Antibacterial 5′-O-(N-dipeptidyl)-sulfamoyladenosines

The aminoacyl-tRNA synthetase (aaRS) class of enzymes is a validated target for antimicrobial development. Aminoacyl analogues of 5′-O-(N-l-aminoacyl)-sulfamoyladenosines are known to be potent inhibitors of aaRS, but whole cell antibacterial activity of these compounds is very limited, and poor penetration into bacteria has been proposed as the main reason for this. Aiming to find derivatives that better penetrate bacteria, we developed a simple and short method to prepare dipeptidyl-derivatives of 5′-O-(N-l-aminoacyl)-sulfamoyladenosines, and used this method to prepare 18 5′-O-(N-dipeptidyl)-sulfamoyladenosines. The antibacterial activity of these derivatives and a number of reference compounds against S. aureus, E. faecalis and E. coli was determined. Several of the new derivatives showed improved antibacterial activity and an altered spectrum of antibacterial activity.     

Synthesis and Biological Effects of 5′-Deoxy-5′-(Cyclo-Propylmethylthio)Adenosine

Abstract

A novel synthesis of the nucleoside analog, 5′-deoxy-5′-(cyclopropylmethylthio)adenosine (CPMTA, 1) has been developed. CPMTA is a closely related structural analog of 5′-deoxy-5′-(isobutylthio)-adenosine (SIBA, 2), which has been widely studied and shown to exert a multitude of biological effects. The in vitro and in vivo antitumor (L1210 leukemia) activity of CPMTA has been found to be comparable to that of SIBA, whereas its in vitro antiviral (HSV and VSV) activity is diminished. These agents are being developed as inhibitors of methylation and/or polyamine synthesis.     

Cobalt-requiring 5′-deoxy-5′-methylthioadenosine nucleosidase from soybean (Glycine max) cotyledon

5??-Deoxy-5??-methylthioadenosine nucleosidase (MTA nucleosidase, EC 3.2.2.9) was purified from soybean (Glycine max) cotyledon. The nucleosidase was a trimer consisting of three identical subunits with a molecular mass of 59.5?kDa. The nucleosidase was a cobalt-requiring enzyme for its catalytic function. The enzymatic activity increased in a dose-dependent manner in the presence of cobalt. Cobalt was bound to the nucleosidase with a stoichiometry of 1 equivalent of cobalt/subunit. A thiol group-specific reagent reduced the enzymatic activity. Four cysteinyl residues of each subunit are considered to play an important role in binding cobalt.     

Acycloadenosine Derivatives as Inhibitors of 5′-Deoxy-5′-Methylthioadenosine Phosphorylase (MesADo PASE)

Abstract

Four classes of acyclo amlogs of 5′-methylthioadenosine were synthesized and tested as inhibitors of mammalian methylthicadenosine phosphorylase. Halogenated dihydroxypropyl acycloadenosires were most potent, i.e. K_i = 0.2 - 0.7 uM.     

癌变过程中酪氨酸转氨酶(TAT)和5′-核苷磷酸二酯酶(5′-NPDase)的变化

本文测定了大鼠及人体胚胎发育和癌变过程中TAT和5′-NPDase活力变化,所得结果表明: (一)5′-NPDase快速同工酶区带在甲胎蛋白(AFP)阴性肝癌患者血清中阳性率较高。(二)TAT,5′-NPDase和AFP也许可作为研究癌、胚以及肝癌癌变过程中基因表达的三个互补生化指标。     

The 5′-Nor Aristeromycin Analogues of 5′-Deoxy-5′-Methylthioadenosine and 5′-Deoxy-5′-Thiophenyladenosine

To extend the potential of 5′-noraristeromycin (and its enantiomer) as potential antiviral candidates, the enantiomers of the carbocyclic 5′-nor derivatives of 5′-methylthio-5′-deoxyadenosine and 5′-phenylthio-5′-deoxyadenosine have been synthesized and evaluated. None of the compounds showed meaningful antiviral activity.     

(5′R)-and (5′S)-purine 5′,8-cyclo-2′-deoxyribonucleosides: reality or artifactual measurements? A reply to Chatgilialoglu’s comments (this issue)

Abstract

This rebuttal letter is aimed at refuting the poor and false arguments elaborated by Chatgilialoglu (preceding article) in his response to the position article (Cadet et al. Free Radic Res 2019;53:574–577) that focussed on the putative reliability of the HPLC-MS/MS measurements of five radiation-induced damage to cellular DNA, which included 8-oxo-7,8-dihydro-2'-deoxyadenosine and the (5′R) and (5′S) diastereomers of 5′,8-cyclo-2′-deoxyadenosine and 5′,8-cyclo-2′-deoxyadenosine (Krokidis et al. Free Radic Res 2017;51:470–482). Unfortunately, none of the main issues we raised on the suitability of the analytical approach and the shortcomings associated with DNA extraction in HPLC based measurement methods of oxidatively generated damage in cells were properly considered in Chatigilialolu’s letter. The main questionable issues include the lack of information on the sensitivity of HPLC-MS/MS analysis, the absence of a dose curve that is essential in the formation of damage and the nonconsideration of artifactual oxidation.     

Radiation chemical studies of sensitization by 5-bromouridine-5′-monophosphate (5-BrUMP)

Summary This study was undertaken to investigate the mechanism of chemical radiosensitization by halogenated bases incorporated into DNA. Radiation-induced base and sugar-phosphate backbone damage to 5-bromouridine-5-monophosphate (5-BrUMP) was monitored using a flow system connected in series with a recording spectrophotometer, a bromide (Br^–)-specific ion analyzer and a Technicon auto-sampler. The system was used to assay loss of UV-absorbing 5,6 double-bond, release of Br^– and inorganic phosphate (Pi) release using an automated colorimetric method, as a function of gamma-ray dose. Results obtained with radical scavengers indicate that, unlike non-halogenated nucleotides where the hydroxyl radical (· OH) is the principal damaging species, 5-BrUMP is damaged by the hydrated electron (e _aq ^– ), hydrogen atom (H·) and · OH, producing a high yield of base damage and Br^– and Pi release in anoxia. Another novel feature of 5-BrUMP radiolysis is that oxygen, by convertinge _aq ^– and H· to the unreactive superoxide radical anion (0 ₂ ^– ), has a protective effect on both base and phosphate ester damage. Under · OH-scavenging conditions, where the radiation yield of reductive debromination is 3.8, there is some Pi release, suggesting the possibility of intramolecular hydrogen atom transfer from the sugar ring to the 5-uracilyl radical and subsequent sugar-phosphate bond cleavage. This hypothesis is supported by the action of oxygen and thiols in modifying thee _aq ^– -mediated sugar-phosphate damage.     

Oligomerization of 3′-amino-3′-deoxyguanosine-5′-phosphorimidazolidate on a d(CpCpCpCpC) template

Summary 3-Amino-3-deoxyguanosine-5-phosphorimidazolidate (ImpGnh ₂) oligomerizes more rapidly and regiospecifically than related nucleotide derivatives on a d(CpCpCpCpC) template. The greater nucleophilicity of the amino group leads to efficient oligomerization even when the structure of the double-helical complex formed by the template and the substrate is not optimal for reaction. The use of amine-containing analogues should permit us to develop models of potentially prebiotic polymerization reactions that cannot be studied easily using natural nucleotides.     

利用~1H-NMR模拟谱研究三核苷酸A3′P(CH_3)5′A3′P(CH_3)5′A的构象性质

根据Altona等人的方法.利用~1H—NMR模拟谱分析了A3′P(CH_3)5A3′P(CH_3)5′A的三种非对映异构体:a、b和C的构象状态.发现:在室温下三个核糖环都是S型构象占优势(X_N≤0.44),而且随温度升高S型构象成分增多;两个二核苷酸片段-PAPA和APAP-的磷酸骨架扭角分别与A3′P(CH_3)5′A两种异构体a或b数值接近.差值约5°左右;二核苷酸片段中核糖环的重叠程度与手性磷原子的构型有关、R构型比S构型的核糖环重叠程度小;从而推测,A3′P(CH_3)5′A3′P(CH_3)5′A各种非对映异构体的稳定性为RR>RS.SR>SS,与化学合成中所见相符合.     

DNA5′端~(32)P标记方法

在DNA的结构与功能研究中,其5′端~(32)P标记是常用的有效技术。下面我们从《Methods in Enzymolgy》Vol 65中摘译了DNA 5′端脱磷及~(32)P标记方法,供大家参考。1.用磷酸单酯酶除去DNA链5′末端磷     

Phosphonoformate Esters of Anti-HIV Nucleosides: 3′-Azido-3′-deoxythymidine and 2′,3′-Dideoxycytidine Derivatives Containing a Small 5′-(0-Alkoxycarbon-ylphosphinyl) or 5′-(O-Cholesterylcarbonylphosphinyl) Substituent

Abstract

A convenient general method of synthesis of 5′-O-(alkoxycarbonyl)phosphonate esters of 2′,3′-dideoxyribonucleosides is presented, using the 5′-O-(methoxycarbonyl)phosphinyl, 5′-0-(ethoxycarbonyl)phosphinyl, and 5′-O-(cholesterylcarbonyl)phosphinyl derivatives of 3′-azido-3′-deoxythymidine (AZT) and the 5′-0-(ethoxycarbonyl)phosphinyl derivative of 2′,3′-dideoxycytidine (ddC) as examples. Reaction of trimethyl phosphonoformate, methyl phosphonoformate, or dimethyl cholesterylcarbonylphosphonate with phosphorus pentachloride in carbon tetrachloride, followed by direct condensation of the resulting phosphonyl chloride with the nucleoside, gave the fully esterified phosphonoformate derivatives, which on treatment with sodium iodide in tetrahydrofuran underwent selective cleavage of the P-OMe or P-OEt groups, leaving the carboxylate esters intact. The resulting products were converted from sodium salts to ammonium salts by ion-exchange chromatography.     

5′-O-Dephosphorylated 2′,5′-oligoadenylate (2-5A) with 8-methyladenosine at the 2′-terminus activates human RNase L

Human ribonuclease L (RNase L), an interferon-induced endoribonuclease, becomes enzymatically active after binding to 2-5A. The 5′-phosphoryl group of 2-5A is reportedly necessary for the conformational change leading to RNase L activation. However, we found that 5′-O-dephosphorylated 2-5A tetramer analogs with 8-methyladenosine at the 2′-terminus were more effective as an activator of RNase L than the parent 2-5A tetramer. Introduction of 8-methyladenosine is thought to induce a dramatic shift of 2-5A in the binding site of RNase L.     

Trifurcated (Four-Center) Hydrogen Bond in Solid State Crystal Structure of 5′-Amino-5′-deoxyadenosine p-Toluenesulfonate

Abstract

The crystal structure of 5′-amino-5′-deoxyadenosine (5′-Am.dA) p-toluenesulfonate has been determined by X-ray crystallographic methods. It belongs to the orthorhombic space group P2₁2₁2₁ with a=7.754(3)Å, b=8.065(l)Å and c=32.481(2)Å. This nucleoside shows a syn conformation about the glycosyl bond and C2′-endo-C3′-exo puckering for the ribose sugar. The orientation of N5′ atom is gauche-trans about the exocyclic C4′-C5′ bond. The amino nitrogen N5′ forms a trifurcated hydrogen bond with N3, O9T and 04′ atoms. Adenine bases form A.A.A triplets through hydrogen bonding between N6, N7 and N1 atoms of symmetry related nucleoside molecules.     

阴离子交换树脂分离制备腺嘌呤核糖核苷(3′，5′-)环磷酸(cAMP)

腺嘌呤核苷3′,5′-环磷酸对癌细胞在特定条件下有抑制作用,对冠心病和牛皮癣等有缓解作用,临床上已证明。本文所介绍的合成、分离、纯化、鉴定等方法,简易而又可靠,比目前国外报道的方法有很大改进,特别是采用国产离子交换树脂,分离简便、容量大、效果好,为大量生产创造了有利条件。——编者     

The influence of CpG (5′-d(CpG)-3′ dinucleotides) methylation on ultrasonic DNA fragmentation

Abstract

DNA methylation is an important way of gene regulation. The variety of methods for DNA methylation analysis based on chemical modification or enzyme digestion has been proposed. However, DNA is able to undergo transformations under physical power. Here, we report that the cytosine methylation in CpG dinucleotides determines the difference in fragmentation rate of methylated and unmethylated DNA under sonication. We found that at the beginning of sonication, methylated DNAs are degraded faster than unmethylated one, and the difference in fragmentation degree can be evaluated with high reliability by quantitative polymerase chain reaction (qPCR). The optimal parameters that provide the greatest difference in amount of amplifiable DNA targets corresponding to fragmentation degree are the following: moderate amplicon size (about 150–250?bp), medium CpG sparseness (one CpG dinucleotide per ～12–14 nucleotides of the chain), and short sonication time (less than 5?min). Along with CpG, the CpA and CpT contents of amplified regions should be taken into account for proper DNA fragmentation by ultrasound as well. The obtained data could be used for elaboration of a method for comparative methylation testing, when there is no need to detect methylation of certain CpG dinucleotides. This method will be simple (can be used by any technician familiar with PCR), low cost (no need to use an expensive reagents), and fast (only brief DNA sonication and conventional qPCR are carried out).

Communicated by Ramaswamy H. Sarma     

The Synthesis of Some 5-Alkyl (Cycloalkyl)-Substituted 2′ -Deoxy-4′-Thiouridines

Abstract

The silylated pyrimidine bases IIa-d were condensed with the benzyl 3,5-di-O-benzyl-2-deoxy-1,4-dithio-d-erythro-pentofuranoside III in acetonitrile under activation by N-iodosuccinimide, giving ca 1.5: 1/α: β anomeric mixtures of the blocked nucleosides IVa-d and Va-d. in yields of 55–58%. After the separation on a silica column the pure anomers were deprotected by BCI₃ or TiCI₄, providing the free nucleosides VIa-d and VIIa,c,d in moderate to good overall yields. The β- or α-anomeric configuration, anti-glycosidic conformation and prevailing C2′endo(S) thiosugar pucker in the synthesized compounds were established by the combined use of the ¹H, ¹³C NMR and X-ray crystallography.

     

Syntheses,properties, and use of fluorescent N-(5′-phospho-4′-pyridoxyl)amines in assay of pyridoxamine (pyridoxine) 5′-phosphate oxidase

A sensitive and simple fluorometric assay has been developed for detection of pyridoxamine (pyridoxine) 5′-phosphate oxidase. This technique utilizes fluorescent N-(5′-phospho-4′-pyridoxyl)amines as substrates that, upon incubation with the oxidase, release the free fluorescent amine. The substrates were prepared by condensation of pyridoxal 5′-phosphate with fluorescent amines and subsequent hydrogenation of the Schiff bases. Since N-(1-naphthyl)ethylenediamine is 15 times less fluorescent in the intramolecularly quenched substrate than the product amine, the direct increase of fluorescence, as well as selective extraction of more fluorescent product, can be utilized for assay. The apparent K_m value for this substrate is 8 μm, which is slightly less than that of pyridoxamine 5′-phosphate; V is larger than the natural substrate value. The greater sensitivity gained by this fluorimetric method allows detection of the oxidase in smaller quantities than can be determined by the conventional colorimetric assay.