led us to the first proposal of a possible mechanism for RNR inhibition by dFdCDP in the absence of reductants. This mechanism turned out to be very similar to the natural substrate reduction pathway and only deviates from the natural course after the formation of the well-known disulphide bridge. This deviation is caused precisely by the F atom in the beta-face, only present in this inhibitor. The essential radical in R2 is lost, and so is the enzyme catalytic activity. The nucleotide-based radical that constitutes the end product of our mechanism has been suggested in the literature as a possible candidate for the one detected experimentally. In fact, all experimental data available has been reproduced by the theoretical calculations performed here.     

Simultaneous determination of deoxycytidine diphosphate and deoxycytidine triphosphate by capillary electrophoresis with transient isotachophoretic stacking: a sensitive monitoring method for ribonucleotide reductase activity

A simple and rapid capillary electrophoretic method was developed for simultaneous determination of sub‐micromolar 2′‐deoxycytidine 5′‐diphosphate (dCDP) and 2′‐deoxycytidine 5′‐triphosphate (dCTP) levels in enzyme assays without using radioactively labeled substrates. The separation was performed at 25°C using MES in the BGE as the terminating ion, the chloride ions in the sample buffer as the leading ion, and PEG 4000 in the BGE as the EOF suppressor for sample stacking by transient isotachophoresis (tITP). Several parameters affecting the separation were investigated, including the pH of the BGE, the concentration of sodium chloride in the sample buffer, and the concentrations of MES and PEG 4000 in the running buffer. Good separation with high separation efficiency was achieved within 6 min under optimal conditions. In comparison with the simple CZE method, the present tITP‐CZE method enabled a 150‐fold increase in the injection time without any decrease in resolution and the sensitivity was enhanced up to two orders of magnitude with the new method. The linear range of the method was 0.1–10 μM for dCDP and dCTP. The limits of detection of dCDP and dCTP were 85 and 73 nM, respectively. The proposed method was successfully applied for the activity assay of ribonucleotide reductase from Hep G2 and Sf9 cells.     

Photoluminescence of 2-(2′-hydroxy-5′-methylbenzoyl)-1,5-diphenylpyrrole in aqueous and β-cyclodextrin environments: manifestation of open and closed conformers

Steady-state fluorometric studies have been performed on 2-(2′-hydroxy-5′-methylbenzoyl)-1,5-diphenylpyrrole (HMBDPP) in aqueous and aqueous β-cyclodextrin (β-CD) environments at ambient temperature. The fluorophore mostly shows a single emission in aqueous solution. Addition of β-CD to the aqueous solution of the fluorophore results in the development of another emission band at higher energy. The difference in the fluorometric behaviour is assigned to a remarkable change in the polarity of the microenvironment within the supramolecular structural environment compared to that of the bulk aqueous phase. Semi-empirical calculation (AM1-SCI) rules out the possibility of intramolecular proton transfer reaction in any of the S₀, S₁ and T₁ states of the fluorophore. It is proposed that HMBDPP exists mostly in the intermolecularly hydrogen-bonded form (open conformer) in aqueous solution while within β-CD environment, it is the intramolecularly hydrogen-bonded form (closed conformer) that predominates.     

Chiral separation of 1,1'-bi-2-naphthol and its analogue on molecular imprinting monolithic columns by HPLC

Two molecular imprinting polymer (MIP) monolithic columns with (S)-(-)-1,1'-bi-2-naphthol and (R)-(+)-5,5',6,6',7,7',8,8'-octahydro-1,1'-bi-2-naphthol as the templating molecules, respectively, have been prepared by in situ polymerization using 4-vinylpyridine and ethylene dimethacrylate as functional monomer and cross-linker, respectively. The columns with good flow-through properties were obtained by changing the molar ratio of the functional monomer and the template molecule. The effects of mobile-phase composition on separation of enantiomers were systematically investigated. The results indicate that hydrophobic interaction in aqueous solution and hydrogen-bonding interaction in ACN between the enantiomers and polymers could play important roles in the retention and resolution. The effects of chromatographic conditions, such as flow rate, column temperature, sample loading, on the enantioseparation were also studied. Further, these two MIP columns show a cross-reactivity.     

Preparative isolation of guaipyridine sesquiterpene alkaloid from Artemisia rupestris L. flowers using high-speed counter-current chromatography

Although the medicinal plant Artemisia rupestris L. has been widely researched for several decades, its alkaloids have never been isolated before. To our surprise, the alkaloids in the plant were not detected in the stems but detected in the flowers. Herein, a novel and strange guaipyridine sesquiterpene alkaloid with a carboxyl group named rupestine was purified successfully from the total alkaloids extracted from the flowers by high-speed counter-current chromatography (HSCCC). The two-phase solvent system used was composed of ethyl acetate-methanol-water (8:1:7, v/v/v). Fifty six milligrams of rupestine was obtained at over 97% purity and 95% recovery from 200 mg of the total alkaloids in one-step separation. Its structure was elucidated by spectroscopic methods including high resolution ESI-MS, (1)H NMR, (13)C NMR, Heteronuclear Multiple Bond Correlation (HMBC), Heteronuclear Single Quantum Coherence (HSQC), and Nuclear Overhauser Enhancement Spectroscopy (NOESY).     

Rapid determination of gemcitabine in plasma and serum using reversed-phase HPLC

Gemcitabine (2'2'-difluorodeoxycytidine) is a pyrimidine analog used in the treatment of a variety of solid tumors. After intravenous (i.v.) administration, it is rapidly inactivated to 2'-deoxy-2',2'-difluorouridine (dFdU). A sensitive analytical method for the quantitation of gemcitabine is required for the assessment of alternative dosage and treatment schemes. A rapid and robust RP-HPLC assay for analysis of gemcitabine in human and animal plasma and serum was developed and validated using 2'-deoxyuridine (dU) and 5-fluoro-2'-deoxyuridine (5FdU) as internal standards. It is based on protein precipitation, the use of an Atlantis dC18 column of 100 mm length (inner diameter, 4.6 mm; particle size, 3 microm) and isocratic elution using a 10 mM phosphate buffer, pH 3.0, followed by isocratic elution with the same buffer containing 3% of ACN. For gemcitabine, RSD values for intraday and interday precision were < 4.4 and 5.3%, respectively, the LOQ was 20 ng/mL, and the assay was linear in the range of 0.020-20 microg/mL with an accuracy of > or =89%. The recovery for gemcitabine, dU and 5FdU was 86-98%. The assay was applied to determine gemcitabine levels in plasma samples of patients collected during and shortly after conventional infusion of 25-30 mg/kg body mass (levels: 2.0-18.9 microg/mL) and rats that received lower doses (1.5 mg/kg) via i.v., subcutaneous and oral drug administration (levels: 0.20-2.60 microg/mL). It could also be applied to estimate dFdU levels in human plasma.     

两个新颖的联环十二烷衍生物的合成及结构表征

2-（2＇-Oxo-3＇-oximidocyclododecyl） cyclododecanone （1） and 2-（1＇-hydroxylcyclododecyl） cyclododecanone （2） were synthesized and characterized. The conformation analysis was carried out based on the NMR, molecular mechanics calculation and X-ray diffraction. The conformation of two cyclododecyl moieties of both 1 and 2 was found to be the [3333]-2-one or [3333] square conformation both in the crystal state and the solution. The dihedral angle between carbonyl and the oxime double bond of the ring B is 180°in the crystal of 1. The protons or hydroxyl group of carbon atoms to link the two cyclododecyl moieties of 1 and 2 constitute dihedral angles of 174°in the crystal, and 175°in the solution, and the C-C 6 bond between two cyclododecyl moieties can not freely rotate in the solid state and the solution. In addition, compound 2 was the first example of a-comer-anti-monosubstituted cyclododecanone. synthesis     

An ab initio theoretical study of electronic structure and properties of 2'-deoxyguanosine in gas phase and aqueous media

Molecular geometries of two structural forms of 2'-deoxyguanosine (keto-N9R and keto-N7R, R = the sugar moiety) considering both the C2'-endo and C3'-endo conformations of the sugar ring and those of the complexes of these species with two water molecules each were optimized employing the ab initio RHF procedure. A mixed basis set consisting of the 6-311+G* basis set for the nitrogen atom of the amino group and the 4-31G basis set for all the other atoms was used. The RHF calculations were followed by correlation correction of the total energy at the MP2 level. Both the structural forms of 2'-deoxyguanosine were solvated using the polarized continuum model (PCM) of the self-consistent reaction field (SCRF) theory and the corresponding RHF optimized geometries at the RHF and MP2 levels. Geometry optimization was also performed in aqueous media using the Onsager model at the RHF level using the above-mentioned mixed basis set, and subsequently, using the reoptimized geometries, single-point MP2 calculations were performed. It is found that both the keto-N9R and keto-N7R forms of 2'-deoxyguanosine as well as their complexes with two water molecules each would occur, particularly at the water-air interface. Though the normal Watson-Crick-type base pairing would not be possible with the keto-N7R form of 2'-deoxyguanosine(G*), two other (G*-C and G*-T) base pairing schemes may occur with this form of the nucleoside, which may cause mutation. The present calculated geometry of the keto-N9R form of the anti-conformation of 2'-deoxyguanosine including the dihedral angle chi(CN) agree satisfactorily with the available crystallographic results. The present results also agree satisfactorily with those obtained by other authors earlier for the keto-N9R form of 2'-deoxyguanosine using B3LYP and MP2 methods employing the 6-31G* basis set. Using transition state calculations, it is shown that tautomerism of guanine and other similar molecules where the tautomers would coexist would be facilitated by the occurrence of the H(+) and OH(-) fragments of water molecules. Further, this coexistence of the two tautomers appears to make the C8 carbon atom located between the N7 and N9 nitrogen atoms susceptible to attack by the OH(-) group. Thus, an explanation is obtained for the efficient formation of the reaction product 8-hydroxy-2'-deoxyguanosine, which serves as a biomarker for oxidative damage to DNA in biological systems.     

Analysis of dideoxyadenosine triphosphate by CE with fluorescence detection. I. Derivatization through the phosphate group

A CZE method was developed, which separates 2',3'-dideoxyadenosine-5'-triphosphate (ddATP) from other metabolites and endogenous nucleotides at high concentrations (20-200 microg/mL) to allow UV detection. To enhance sensitivity, fluorescence detection which requires prior derivatization of compounds was examined. Precapillary derivatization of ddATP in the presence of N-(3-dimethylaminopropyl)-N'-ethylcarbodiimide hydrochloride (EDAC) with dansyl ethylenediamine (dansyl EDA) was faster and stable compared to that of 4,4-difluoro-5,7-dimethyl-4-bora-3a,4a-diaza-s-indacene-3-propionyl ethylenediamine (BODIPY FL EDA). Reaction conditions, reagent concentrations and detection parameters were optimized and highest derivatization efficiency was achieved in 0.1 M 1-methylimidazole buffer (pH 8.0) with 140 mM EDAC in 1-methylimidazole buffer and 30 mM dansyl EDA in DMF for 90 min at 60 degrees C. Dansyl EDA derivatives of ddATP, 2'-deoxyadenosine-5'-triphosphate (dATP) and ATP were comigrating with the CZE method; therefore, a MEKC method was developed and optimized for repeatable separations. Upon dansylation, sensitivity of ddATP with fluorescence detection (LOQ = 12 ng/mL) was 160 times higher than UV detection (LOQ = 1.9 microg/mL).     

首次合成来源于鼠李属植物中的两个新颖的蒽环鼠李糖苷，2’, 3’-Di-O-acetylfrangulin A 和 Prinoidin

首次全合成来源于鼠李属植物中的两个天然产物2’, 3’-di-O-acetylfrangulin A (1) 和 prinoidin (2),它们对KB细胞表现出较好的细胞毒活性。通过1H NMR, 13C NMR, 1H-1H COSY, HMQC 和 HMBC确证了两个化合物的结构。     

Quantification of polyamines in human erythrocytes using a new near-infrared cyanine 1-(epsilon-succinimidyl-hexanoate)-1'-methyl-3,3,3',3'-tetramethyl-indocarbocyanine-5,5'-disulfonate potassium with CE-LIF detection

A novel near-infrared (NIR) cyanine 1-(epsilon-succinimidyl-hexanoate)-1'-methyl-3,3,3',3'-tetramethyl-indocarbocyanine-5,5'-disulfonate potassium (MeCy5-OSu) has been developed in our laboratory. Simultaneous determination of MeCy5-OSu-derivatized polyamines spermine (Spm), spermidine (Spd), cadaverine (Cad), and putrescine (Put) based on the separation by CE combined with diode LIF detection has been accomplished. The highest derivatization efficiency was achieved in 0.2 mol/L borate buffer (pH 8.8) for 20 min at 25 degrees C. Polyamine derivatives were separated within 14 min in the phosphate running buffer (pH 3) containing 50 mmol/L phosphoric acid, 40 mmol/L SDS, and 35% methanol v/v. Linearity of response was obtained in the range of 10-200 nmol/L. The detection limits (S/N = 3) for Spm, Spd, Cad, and Put were 0.8, 1, 3, and 2 nmol/L, respectively. The proposed method has been successfully applied to the analysis of polyamines in erythrocytes of two healthy persons and one cancer patient. Average recoveries for erythrocyte samples were 93.6-106% and coefficients of variation ranged from 1.8 to 5.4%. The analysis of polyamines in erythrocytes can be used for studying the relationship between their changes and the carcinogenesis process involved in erythrocytes.     

Use of Adsorptive Transfer Stripping Voltammetry for Analyzing Variations of Cytosine Methylation in DNA

The electrochemical behavior and thermal stability of double stranded oligonucleotides containing 5‐methyl‐cytosine and 7‐deaza‐guanosine as nucleotide analogues, as well as of Jurkat genomic DNAs methylated to different degree were studied by ACV and SWV and by thernal denaturation analysis. ACV and SWV combined with thermal denaturation analysis of the natural and modified oligonucleotides gave information regarding the presence of methylation and the concomitant conformational changes. ACV and SWV of Jurkat DNA mixtures methylated to different degrees revealed a decrease of the peak heights with increasing methylation, indicating an increase of structural rigidity, in agreement with the thermal denaturation data. These results verify the, possibly local, conformational changes introduced by DNA methylation. The results obtained in all cases were reproducible.     

Synthesis of (+) or (-)-2-(8′-Diphenylphosphino-1′-naphthyl)oxazoline Ligands and Their Application in Pd-Catalyzed Allylic Alkylation Reaction

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Quantification of oxyresveratrol analog trans-2,4,3',5'-tetramethoxystilbene in rat plasma by a rapid HPLC method: application in a pre-clinical pharmacokinetic study

A rapid HPLC method was developed and validated for the quantification of oxyresveratrol analog trans‐2,4,3′,5′‐tetramethoxystilbene (oxyresveratrol tetramethyl ether, OTE) in rat plasma. Chromatographic separation was achieved on an RP‐HPLC column, which was protected by a guard column through a 12 min gradient delivery of a mixture of acetonitrile–water at 50°C. The UV absorbance at 325 nm was recorded. The retention time of OTE and trans‐stilbene (internal standard) was about 7.7 and 8.4 min, respectively. The calibration curves were linear (R² ≥ 0.9986) with a lower limit of quantification of 15 ng/mL. The intra‐ and inter‐day variations, in terms of RSD, were all lower than 9.8% while the intra‐day and inter‐day bias ranged from ?8.3 to +9.2%. The pharmacokinetics of OTE was assessed in rats using 2‐hydroxypropyl‐β‐cyclodextrin as a dosing vehicle. After intravenous administration, OTE possessed a long terminal elimination half‐life (t_{1/2 λz} = 481 ± 137 min) and slow clearance (Cl = 29.1 ± 3.7 mL/min/kg). Upon oral administration, OTE was rapidly absorbed. However, it only displayed minimal plasma exposure and its absolute oral bioavailability (F) was as low as 4.5 ± 3.2%. Fortunately, the levels of OTE after single oral administration were sufficient to inhibit human cytochrome P450 1B1. Copyright © 2010 John Wiley & Sons, Ltd.     

An Efficient and Economical Method for the Preparation of Fmoc-Argω,ω'(Boc)2-OH

The arginine derivative Fmoc‐Arg^ω,ω′(Boc)₂‐OH has been prepared in perfect yield starting from Fmoc‐Orn·HCl and N,N′‐di‐Boc‐N′′‐triflyguanidine with the presence of diisopropylethylamine (DIEA). This work provides an efficient and economical method for the preparation of this compound.     

Synthesis of Dinaphtho-dioxaphosphepin-4-oxides, Epoxides and Bisphosphonates

A few new seven-membered phosphorus heterocyclic compounds and bis-phosphonates (5a—5g, 5f’, 5g’, 9 and 10) were prepared by the reaction of 4-bromo dioxaphosphepin (2) with various Grignard reagents followed by their oxidation with H2O2. All the compounds were thoroughly characterized by elemental analysis, IR, 1H, 13C, 31P NMR and mass spectral data. Their antimicrobial activity was evaluated and some of them possess significant activity.     

Optical Rotatory Feature of （R or S）—1,1’—Binaphthalene—2,2’—diol（BINOL）in various Solvents

The changes of the specific rotation and sign of optically active BINOL have been studied in polar/non-polar solvents and at the different pH values of solvent.It is considered that these changes are determined by the equilibriurn studies between cisoid and transoid conformations of BINOL with the same configuration(R or S) which related to the change of the dihedral angle between two naphthalene ring planes of BINOL.     

Identification and determination of major flavonoids in rat urine by HPLC-UV and HPLC-MS methods following oral administration of Dalbergia odorifera extract

Flavonoids are the main active constituents of Dalbergia odorifera. The excretion of the major flavonoids in rat urine after oral administration of D. odorifera extract was investigated by HPLC-UV and HPLC-MS methods. Utilizing the HPLC-MS technique, 18 flavonoids, including five isoflavones, four isoflavanones, four neoflavones, two flavanones, two chalcones and one isoflavanonol were identified in free form in a urine sample based on the direct comparison of the corresponding tR, UV maximum absorbance (lambda(max)) values and MS data with the authentic standards. The amounts of the prominent flavonoids, (3R)-4'-methoxy-2',3,7-trihydroxyisoflavanone and vestitone, were determined by HPLC-UV with the internal standard method, and the validation procedure confirmed that it afforded reliable analysis of these two analytes in urine after oral administration of D. odorifera extract.