One-step to get 5-azidomethyl-2′-deoxyuridine from 5-hydroxymethyl-2′-deoxyuridine and detection of it through click reaction

Nowadays a few ways to synthesize 5-azidomethyl-2′-deoxyuridine from 5-hydroxymethyl-2′-deoxyuridine have been reported. But none of them was one-step. And many of them need to protect the hydroxyl group on the pentose ring. The detection of 5-hydroxymethyl-2′-deoxyuridine is also very important in many biological processes. However few fluorescence detection strategies have been tried to do this. Herein, we reported a one-step protocol to synthesize 5-azidomethyl-2′-deoxyuridine, which was then used for detecting 5-hydroxymethyl-2′-deoxyuridine through a click reaction.     

Synthesis,cytotoxicity and antiviral activity studies of the conjugates of cobalt bis(1,2-dicarbollide)(-I) with 5-ethynyl-2′-deoxyuridine and its cyclic derivatives

A series of novel conjugates of cobalt bis(1,2-dicarbollide)(-I) with 5-ethynyl-2′-deoxyuridine and its cyclic derivatives were synthesized. Conjugates with 5-ethynyl-2-deoxyuridine were prepared by the direct Sonogashira coupling of a series of cobalt bis(1,2-dicarbollide)(-I) terminal alkynes and 5-iodo-2′-deoxyuridine. Their furo[2,3-d]pyrimidin-2(3H)-one isomers were obtained either by intermolecular cyclization of the above conjugates or by Sonogashira coupling using Pd/C as a catalyst. Action of ammonia on these furo[2,3-d]pyrimidin-2(3H)-one conjugates resulted in pyrrolo[2,3-d]pyrimidin-2(3H)-one conjugates. Most of the designed compounds have shown low cytotoxicity in several cell lines. Some 5-ethynyl-2-deoxyuridine and furo[2,3-d]pyrimidin-2(3H)-one conjugates have also presented antiviral activity.     

Parallel G-quadruplex Structures Increase Cellular Uptake and Cytotoxicity of 5-Fluoro-2′-deoxyuridine Oligomers in 5-Fluorouracil Resistant Cells

Fluoropyrimidines, such as 5-fluorouracil (5-FU) and related prodrugs have been considered first-line chemotherapy agents for the treatment of colorectal cancer. However, poor specificity and tumor cell resistance remain major limiting bottlenecks. G-quadruplexes, have been suggested as preferred nanostructures for enhancing cellular uptake mediated by G-quadruplex binding proteins which are abundant at the membranes of some tumor cells. In the current study, we propose a new strategy to deliver 5-fluoro-2′-deoxyuridine (5-FdU) monophosphate, the main active drug from 5-FU derivatives that may circumvent the cellular mechanisms of FU-resistant cancer cells. Two G-quadruplexes delivery systems containing four and six G-tetrads ((TG₄T) and (TG₆T)) linked to a FdU oligonucleotide were synthesized. Biophysical studies show that the G-quadruplex parallel structures are not affected by the incorporation of the 5 units of FdU at the 5’-end. Internalization studies confirmed the ability of such G-quadruplex nanostructures to facilitate the transport of the FdU pentamer and increase its cytotoxic effect relative to conventional FU drug in FU-resistant colorectal cancer cells. These results suggest that FdU oligomers linked to G-quadruplex parallel sequences may be a promising strategy to deliver fluoropyrimidines to cancer cells.     

Synthesis of tricarbonyl rhenium and technetium complexes of a 5′-carboxamide 5-ethyl-2′-deoxyuridine for selective inhibition of herpes simplex virus thymidine kinase 1

Herpes simplex virus thymidine kinase type 1 (HSV1-TK) is frequently used as reporter protein in gene therapy. Our aim is to produce single photon emitting reporter probe based on technetium-99m. The synthesis of organometallic technetium and rhenium complexes of a 5′-carboxamide 5-ethyl-2′-deoxyuridine derivative able to selectively inhibit HSV1-TK is presented. The 5-ethyl-2′-deoxyuridine functionalized with a suitable tridentate chelating system at position 5′ was synthesized from commercial 2′-deoxyuridine in seven steps. The 5-ethyl-2′-deoxyuridine derivative was labeled with the fac-M(CO)₃-core (M = Tc, Re). The resulting rhenium complex was found to be a selective competitive inhibitor of HSV1-TK (K_i = 4.56 μM). Inhibition of the human cytosolic thymidine kinase (hTK1) previously reported with organometallic rhenium and technetium complexes of 5′-carboxamide thymidine derivative was not observed. The uptake of the technetium-99m complex in transfected cells expressing HSV1-TK has been evaluated to assess its possible use as reporter.     

Uracil ring opening in the reaction of 5-formyl-2′-deoxyuridine with primary alkyl amines

Treatment of 5-formyl-2′-deoxyuridine (f⁵dU) with stoichiometric amounts of strongly nucleophilic, non-hindered primary alkyl amines led to fast and quantitative formation of the corresponding Schiff bases. In the presence of excess amines, novel nucleosides with ring opened pyrimidine bases were formed as a result of the Michael addition of a second amine to the pre-formed imines. In the reaction of f⁵dU with aromatic amines, the formation of Schiff base derivatives was slower and even under prolonged treatment with an excess of amine the uracil ring remained intact.     

5-Alkynyl-2′-deoxyuridines, containing bulky aryl groups: evaluation of structure-anti-HSV-1 activity relationship

Four 5-alkynyl-2′-deoxyuridines containing different bulky substituents and flexible linkers between the triple bond and the aromatic residue have been prepared and tested against HSV-1 in Vero cells. Two nucleosides containing carbonyl groups, 5-(4-benzoylphenoxypropyn-1-yl)-2′-deoxyuridine (19a) and 5-(estron-3-yloxypropyn-1-yl)-2′-deoxyuridine (19c), showed low cytotoxicity and moderate antiviral activity. The flexible linker appears not to be favorable for antiviral properties of 5-alkynyl-2′deoxyuridines: 5-[(perylen-3-yl)methoxypropyn-1-yl]-2′-deoxyuridine (19d) showed considerable cytotoxicity and no antiviral activity in contrast to the active and nontoxic 5-(perylen-3-ylethynyl)-2′-deoxyuridine (9), a nucleoside with a rigid triple-bond-connection of the aromatic system to the nucleobase.     

Synthesis of hapten-phosphoramidites from 2′-deoxyuridine

A total of 11 novel phosphoramidites, 3a-d, 4a-d and 14a-c were prepared from 2′-deoxyuridine functionalized at 5 and 6-position of the pyrimidine ring with hapten reporter groups, e.g. adamantane, carbazole, dansyl and dabsyl, suitable for use in immunodetection nucleic acid testing assays.     

Proton Nuclear Magnetic Resonance Measurements of 2′-Aminodeoxyuridylyl-3′,5′-Deoxyuridine

A dideoxyribonucleotide, 2′-amino-2′-deoxyuridylyl 3′,5′-deoxyuridine, containing an unsual base (2′-amino-2′-deoxyuridine) that isresistant to nucleases was investigated by ′H NMR. The pK_a of the protonation of the amino group (5.8) was determined by profiles of chemical shifts of protons in the vicinity of amino group versus pH. However, protonation of the amino group has little effect on the conformation of the dimer, assumed to be B-form DNA. This conclusion is drawn from the chemical shift data and coupling constants of H₁-H₂. Thus, 2′-amino-2′-deoxyuridine can be used in antisense and anticode oligonucleotides.     

Synthesis of Thymidine Dimer Containing Novel (N‐Acetyl)imino Linkage

By starting with 3′‐keto‐5′‐O‐protected thymidine, 3′‐O‐amino‐5′‐t‐butyl‐diphenylsilyl thymidine ( 9 ) was prepared and coupled with 3′‐O‐t‐butyl‐diphenylsilyl‐5′‐formyl thymidine to form a nucleoside dimer ( 11 ) containing oxime linkage. The back bone of this dimer, then, under went reduction followed by acetylation to give an (N‐acetyl)imino linkage, and a novel dinucleotide ( 13 ) was obtained.     

Synthesis of a technetium-99m-labeled thymidine analog: a potential HSV1-TK substrate for non-invasive reporter gene expression imaging

{2-[5-(2′-Fluoro-2′-deoxyuridin-5-yl)pent-4(E)-enyl] [2-(2-mercaptoethyl)aminoethyl]aminoethanethiolato(3)-N,N′,S,S′}oxo-[^99mTc]technetium(V), a potential viral thymidine kinase substrate, was synthesized by coupling 2′-fluoro-2′-deoxyuridine analog with a N2S2 radiometal chelator, followed by [Tc-99m]technetium conjugation. The chemical structure of the radioactive probe was characterized by ¹H NMR and high resolution MS using Re-188 conjugated mimics. The radiochemical purity and yield were identified as 98% and 42%, respectively.     

Furan Decorated Nucleoside Analogues as Fluorescent Probes: synthesis, photophysical evaluation and site-specific incorporation

The synthesis and photophysical evaluation of modified nucleoside analogues in which a five-membered heterocycle (furan, thiophene, oxazole, and thiazole) is attached to the 5-position of 2′-deoxyuridine are reported. The furan-containing derivative is identified as the most promising responsive nucleoside of this family due to its emission quantum efficiency and degree of sensitivity to its microenvironment. The furan moiety was then attached to the 5-position of 2′-deoxycytidine as well as the 8-position of adenosine and guanosine. Photophysical evaluation of these four furan-containing nucleoside analogues reveals distinct differences in the absorption, emission, and quantum efficiency depending upon the class of nucleoside (pyrimidine or purine). Comparing the photophysical properties of all furan-containing nucleosides, identifies the furan thymidine analogue, 5-(fur-2-yl)-2′-deoxyuridine, as the best candidate for use as a responsive fluorescent probe in nucleic acids. 5-(Fur-2-yl)-2′-deoxyuridine was then converted to the corresponding phosphoramidite and site specifically incorporated into DNA oligonucleotides with greater than 88% coupling efficiency. Such furan-modified oligonucleotides form stable duplexes upon hybridization to their complementary DNA strands and display favorable fluorescent features.     

2’-脱氧胞苷-5’-磷酸羟基加合物的分子结构与电子结构

使用密度泛函理论(DFT)的B3LYP/DZP++研究了羟基自由基与2’-脱氧胞苷-5’-磷酸(dCMP)的胞嘧啶环加成产物的分子结构与电子结构. 结果表明, dCMP胞嘧啶环中各C原子上的单羟基加合物的相对稳定性顺序为C5>C6>>C4≥C2. 加合物的稳定性、自旋密度、静电势以及dCMP的电子密度、静电势、电荷分布分析表明, dCMP遭遇多个羟基自由基攻击时, 第一个羟基自由基加在dCMP的C5上, 而C6则成为第二个羟基自由基的进攻目标. 反应中一旦形成了C2-位单羟基加合物, 则极有可能在DNA复制过程中引起致命的基因突变, 也可能诱发DNA-DNA以及DNA-蛋白质的链间交联, 引起更复杂的损伤. 相反, C5、C6-位上单羟基加合物的形成对DNA的稳定性不构成直接威胁.     

Anomeric 5-Aza-7-deaza-2′-deoxyguanosines in Silver-Ion-Mediated Homo and Hybrid Base Pairs: Impact of Mismatch Structure,Helical Environment,and Nucleobase Substituents on DNA Stability

Nucleoside configuration (α-d vs. β-d ), nucleobase substituents, and the helical DNA environment of silver-mediated 5-aza-7-deazaguanine-cytosine base pairs have a strong impact on DNA stability. This has been demonstrated by investigations on oligonucleotide duplexes with silver-mediated base pairs of α-d and β-d anomeric 5-aza-7-deaza-2′-deoxyguanosines and anomeric 2′-deoxycytidines incorporated in 12-mer duplexes. To this end, a new synthetic protocol has been developed to access the pure anomers of 5-aza-7-deaza-2′-deoxyguanosine by glycosylation of either the protected nucleobase or its salt followed by separation of the glycosylation products by crystallization and chromatography. Thermal stability measurements were performed on duplexes with α-d /α-d and β-d /β-d homo base pairs or α-d /β-d and β-d /α-d hybrid pairs within two sequence environments, positions 6 or 7, of oligonucleotide duplexes. The respective T_m stability increases observed after silver ion addition differ significantly. Homo base pairs with β-d /β-d or α-d /α-d nucleoside combinations are more stable than α-d /β-d hybrid base pairs. The positional switch of silver-ion-mediated base pairs has a significant impact on stability. Nucleobase substituents introduced at the 5-position of the dC site of silver-mediated base pairs affect base pair stability to a minor extent. Our investigation might lead to applications in the construction of bioinspired nanodevices, in DNA diagnostics, or metal-DNA hybrid materials.     

Efficient bioactive oligonucleotide-protein conjugation for cell-targeted cancer therapy

Oligonucleotide-protein conjugates have important applications in biomedicine. Simple and efficient methods are described for the preparation of these conjugates. Specifically, we describe a new method in which a bifunctional linker is attached to thiol-oligonucleotide to generate a reactive intermediate that is used to link to the protein. Having similar conjugation efficacy compared with the classical method in which the bifunctional linker is attached first to the protein, this new approach produces significantly more active conjugates with higher batch to batch reproducibility. In a second approach, direct conjugation is proposed using oligonucleotides carrying carboxyl groups. These methodologies have been applied to prepare nanoconjugates of an engineered nanoparticle protein carrying a T22 peptide with affinity for the CXCR4 chemokine receptor and oligomers of the antiproliferative nucleotide 2’-deoxy-5-fluorouridine in a very efficient way. The protocols have potential uses for the functionalization of proteins, amino-containing polymers or amino-lipids in order to produce complex therapeutic nucleic acid delivery systems.     

5-卤代-2’-脱氧-2’-β-氟-4’-叠氮嘧啶核苷的合成与抗乙肝病毒活性研究

以(间氯)苯甲酰基保护的2’-脱氧-2’-β-氟-4’-叠氮尿苷为起始原料,经过硝酸铈铵(CAN)介导的卤代、三氮唑活化、胺化、脱保护合成了一系列5-卤代的2’-脱氧-2’-β-氟-4’-叠氮嘧啶核苷类化合物.体外生物活性评价研究表明, 5-氯代(6a)和5-碘代(6c)核苷衍生物具有很好的抗乙肝病毒活性,而且细胞毒性较小.     

Efficient synthesis of terminal 4-methylumbelliferyl labeled 5-fluoro-2′-deoxyuridine-5′-O-tetraphosphate (Um-PPPP-FdU): a potential probe for homogenous fluorescent assay

Efficient synthesis of 5-fluoro-2′-deoxyuridine-5′-O-tetraphosphate bearing 4-methylumbelliferyl label on the terminal phosphate is reported. This compound has the potential as a promising probe molecule for homogenous fluorescent polymerase assay. This class of compounds will aid in quantification of cellular internalization and DNA incorporation of nucleotide based chemotherapeutic agents to offer mechanistic insights.     

靛红Morita-Baylis-Hillman碳酸酯与环状N-磺酰亚胺的不对称烯丙基烷基化反应研究

本课题组近年来发展的通过路易斯碱催化靛红Morita-Baylis-Hillman(MBH)碳酸酯的烯丙基烷基化反应是合成光学纯3,3-二取代2-氧化吲哚化合物的一种有效方法. 在此基础上, 本文研究了手性叔胺催化靛红MBH碳酸酯与环状N-磺酰亚胺的不对称烯丙基烷基化反应, 通过亲电反应途径以较高的立体选择性(达86% ee, dr＞95∶5)和高收率(达96%)合成C-3位含季碳手性中心的多官能团氧化吲哚产物. 通过简单的转化可以得到含多个手性中心的2-吲哚酮-3,4'-哌啶环类骨架, 这为进一步合成生理活性物质研究奠定了基础.     

Independent generation of C5'-nucleosidyl radicals in thymidine and 2'-deoxyguanosine

The synthesis of the C5' tert-butyl ketone of thymidine 1a and 2'-deoxyguanosine 2 is achieved by reaction of 5'-C-cyano derivatives with tert-butyl lithium followed by acid hydrolysis. The 5'R configuration is assigned by X-ray crystal structure determination of an opportunely protected derivative of 1a. The (5'S)-isomers of both nucleosides are not stable, and a complete decomposition occurs in the reaction medium. The photochemistry of 1a and 2 effectively produced the thymidin-5'-yl radical and the 2'-deoxyguanosin-5'-yl radical, respectively. In the thymidine system, the C5' radical is fully quenched in the presence of a physiological concentration of thiols. In the 2'-deoxyguanosine system, the C5' radical undergoes intramolecular attack onto the C8-N7 double bond of guanine leading ultimately to the 5',8-cyclo-2'-deoxyguanosine derivative. The cyclization of the 2'-deoxyguanosin-5'-yl radical occurs with a rate constant of ca. 1x10(6) s-1 and is highly stereoselective affording only the (5'S)-diastereomer.     

Synthesis and Biological Activities of C (5)-N-Spin-Labeled Uridines and Related Derivatives

Direct introduction of a N-atom in one step at C (5) of 5-hydroxyuridine (4a) or 5-hydroxy-2′-deoxyuridine (4b) by certain primary amines led to the synthesis of two novel C(5)-N-spin-labeled nucleoside analogs and to several C(5)-N-aryl adducts. Substitution by 4-amino-2,2,6,6-tetramethylpiperidinooxyl (3) at C(5) of 4a or 4b led to the spin-labeled nucleosides 5-[(1-oxyl-2,2,6,6-tetramethyl-4-piperidinyl)amino]uridine and -2′-deoxyuridine ( 2a and 2b , respectively). The analogous C(5)-substituted aniline adducts 5-anilino uridine (5a) and 5-anilino-2′-deoxyuridine (5b) and the p-toluidine adducts 5-(p-toluidino)uridine (6a) and 5-(p-toluidino)-2-deoxyuridine (6b) were also prepared. In addition, results of the antiviral and antimetabolic activity of some of these analogs are reported.