Polynucleotides and Their Components in the Processes of Aromatic Nucleophilic Substitution: I. Chemistry and Dynamics of Nucleotide Arylation with Pentafluoropyridine; Obtaining of Synthons for Molecular Design of Nucleic Acid Analogues

Pentafluoropyridine reacts with thymidine, adenosine, and uridine hydroxy groups to give quantitative yields of the corresponding nucleoside di- and triaryl ethers. The nucleophilic substitution reactions proceed successively and in parallel, with the slowest step being the nucleophilic substitution of the nucleoside secondary hydroxyls. The resulting ethers contain tetrafluoropyridyl moieties, which could be smoothly modified by nucleophilic substitution of fluorine atoms. The ethers are useful intermediate synthons (both isolated and in situ) for molecular design of oligonucleotide analogues.     

Stereocontrolled Synthesis of Diene and Enyne Sugar-Modified Nucleosides and Their Interaction with S-Adenosyl-L-homocysteine Hydrolase

Abstract

Conjugated diene 5–7 and enyne 8 analogs derived from adenosine and uridine were synthesized employing Pd-catalyzed cross-coupling reactions.     

Cobalt(III) complexes with linear hexadentate N6 or N4S2 donor set atoms providing pyridyl-amide-amine/thioether coordination

Two new cobalt(III) complexes of symmetric hexadentate ligand with N₆ [1,10-bis(2-picolinamide)-4,7-diazadecane (pycdpnen)] and N₄S₂ [1,8-bis(2-picolinamide)-3,6-dithiaoctane (pycdadt)] donor set atoms have been synthesized as perchlorate salts and characterized by spectroscopic methods. All two ligands with strong-field pyridylcarboxamido N donor stabilize Co(III) as demonstrated by the facile oxidation of the cobalt center. The structures of [Co(pycdpnenH₋₂)](ClO₄) (1) and [Co(pycdadtH₋₂)](ClO₄) · H₂O (2) investigated by COSY, HMBC, HMQC and NOESY NMR studies show that compounds 1 and 2 have the same geometrical configuration. The X-ray analysis reveals that complex 2 crystallizes in a orthorhombic space group Pccn. The cation [Co(pycdadtH₋₂)]⁺ is distorted octahedral with the two pyridyl groups in cis position.     

First Synthesis and Anti-HIV Evaluation of 4′-Methyl-Cyclopentanyl 9-Deazaadenosine

The first synthesis of a 4′-methylated carbocyclic C-nucleoside 16 was achieved via the mesylate intermediate 10, which was prepared using ring-closing metathesis and S_N2 alkylation from acetol 5. When antiviral evaluation of synthesized compound 16 was performed against various viruses such as HIV, HSV-1, HSV-2, and HCMV, it showed moderate anti-HIV activity in MT-4 cell line (EC₅₀ = 14.7 μmol).     

Synthesis and Anti-Hiv Activity of 4′-Modified Cyclopentenyl Pyrimidine C-Nucleosides

Novel syntheses of 4′-modified cyclopentenyl pyrimidine C-nucleosides were performed via C-C bond formation using S_N2 alkylation via the key intermediate mesylates 6 and 16, which were prepared from acyclic ketone derivatives. When antiviral evaluation of synthesized compound was performed against various viruses such as HIV-1, HSV-1 and HSV-2, isocytidine analogue 20 showed moderate anti-HIV activity in CEM cell line (EC₅₀ = 13.1 μmol).7     

Surprising unreactivity of cholesterol-5,6-epoxides towards nucleophiles

We recently established that drugs used for the treatment and the prophylaxis of breast cancers, such as tamoxifen, were potent inhibitors of cholesterol-5,6-epoxide hydrolase (ChEH), which led to the accumulation of 5,6α-epoxy-cholesterol (5,6α-EC) and 5,6β-epoxy-cholesterol (5,6β-EC). This could be considered a paradox because epoxides are known as alkylating agents with putative carcinogenic properties. We report here that, as opposed to the carcinogen styrene-oxide, neither of the ECs reacted spontaneously with nucleophiles. Under catalytic conditions, 5,6β-EC remains unreactive whereas 5,6α-EC gives cholestan-3β,5α-diol-6β-substituted compounds. These data showed that 5,6-ECs are stable epoxides and unreactive toward nucleophiles in the absence of a catalyst, which contrasts with the well-known reactivity of aromatic and aliphatic epoxides. These data rule out 5,6-EC acting as spontaneous alkylating agents. In addition, these data support the existence of a stereoselective metabolism of 5,6α-EC.     

Molecular Dynamics Study of High Temperature Phase-Separation in a H2O/N2 Mixture with Exp-6 Interactions

Abstract

Equimolar H₂O/N₂ fluid mixture was studied by molecular dynamics simulations for NVT ensemble. Calculations were performed with the modified Buckingham (exp-6) potentials at T = 2000 K. Particular attention was given to the phase separation at very high pressures relevant to a detonation environment. Calculations of pair correlation functions and local mole fractions clearly indicated the occurrence of the fluid separation into N₂-rich and H₂O-rich phase. The density at the phase boundary between homogeneous and inhomogeneous phase-separated state was determined to be p = 1.35 g/cm³ on the basis of the static cross correlation factor which is defined by the sum of the local mole fractions. The ratio of the self-diffusion coefficients of N₂ and H₂O at p < 1.35 g/cm³ was found to be approximately equal to the value predicted by the kinetic theory of the ideal gas, whereas the ratio was close to unity at the phase-separated state (p > 1.35 g/cm³). In addition, two distinctive behaviors of the system could be observed for the relaxation from the initial uniform mixture to the phase-separated fluid: at lower densities (1.35 < p < 2.0 g/cm³) the fluid mixture began to relax into the phase-separated system without obvious incubation time, while clear incubation period was associated for the separation at higher densities. During this incubation period, discontinuous jumps in the mean square displacements were found.     

Interspecific Competition for Soil N and its Interaction with N2 Fixation, Leaf Expansion and Crop Growth in Pea–Barley Intercrops

Field experiments were carried out during three successive years to study through a dynamic approach the competition for soil N and its interaction with N₂ fixation, leaf expansion and crop growth in pea–barley intercrops. The intensity of competition for soil N varied between experiments according to soil N supply and plant densities. This study demonstrates the key role of competition for soil N which occurs early in the crop cycle and greatly influences the subsequent growth and final performance of both species. Relative yield values for grain yield and N accumulation increased with the intensity of competition for soil N. Barley competed strongly for soil N in the intercrop. Its competitive ability increased steadily during the vegetative phase and remained constant after the beginning of pea flowering. The period of strong competition for soil N (500–800 degree-days after sowing) also corresponded to the period of rapid growth in leaf area for both species and therefore an increasing N demand. For each species, the leaf area per plant at the beginning of pea flowering was well correlated with crop nitrogen status. Barley may meet its N needs more easily in intercrops (IC) and has greater leaf area per plant than in sole crops (SC). Barley having a greater soil N supply results in an even higher crop N status and greater competitive ability relative to pea in intercrop. Competition by barley for soil N increased the proportion of pea N derived from fixation. The nitrogen nutrition index (NNI) values of pea were close to 1 whatever the soil N availability in contrast to barley. However N₂ fixation started later than soil N uptake of pea and barley and was low when barley was very competitive for soil N. Due to the time necessary for the progressive development and activity of nodules, N₂ fixation could not completely satisfy N demand at the beginning of the crop cycle. The amount of N₂ fixed per plant in intercrops was not only a response to soil N availability but was largely determined by pea growth and was greatly affected when barley was too competitive.     

Fast Accumulation of Nonsynonymous Mutations on the Female-Specific W Chromosome in Birds

Following cessation of recombination during sex chromosome evolution, the nonrecombining sex chromosome is affected by a number of degenerative forces, possibly resulting in the fixation of deleterious mutations. This might take place because of weak selection against recessive or partly recessive deleterious mutations due to permanent heterozygosity of nonrecombining chromosomes. Furthermore, population genetic processes, such as selective sweeps, background selection, and Muller’s ratchet, result in a reduction in N_e, which increase the likelihood of fixation of deleterious mutations. Theory thus predicts that nonrecombining genes should show increased levels of nonsynonymous (d_N) to synonymous substitutions (d_S). We tested this in an avian system by estimating the ratio between d_N and d_S in six gametologous gene pairs located on the Z chromosome and the nonrecombining, female-specific W chromosome. In comparisons, we found a significantly higher d_N/d_S ratio for the W-linked than the Z-linked copy in three of the investigated genes. In a concatenated alignment of all six genes, the d_N/d_S ratio was six times higher for W-linked than Z-linked genes. By using human and mouse as outgroup in maximum likelihood analyses, W-linked genes were found to evolve differently compared with their Z-linked gametologues and outgroup sequences. This seems not to be a consequence of functional diversification because d_N/d_S ratios between gametologous gene copies were consistently low. We conclude that deleterious mutations are accumulating at a high rate on the avian W chromosome, probably as a result of the lack of recombination in this female-specific chromosome. Electronic Supplementary Material Electronic Supplementary material is available for this article at and accessible for authorised users. [Reviewing Editor: Dr. Deborah Charlesworth]     

Balancing oral exposure with Cyp3A4 inhibition in benzimidazole-based IGF-IR inhibitors

3-(Benzimidazol-2-yl)-pyridine-2-one-based ATP competitive inhibitors of Insulin-like Growth Factor 1 Kinase (IGF-IR) were optimized for reduced Cyp3A4 inhibition and improved oral exposure. The use of malonate as methyl anion synthon via S_NAr reaction and double decarboxylation under mild conditions is demonstrated.     

Interaction of pyrophosphate with catalytic and noncatalytic sites of chloroplast ATP synthase

The effect of pyrophosphate (PP_i) on labeled nucleotide incorporation into noncatalytic sites of chloroplast ATP synthase was studied. In illuminated thylakoid membranes, PP_i competed with nucleotides for binding to noncatalytic sites. In the dark, PP_i was capable of tight binding to noncatalytic sites previously vacated by endogenous nucleotides, thereby preventing their subsequent interaction with ADP and ATP. The effect of PP_i on ATP hydrolysis kinetics was also elucidated. In the dark at micromolar ATP concentrations, PP_i inhibited ATPase activity of ATP synthase. Addition of PP_i to the reaction mixture at the step of preliminary illumination inhibited high initial activity of the enzyme, but stimulated its activity during prolonged incubation. These results indicate that the stimulating effect of PP_i light preincubation with thylakoid membranes on ATPase activity is caused by its binding to ATP synthase noncatalytic sites. The inhibition of ATP synthase results from competition between PP_i and ATP for binding to catalytic sites. Published in Russian in Biokhimiya, 2009, Vol. 74, No. 7, pp. 956–962.     

Nitrogen Dynamics in the Steeply Stratified,Temperate Lake Verevi,Estonia

The dynamics of different nitrogen compounds and nitrification in diverse habitats of a stratified Lake Verevi (Estonia) was investigated in 2000–2001. Also planktonic N₂-fixation (N₂fix) was measured in August of the observed years. The nitrogen that accumulated in the hypolimnion was trapped in the non-mixed layer during most of the vegetation period causing a concentration of an order of magnitude higher than in the epilimnion. The ammonium level remained low in the epilimnion (maximum 577 mgN m⁻³, average 115 mgN m⁻³) in spite of high concentrations in the hypolimnion (maximum 12223 mgN m⁻³, average 4807 mgN m⁻³). The concentrations of NO₂⁻ and NO₃⁻ remained on a low level both in the epilimnion (average 0.94 and 9.09 mgN m⁻³, respectively) and hypolimnion (average 0.47 and 5.05 mgN m⁻³, respectively). N₂fix and nitrification ranged from 0.30 to 2.80 mgN m⁻³ day⁻¹ and 6.0 to 107 mgN m⁻³ day⁻¹, respectively; the most intensive processes occurred in 07.08.00 at depths of 2 and 5 m, accordingly. The role of N₂fix in the total nitrogen budget of Lake Verevi (in August 2000 and 2001) was negligible while episodically in the nitrogen-depleted epilimnion the N₂fix could substantially contribute to the pool of mineral nitrogen. Nitrification was unable to influence nitrogen dynamics in the epilimnion while some temporary coupling with ammonium dynamics in the hypolimnion was documented.     

Ab initio computational insight into the ion-pair SN2 reaction of lithium isothiocyanate and methyl fluoride in the gas phase and in acetone solution

The ion-pair S_N2 reaction LiNCS + CH₃F with two mechanisms, inversion and retention, was investigated at the MP2(full)/6-311+G**//HF/6-311+G** level in the gas phase and in acetone solution. All HF-optimized structures were confirmed by vibrational frequency analysis. Based on IRC analyses, eight possible reaction pathways in the title reaction are proposed. The inversion mechanism through a six-membered-ring transition-state structure is the most favorable. Methyl thiocyanate should form preferentially in the gas phase and the more stable methyl isothiocyanate will be the main product in CH₃COCH₃. The retardation of the reaction in CH₃COCH₃ solution was attributed to the differences in the solvation free energies in the separated reactants and transition structures. All of the theoretical results are consistent with the experiment.     

Heterometal cubane-type WFe3S4 and related clusters trigonally symmetrized with hydrotris(3,5-dimethylpyrazolyl)borate

The scope of formation and structures of tungsten-iron-sulfur clusters has been explored using reactions based on [(Tp*)WS₃]¹⁻ (1) as the ultimate precursor. The reaction system 1/FeCl₂/NaSEt/S affords the cubane cluster [(Tp*)WFe₃S₄Cl₃]¹⁻ (2), which with NaSEt is converted to [(Tp*)WFe₃S₄(SEt)₃]¹⁻ (3).Clusters 2 and 3 contain the cubane [WFe₃(μ₃-S)₄]³⁺ core.Complex 1 with FeCl₂/NaSEt forms [(Tp*)WFe₂S₃Cl₂(SEt)]¹⁻ (4) with the cuboidal [WFe₂(μ₂-S)₂(μ₃-S)(μ₂-SR)]²⁺ core.Treatment of 2 with excess Et₃P yields the edge-bridged double [(Tp*)₂W₂Fe₆S₈(PEt₃)₄] (5) with the [W₂Fe₆(μ₃-S)₆(μ₄-S)₂] core. Reaction of 2 with excess leads a mixture of products, from which [(Tp*)₂W₂Fe₅S₉Na(SH)(MeCN)]³⁻(6) was identified.This cluster, as closely related [(Tp)₂Mo₂Fe₆S₉(SH)₂]³⁻, exhibits a core topology [W₂Fe₅Na(μ₂-S)₂(μ₃-S)₆(μ₆-S)] very similar to the P^N cluster of nitrogenase. All reactions were carried out in acetonitrile. The structures of 2-6 were established crystallographically as Et₄N⁺ salts. In the cubane series, substitution of tungsten for molybdenum decreases the [MFe₃S₄]^3+/2+ redox potential by ca. 0.20 V but has a negligible effect on electron distribution. This work expands the small set of previously known weak-field W-Fe-S clusters, demonstrates the existence of tungsten-containing edge-bridged double cubanes and clusters with the P^N core topology, and introduces a new cuboidal core structure as found in 4 (Tp = hydrotris(pyrazolyl)borate, Tp* = hydrotris(3,5-dimethylpyrazolyl)borate).     

Chemistry of selenium and tellurium with tetrachelate and macrocyclic ligands

Treatment of meso(tetra-p-tolyl)porphryin, H₂(TTP), or Li₂(TTP) with OSeCl₂ or OSe(NMe₂)₂ in toluene or THF resulted in the formation of the diprotonated porphyrin, [H₄(TTP)]Cl₂ and indicated the reluctance of selenium to insert into the porphyrin core. The molecular structure of [H₄(TTP)]Cl₂ was determined by single-crystal X-ray diffraction and exhibited the typical saddle-shape distortion of diprotonated porphyrins. The molecular structure of (p-MeO-Ph)₂Te(salen) was reexamined by X-ray diffraction. The geometry of the Te(IV) center is strongly influenced by a stereochemically active lone pair and is best described as having an AX₄E disphenoid structure in which the salen oxygen atoms occupy axial positions and the two anisyl ligands reside in equatorial sites. Distances between Te and the salen nitrogen atoms are 2.852(3) and 2.984(3) Å and are largely nonbonding.     

Interaction of the tylosin-resistance methyltransferase RlmA II at its rRNA target differs from the orthologue RlmA I

RlmA^II methylates the N1-position of nucleotide G748 in hairpin 35 of 23 S rRNA. The resultant methyl group extends into the peptide channel of the 50 S ribosomal subunit and confers resistance to tylosin and other mycinosylated macrolide antibiotics. Methylation at G748 occurs in several groups of Gram-positive bacteria, including the tylosin-producer Streptomyces fradiae and the pathogen Streptococcus pneumoniae. Recombinant S. pneumoniae RlmA^II was purified and shown to retain its activity and specificity in vitro when tested on unmethylated 23 S rRNA substrates. RlmA^II makes multiple footprint contacts with nucleotides in stem-loops 33, 34 and 35, and does not interact elsewhere in the rRNA. Binding of RlmA^II to the rRNA is dependent on the cofactor S-adenosylmethionine (or S-adenosylhomocysteine). RlmA^II interacts with the same rRNA region as the orthologous enzyme RlmA^I that methylates at nucleotide G745. Differences in nucleotide contacts within hairpin 35 indicate how the two methyltransferases recognize their distinct targets.     

2‐Azapurine Nucleosides: Synthesis,Properties, and Base Pairing of Oligonucleotides

This review deals with 2‐azapurine (imidazo[4,5‐d] [1,2,3]triazine) nucleosides and closely related analogs. Different routes are described to yield the desired target compounds, including a sequence of ring‐opening and ring‐closure reactions performed on purine nucleosides or direct glycosylation of a 2‐azapurine nucleobase with a sugar halide. Further, physical and spectroscopic properties of 2‐azapurine nucleosides are discussed, including fluorescence, ¹³C‐NMR data, single‐crystal X‐ray analyses, and conformation studies on selected compounds; new biological data are presented. The second part of this review is dedicated to oligonucleotides containing 2‐azapurines, including building‐block (phosphoramidite) preparation and their use in solid‐phase oligonucleotide synthesis. Base‐pairing properties of 2‐azapurine nucleosides as surrogates of canonical constituents of DNA were evaluated.     

Cell death induced by N-methyl-N-nitrosourea, a model SN1 methylating agent, in two lung cancer cell lines of human origin

New therapeutic approaches are needed for lung cancer, the leading cause of cancer death. Methylating agents constitute a widely used class of anticancer drugs, the effect of which on human non small cell lung cancer (NSCLC) has not been adequately studied. N-methyl-N-nitrosourea (MNU), a model S_N1 methylating agent, induced cell death through a distinct mechanism in two human NSCLC cell lines studied, A549(p53^wt) and H157(p53^null). In A549(p53^wt), MNU induced G2/M arrest, accompanied by cdc25A degradation, hnRNP B1 induction, hnRNP C1/C2 downregulation. Non-apoptotic cell death was confirmed by the lack of increase in the sub-G1 DNA content, Poly (ADP-ribose) polymerase cleavage and caspase-3, -7 activation. In H157(p53^null), MNU induced apoptotic cell death, confirmed by cytofluorometry of DNA content and immunodetection of apoptotic markers, accompanied by overexpression of hnRNP B1 and C1/C2. Thus, the mechanism of the cell death induced by S_N1 methylating agents is cell type-dependent and must be assessed prior treatment.