Mineral Supported Facile Synthesis of Novel 4-Hydroxybenzoxazin-2-Thione N-Nucleosides

One-pot montmorillonite K-10 clay-supported reactions of substituted/unsubstituted salicylaldehyde and ribosyl/deoxyribosyl thioureas expeditiously yielded novel N-nucleosides, 4-hydroxy-3,4-dihydro-3-(β-D-ribofuranosyl or β-D-2 ′-deoxyribofuranosyl)-2 ^″-benz[e]-1,3-oxazin-2-thione via cycloisomerization of aldehyde intermediate under solvent-free microwave irradiation conditions.     

Artificially expanded genetic information system: a new base pair with an alternative hydrogen bonding pattern

To support efforts to develop a ‘synthetic biology’ based on an artificially expanded genetic information system (AEGIS), we have developed a route to two components of a non-standard nucleobase pair, the pyrimidine analog 6-amino-5-nitro-3-(1′-β-D-2′-deoxyribofuranosyl)-2(1H)-pyridone (dZ) and its Watson–Crick complement, the purine analog 2-amino-8-(1′-β-D-2′-deoxyribofuranosyl)-imidazo[1,2-a]-1,3,5-triazin-4(8H)-one (dP). These implement the pyDDA:puAAD hydrogen bonding pattern (where ‘py’ indicates a pyrimidine analog and ‘pu’ indicates a purine analog, while A and D indicate the hydrogen bonding patterns of acceptor and donor groups presented to the complementary nucleobases, from the major to the minor groove). Also described is the synthesis of the triphosphates and protected phosphoramidites of these two nucleosides. We also describe the use of the protected phosphoramidites to synthesize DNA oligonucleotides containing these AEGIS components, verify the absence of epimerization of dZ in those oligonucleotides, and report some hybridization properties of the dZ:dP nucleobase pair, which is rather strong, and the ability of each to effectively discriminate against mismatches in short duplex DNA.     

Synthesis of fluorescent nucleoside analogs as probes for 2′-deoxyribonucleoside kinases

We are reporting on the synthesis of fluorescent nucleoside analogs with modified sugar moieties (e.g., sugars other than ribose and 2′-deoxyribose). Four novel derivatives of the fluorescent thymidine analog 6-methyl-3-(β-D-2′-deoxyribofuranosyl) furano-[2,3-d]pyrimidin-2-one were synthesized via Sonogashira reaction and subsequent copper-catalyzed cycloaddition. These compounds represent promising tools for studying nucleoside metabolism inside living cells, as well as for screening directed evolution libraries of 2′-deoxyribonucleoside kinases with new and improved activity for the corresponding nucleoside analogs.     

NOVEL NUCLEOSIDE TRIPHOSPHATE ANALOGS FOR THE ENZYMATIC LABELING OF NUCLEIC ACIDS

We have evaluated several novel nucleotide analogs suitable for enzymatic labeling of nucleic acid targets for a variety of array-based assays. Two new reagents in particular, a C4-labeled 1-(2′,3′-dideoxy-β-D-ribofuranosyl) imid- azole-4-carboxamide 5′-triphosphate 5 and an N1-labeled 5-(β-D- ribofuranosyl)-2,4(1H,3H)-pyrimidinedione 5′-triphosphate 3, were found to be excellent substrates for labeling with terminal deoxynucleotidyl transferase and T7 RNA polymerase, respectively.     

Recognition of an expanded genetic alphabet by type-II restriction endonucleases and their application to analyze polymerase fidelity

To explore the possibility of using restriction enzymes in a synthetic biology based on artificially expanded genetic information systems (AEGIS), 24 type-II restriction endonucleases (REases) were challenged to digest DNA duplexes containing recognition sites where individual Cs and Gs were replaced by the AEGIS nucleotides Z and P [respectively, 6-amino-5-nitro-3-(1'-β-D-2'-deoxyribofuranosyl)-2(1H)-pyridone and 2-amino-8-(1'-β-D-2'-deoxyribofuranosyl)-imidazo[1,2-a]-1,3,5-triazin-4(8H)-one]. These AEGIS nucleotides implement complementary hydrogen bond donor-donor-acceptor and acceptor-acceptor-donor patterns. Results allowed us to classify type-II REases into five groups based on their performance, and to infer some specifics of their interactions with functional groups in the major and minor grooves of the target DNA. For three enzymes among these 24 where crystal structures are available (BcnI, EcoO109I and NotI), these interactions were modeled. Further, we applied a type-II REase to quantitate the fidelity polymerases challenged to maintain in a DNA duplex C:G, T:A and Z:P pairs through repetitive PCR cycles. This work thus adds tools that are able to manipulate this expanded genetic alphabet in vitro, provides some structural insights into the working of restriction enzymes, and offers some preliminary data needed to take the next step in synthetic biology to use an artificial genetic system inside of living bacterial cells.     

A facile synthesis of nucleoside derivatives of 1,4-oxathiane

Adenosine-5′-carboxaldehyde (1a) was treated with nitromethane under alkaline conditions, to give the two stereoisomeric 5′-C-(nitromethyl) derivatives (2 and 3) of adenosine. Catalytic hydrogenation of 2 gave 9-(6-amino-6-deoxy-β-D-allofuranosyl)adenine (4), which, on treatment with nitrous acid, yielded 9-(β-D-allofuranosyl)hypoxanthine (6). Similar treatment of 3 gave the α-L-talo nucleosides 5 and 7. Reaction of 2′,3′-O-p-anisylidene adenosine-5′-carboxaldehyde (1b) with ethoxycarbonylmethylene-triphenylphosphorane afforded 9-(ethyl 5,6-dideoxy-β-D- ribo-hept-5-enofuranosyluronate)adenine (8), which was hydrolyzed to the corresponding uronic acid (9). Catalytic hydrogenation of 8 gave 9-(ethyl 5,6-dideoxy-β-D-ribo-heptofuranosyluronate)adenine (10). Reduction of 8 with lithium aluminum hydride yielded two new analogs of adenosine: 9-(5,6-dideoxy-β-D-ribo-heptofuranosyl)adenine (12) and 9-(5,6-dideoxy-β-D-ribo-hept-5-enofuranosyl)adenine (13).     

Structures of verbascoside and orobanchoside,caffeic acid sugar esters from Orobanche rapum-genistae

The complete structural elucidation of the two caffeic acid sugar esters verbascoside and orobanchoside, has been realized by ¹H and ¹³C NMR studies. It has been demonstrated that verbascoside is β-(3′,4′-dihydroxyphenyl)ethyl-O-α-L-rhamnopyranosyl(1→3)-β-D-(4-O-caffeoyl)-glucopyranoside, and orobanchoside is β-hydroxy-β-(3′,4′-dihydroxyphenyl)-ethyl-O-α-L-rhamnopyranosyl(1→2)-β-D-(4-O-caffeoyl)-glucopyranoside.     

Nucleosides. IL. Synthesis and Properties of 2,4-Quinazolinedione N-1-2′ Deoxy-, 3′-Deoxy- and 2′,3′-Dideoxynucleosides

Abstract

A series of 6- and/or 7-substituted 2,4-quinazoline-dione N-1-deoxyribofuranosides have been synthesized and characterized. The 2′-deoxy-β-D-ribofuranosides 23–28 have been prepared by transformation of the corresponding ribofuranosides by chemical deoxygenation. Direct glycosidation to the β-anomers with a 2′-deoxyribofuranosyl donor to pure anomers failed due to missing diastereoselectivity and difficult separation of the reaction products. The synthesis of the 3′-deoxy-β-D-ribofuranosides 54–58, however, was achieved by glycosidation of the trimethylsilylated 2,4-quinazolinediones 43–47 with an appropriate 3′-deoxyribofuranosyl donor (48). The 2′,3′-dideoxy-β-D-ribofuranosyl derivatives 63–66 were again obtained by chemical deoxygenation of the corresponding 2′-deoxy-β-D-nucleosides, since all experiments of direct glycosidation with a 2′,3′-dideoxyribofuranosyl donor as well as the chemical conversion of the corresponding ribonucleosides into the 2′,3′-dideoxynucleosides failed due to side reactions. The newly synthesized compounds have been identified by UV and ¹H-NMR spectra as well as elemental analyses.     

Nucleosides 137. Synthetic Modifications at the 2′Position of Pyrrolo[3,2-D]Pyrimidine and Thieno[3,2-D]Pyrimidine C-Nucleosides,Synthesis of “2′-Deoxy-9-Deazzadenosine” and of “9-Deaza ARA-A”

Abstract

The syntheses and preliminary biological evaluation of several novel pyrrolo[3,2-d]pyrimidine and thieno[3,2-d]pyrimidine C-nucleosides incorporating the arabinofuranosyl or 2′-deoxyribofuranosyl sugar moiety are described. The 2′-deoxy thieno[3,2-d]pyrimidine C-nucleosides (15 and 16) were obtained from 7-(β-D-ribofuranosyl)-4-oxo-3H-thieno[3,2-d]pyrimidine (3) and its 4-SMe derivative 8. “2”-Deoxy-9-deazaadenosine (31), “9-Deaza ara-A” (38) and the 2′-substituted arabinosyl pyrrolo[3,2-d]pyrimidine C-nucleosides (42 - 44) were synthesized from 4-amino-7-(2,3-O-isopropylidene-5-O-trityl-β-D-ribofuranosyl)-5H-pyrrolo[3,2-d]pyrimidine (21)     

南海柳珊瑚鳞海底柏化学成分的研究

本文对南海柳珊瑚鳞海底柏Melitodes squarnata Nutting进行了化学成分的研究.通过用工业乙醇:二氯甲烷(2∶1)进行了提取,采用硅胶柱色谱、Sephadex LH-20凝胶色谱、高效液相半制备色谱和薄层制备等方法对鳞海底柏的化学成分进行了分离,并利用波谱分析技术和文献对照鉴定其结构.从鳞海底柏中分离得到了17个化合物,分别鉴定为:malonganenone E(1),malonganenone D(2),nuttingin A(3),腺嘌呤核苷(4),1,3,7-三甲基黄嘌呤(5),2'-脱氧胸腺嘧啶核苷(6),3-甲基-6-次黄嘌呤(7),2'-脱氧尿苷(8),(22E,24R)-ergosta-8 (14),22-dien-3β,5α,6β,7α-tetrol(9),(22E)-胆甾-5,22-二烯-3β-醇(10),胆甾醇(11),(2S,3S,4R)-N-hexadecanoyl-2-amino-1,3,4-eicosanetriol( 12),(2S,2'R,3R,4E,8E)-N-2'- Hydroxytetradecanoyl-2-amino-9-methyl-4,8-octadecaa-diene-1,3-diol(13),鲨肝醇(14),十六烷基甘油醚(15),三油酸甘油酯(16)和4-hydroxy-2,3-dimetlhy1-2-nonen-4-olide(17).     

牛心朴子须根的化学成分研究

从采自宁夏的萝摩科鹅绒藤属植物牛心朴子 (CynanchumkomaroviiAl.Iljinski.)须根的乙醇提取物中分离鉴定了十个非C2 1 甾体类化合物 :β D 呋喃果糖基 (2→ 1) α D [6 O 芥子酰基 ] 吡喃葡萄糖甙 (1) ,β D (3 O 芥子酰基 ) 呋喃果糖基 (2→ 1) α D [6 O 芥子酰基 ] 吡喃葡萄糖甙 (2 ) ,[6 O β D 吡喃葡萄糖基 (1→ 6 ) β D 吡喃葡萄糖基 1,2 双氧 (4 羟基 3,5 二甲氧基肉桂酰 ) (3) ,7 脱甲氧基娃儿藤碱 (4) ,9 羟基 芳樟醇 3 O β D 吡喃木糖基 (1→ 6 ) β D 吡喃葡萄糖甙 (5 ) ,(2E ,6R) 2 ,6 二甲基 2 ,7 辛二烯 1,6 二醇 (6 ) ,[(+) 丁香素 ](7) ,4′ O demethylepiyangambin(8) ,4′ 羟基 2′ 甲氧基苯乙酮 (9) ,(2S ,3S ,4R ,12E) N [2′ (R) 羟基二十二碳烷基 ] 1,3,4 三羟基 2 酰胺 二十碳烷基 12 烯 (10 )。除化合物 4和 9外 ,其余化合物均为首次从该植物中分离得到。     

Pteridine Nucleosides—New Versatile Building Blocks in Oligonucleotide Synthesis

Abstract

Chemical syntheses of 1-(2-deoxy-β-D-ribofuranosyl)lumazines and isopterins as well as 8-(2-deoxy-β-D-ribofuranosyl)-4-amino-7(8H)pteridones and -isoxanthopterins have been developed to make the structural analogs of the naturally occurring 2′-deoxyribonucleosides in the pteridine series available. The corresponding phosphoramidites have been used in machine-aided solid-support syntheses leading to new types of fluorescence labeled oligonucleotides. The effects of the various fluorophors on duplex formation and as labels for enzyme reactions is demonstrated.     

Further probing of the substrate specificities and inhibition of enzymes involved at an early stage of glycosylphosphatidylinositol (GPI) biosynthesis

1-D-6-O-(2-amino-2-deoxy-alpha-D-glucopyranosyl)-1-O-hexadecyl-myo-inositol (14), 1-D-6-O-(2-amino-2-deoxy-alpha-D-glucopyranosyl)-myo-inositol 1-(octadecyl phosphate) (18), 1-D-6-O-(2-amino-2-deoxy-beta-D-glucopyranosyl)-myo-inositol 1-(1,2-di-O-hexadecanoyl-sn-glycerol 3-phosphate) (24), 1-D-6-O-(2-amino-2-deoxy-alpha-D-mannopyranosyl)-myo-inositol 1-(1,2-di-O-hexadecanoyl-sn-glycerol 3-phosphate) (30) and the corresponding 2-amino-2-deoxy-alpha-D-galactopyranosyl analogue 36 have been prepared and tested in cell-free assays as substrate analogues/inhibitors of alpha-(1 --> 4)-D-mannosyltransferases that are active early on in the glycosylphosphatidylinositol (GPI) biosynthetic pathways of Trypanosoma brucei and HeLa (human) cells. The corresponding N-acetyl derivatives of these compounds were similarly tested as candidate substrate analogues/inhibitors of the N-deacetylases present in both systems. Following on from an early study, 1-L-6-O-(2-amino-2-deoxy-alpha-D-glucopyranosyl)-2-O-methyl-myo-inositol 1-(1,2-di-O-hexadecanoyl-sn-glycerol 3-phosphate) (44) was prepared and tested as an inhibitor of the trypanosomal alpha-(1 --> 4)-D-mannosyltransferase. A brief summary of the biological evaluation of the various analogues is provided.     

Aloeresin c,a bitter c,o-diglucoside from cape aloe

A new bitter C,O-diglucoside, aloeresin C, was isolated from commercial Cape aloe. Its structure, 2-acetonyl-7-O-β-D-glucopyranosyl-8-C-β-D-[2′-O-(E)-p-coumaroyl]glucopyranosyl-5-methylchromone, was established by spectral and chemical methods.     

Acylated protopanaxadiol-type ginsenosides from the root of Panax ginseng

Six new protopanaxadiol-type ginsenosides, named ginsenosides Ra(4) -Ra(9) (1-6, resp.), along with 14 known dammarane-type triterpene saponins, were isolated from the root of Panax ginseng, one of the most important Chinese medicinal herbs. The structures of the new compounds were determined by spectroscopic methods, including 1D- and 2D-NMR, HR-MS, and chemical transformation as (20S)- 3-O-{β-D-6-O-[(E)-but-2-enoyl]glucopyranosyl-(1→2)-β-D-glucopyranosyl}-20-O-[β-D-xylopyranosyl-(1→4)-α-L-arabinopyranosyl-(1→6)-β-D-glucopyranosyl]protopanaxadiol (1), (20S)-3-O-[β-D-6-O-acetylglucopyranosyl-(1→2)-β-D-glucopyranosyl]-20-O-[β-D-xylopyranosyl-(1→4)-α-L-arabinopyranosyl-(1→6)-β-D-glucopyranosyl]protopanaxadiol (2), (20S)-3-O-{β-D-6-O-[(E)-but-2-enoyl]glucopyranosyl-(1→2)-β-D-glucopyranosyl}-20-O-[β-D-glucopyranosyl-(1→6)-β-D-glucopyranosyl]protopanaxadiol (3), (20S)-3-O-{β-D-6-O-[(E)-but-2-enoyl]glucopyranosyl-(1→2)-β-D-glucopyranosyl}-20-O-[α-L-arabinopyranosyl-(1→6)-β-D-glucopyranosyl]protopanaxadiol (4), (20S)-3-O-{β-D-4-O-[(E)-but-2-enoyl]glucopyranosyl-(1→2)-β-D-glucopyranosyl}-20-O-[α-L-arabinofuranosyl-(1→6)-β-D-glucopyranosyl]protopanaxadiol (5), (20S)-3-O-{β-D-6-O-[(E)-but-2-enoyl]glucopyranosyl-(1→2)-β-D-glucopyranosyl}-20-O-[α-L-arabinofuranosyl-(1→6)-β-D-glucopyranosyl]protopanaxadiol (6). The sugar moiety at C(3) of the aglycone of each new ginsenoside is butenoylated or acetylated.     

A synthesis of prumycin

Prumycin, 4-D-(alanylamino)-2-amino-2,4-dideoxy-L-arabinose, was synthesized from D-xylose by nine-step conversion via a key intermediate, benzyl 2,3-anhydro-4-azido-4-deoxy-β-L-ribopyranoside. An isomer of prumycin, 4-D-alanylamino-3-amino-3,4-dideoxy-L-xylose, was also synthesized from the same intermediate.     

云芝子实体多糖(CVP)化学结构的研究III.*

通过化学、IR和UV光谱等方法发现云芝子实体的热水提取物 CVP 是由多糖、核酸和蛋白质等组成的混合物。通过柱层析方法从 CVP 中纯化出一个多糖组份 B-2-3,经完全水解证实组成它的单糖残基主要为Glc。用 HPLC 方法测得其分子量为 5.01×105。通过对甲基化及 1H 和 13C NMR 数据的分析发现 B-2-3 为一个以β-D-1, 4-Glc、β-D-1, 3-Glc 和β-D-1, 6-Glc 残基构成主链,同时在β-D-1, 3, 6-Glc 及β-D-1, 4, 6-Glc 处产生分枝的多糖。     

DNA damage by the sulfate radical anion: hydrogen abstraction from the sugar moiety versus one-electron oxidation of guanine

The products of oxidative damage to double-stranded (ds) DNA initiated by photolytically generated sulfate radical anions SO₄^?? were analyzed using reverse-phase (RP) high-performance liquid chromatography (HPLC). Relative efficiencies of two major pathways were compared: production of 8-oxoguanine (8oxoG) and hydrogen abstraction from the DNA 2-deoxyribose moiety (dR) at C1,′ C4,′ and C5′ positions. The formation of 8oxoG was found to account for 87% of all quantified lesions at low illumination doses. The concentration of 8oxoG quickly reaches a steady state at about one 8oxoG per 100 base pairs due to further oxidation of its products. It was found that another guanine oxidation product identified as 2-amino-5-(2′-alkylamino)-4H-imidazol-4-one (X) was released in significant quantities from its tentative precursor 2-amino-5-[(2′-deoxy-β-d-erythro-pentofuranosyl)amino]-4H-imidazol-4-one (dIz) upon treatment with primary amines in neutral solutions. The linear dose dependence of X release points to the formation of dIz directly from guanine and not through oxidation of 8oxoG. The damage to dR was found to account for about 13% of the total damage, with majority of lesions (33%) originating from the C4′ oxidation. The contribution of C1′ oxidation also turned out to be significant (17% of all dR damages) despite of the steric problems associated with the abstraction of the C1′-hydrogen. However, no evidence of base-to-sugar free valence transfer as a possible alternative to direct hydrogen abstraction at C1′ was found.     

Interaction of Escherichia Coli Ribonuclease H With Hybrid Duplexes Containing 2′-Deoxyxylotrymidine, 2′-Deoxy-2′ Fluorouridine or Alpha-Thymidine

Abstract

Oligothymidilates with repeating inserts of 1-(β-D-2′-deoxy-2′-fluoropentafuranosyl) uracil(fU),1-(β-D-2′-deoxy-threo-pentafuranosyl) thymine(xT) an d α-oligodeoxyribonucleotide α(G₂T₁₂G₂) were synthesized. Hybrid duplexes were obtained to study the physico-chemical properties (melting curves, CD-spectra) and the interaction with E. coli ribonuclease H. It was found that the modified hybrid duplex prA₁₈/TT(fUTT)₆ did not bind the enzyme, the modified hybrid duplex prA₁₈/(xTTT)₆ inhibited oligoriboadenylate cleavage by RNase H in hybrid duplexes prA₁₈/(G₂T₂₀) and prA₁₄/T₁₆ as well as the modified hybrid duplex prA₁₄/α(G₂T₁₂G₂).     

Bitter phenylpropanoid glycosides from Conandron ramoidioides

A new bitter glycoside, conandroside and a known glycoside, acteoside were isolated from Conandron ramoidioides. On the basis of the chemical and spectral evidence, conandroside was shown to be 2-(3′,4′-dihydroxy-phenyl)-ethanol 1-O-β-D-xylosyl-(1 → 3)-β-D-(4-caffeyl)-glucoside.