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.     

Norbornane as the novel pseudoglycone moiety in nucleosides

Novel nucleoside analogues based on bicyclo[2.2.1]heptene/heptane were prepared by linear synthesis starting from commercially available 1,2,3,4-tetrachloro-5,5-dimethoxycyclopentadiene 1. The crucial step of the synthesis was insertion of the amino group to the position 7 of the substituted bicyclo[2.2.1]heptene with anti-configuration by a Ritter reaction (H₂SO₄, AcOH, CH₃CN). All nucleobases were constructed at this amino function. The prepared family of the target nucleosides was tested for cytostatic and antiviral activity.     

Synthesis and EPR Studies of 2′‐Deoxyuridines with Alkynyl,Rodlike Linkages

Sonogashira coupling of diacetyl 5‐ethynyl‐2′‐deoxyuridine with diacetyl 5‐iodo‐2′‐deoxyuridine gave the acylated ethynediyl‐linked 2′‐deoxyuridine dimer ( 3 b ; 63 %), which was deprotected with ammonia/methanol to give ethynediyl‐linked 2′‐deoxyuridines ( 3 a ; 79 %). Treatment of 5‐ethynyl‐2′‐deoxyuridine ( 1 a ) with 5‐iodo‐2′‐deoxyuridine gave the furopyrimidine linked to 2′‐deoxyuridine (78 %). Catalytic oxidative coupling of 1 a (O₂, CuI, Pd/C, N,N‐dimethylformamide) gave butadiynediyl‐linked 2′‐deoxyuridines ( 4 ; 84 %). Double Sonogashira coupling of 5‐iodo‐2′‐deoxyuridine with 1,4‐diethynylbenzene gave 1,4‐phenylenediethynediyl‐bridged 2′‐deoxyuridines ( 5 ; 83 %). Cu‐catalyzed cycloisomerization of dimers 4 and 5 gave their furopyrimidine derivatives. One‐electron addition to 1 a , 3 a , and 4 gave the anion radical, the EPR spectra of which showed that the unpaired electron is largely localized at C6 of one uracil ring (17 G doublet) at 77 K. The EPR spectra of the one‐electron‐oxidized derivatives of ethynediyl‐ and butadiynediyl‐linked uridines 3 a and 4 at 77 K showed that the unpaired electron is delocalized over both rings. Therefore, structures 3 a and 4 provide an efficient electronic link for hole conduction between the uracil rings. However, for the excess electron, an activation barrier prevents coupling to both rings. These dimeric structures could provide a gate that would separate hole transfer from electron transport between strands in DNA systems. In the crystal structure of acylated dimer 3 b , the bases were found in the anti position relative to each other across the ethynyl link, and similar anti conformation was preserved in the derived furopyrimidine–deoxyuridine dinucleoside.     

The Mitsunobu reaction in preparing 3-deazapurine carbocyclic nucleosides

The coupling reaction of 4-chloro-1H-imidazo[4,5-c]pyridine (6-chloro-3-deazapurine, 3) with several cyclopentyl derivatives under Mitsunubo reaction conditions provides an efficient entry into N-7 and N-9 substituted 3-deazapurine carbocyclic nucleosides of antiviral potential. The versatility of this procedure is illustrated with a new and efficient synthesis of (−)-3-deazaaristeromycin, a formal preparation of 3-deazaneplanocin A, and a route to 3-deaza-5′-homoaristeromycin.     

Synthesis of Deoxynucleoside Triphosphates that Include Proline,Urea, or Sulfonamide Groups and Their Polymerase Incorporation into DNA

To expand the chemical array available for DNA sequences in the context of in vitro selection, I present herein the synthesis of five nucleoside triphosphate analogues containing side chains capable of organocatalysis. The synthesis involved the coupling of L ‐proline‐containing residues (dU^tPTP and dU^cPTP), a dipeptide (dU^FPTP), a urea derivative (dU^BpuTP), and a sulfamide residue (dU^BsTP) to a suitably protected common intermediate, followed by triphosphorylation. These modified dNTPs were shown to be excellent substrates for the Vent (exo^?) and Pwo DNA polymerases, as well as the Klenow fragment of E. coli DNA polymerase I, although they were only acceptable substrates for the 9°N_m polymerase. All of the modified dNTPs, with the exception of dU^BpuTP, were readily incorporated into DNA by the polymerase chain reaction (PCR). Modified oligonucleotides efficiently served as templates for PCR for the regeneration of unmodified DNA. Thermal denaturation experiments showed that these modifications are tolerated in the major groove. Overall, these heavily modified dNTPs are excellent candidates for SELEX.     

Dinucleosides with Non‐Natural Backbones: A New Class of Ribonuclease A and Angiogenin Inhibitors

Ribonuclease A (RNase A) serves as a convenient model enzyme in the identification and development of inhibitors of proteins that are members of the ribonuclease superfamily. This is principally because the biological activity of these proteins, such as angiogenin, is linked to their catalytic ribonucleolytic activity. In an attempt to inhibit the biological activity of angiogenin, which involves new blood vessel formation, we employed different dinucleosides with varied non‐natural backbones. These compounds were synthesized by coupling aminonucleosides with dicarboxylic acids and amino‐ and carboxynucleosides with an amino acid. These molecules show competitive inhibition with inhibition constant (K_i) values of (59±3) and (155±5) μM for RNase A. The compounds were also found to inhibit angiogenin in a competitive fashion with corresponding K_i values in the micromolar range. The presence of an additional polar group attached to the backbone of dinucleosides was found to be responsible for the tight binding with both proteins. The specificity of different ribonucleolytic subsites were found to be altered because of the incorporation of a non‐natural backbone in between the two nucleosidic moieties. In spite of the replacement of the phosphate group by non‐natural linkers, these molecules were found to selectively interact with the ribonucleolytic site residues of angiogenin, whereas the cell binding site and nuclear translocation site residues remain unperturbed. Docked conformations of the synthesized compounds with RNase A and angiogenin suggest a binding preference for the thymine–adenine pair over the thymine–thymine pair.     

双环及三环核苷的合成

摘要综述了天然双环核苷、抗病毒构效研究中的双环核苷和反义寡核苷酸领域中双环及三环核苷的合成研究进展,介绍了常规官能团转化法及近年来出现的自由基环合、1,3-偶极环加成和烯烃复分解等新方法。     

[2+2+2]-Co-cyclotrimerization 6-alkynylpurines with diynes: a method for preparation of 6-arylpurines

A novel approach to 6-arylpurines based on [2+2+2]-co-cyclotrimerization of 6-alkynylpurines with various α,ω-diynes is described. Co-cyclotrimerization is catalyzed by Ni- and Co-phosphine catalysts and their choice depends on the substitution pattern of the both reactants.