Efficient conjugation and preferential DNA binding of oligonucleotides containing 2′-O-(2-oxoethyl)arabinouridine

Oligodeoxyribonucleotides were synthesized that contain a novel nucleoside, 2′-O-(2-oxoethyl)arabinouridine. Whereas such oligonucleotides showed only a slight reduction in the T_M values of their complexes with complementary DNA, a significant destabilization was observed in the case of duplexes formed with RNA. This may be explained by the C_2′-endo conformation of 2′-O-(2,3-dihydroxypropyl)arabinouridine as demonstrated by NMR experiments in D₂O. The modified oligonucleotides were used to synthesize a number of conjugates with dyes, biotin and a N-modified laminin peptide, by hydrazone and oxime formation. We suggest that the 2′-arabinoaldehyde-containing DNA duplexes may be valuable tools for affinity modification of DNA-binding proteins.     

Synthesis of phosphamide conjugates of 5"-mononucleotides with carcinine and its analogs

The reactions of histamine, the natural dipeptide carcinine (-Ala-HA), and its analogs with 5"-monodeoxyribonucleotides (dNMP) in the presence of triphenylphosphine, 2,2"-dipyridyl disulfide, and N-methylimidazole were studied. The yield of phosphamide derivatives decreases from 72% to 17% as the length of the linker group between the imidazole ring and the terminal aliphatic amino group is increased. Hydrolytic stability of the resulting conjugates was examined. The stability of the bonds in the —O—P(O)₂—NH— group linking the nucleotide and peptide portions of the conjugate depends on the nature of the heterocyclic base of the nucleotide and decreases in the series dTMP > dCMP > dAMP.     

Solid state N and C NMR study of dioxomolybdenum (VI) complexes of Schiff bases derived from trans-1,2-cyclohexanediamine

The ¹³C, ¹⁵N CP MAS NMR and FT-IR spectra of dioxomolybdenum (VI) complexes of trans-N,N′-bis-(R-salicylidene)-1,2-cyclohexanediamine (R=H, R=3,5-diCl, R=3,5-diBr, R=4,6-diOCH₃), trans-N,N′-bis-(2-OH-naphthylidene)-1,2-cyclohexanediamine and trans-N-(salicylidene)-N′-(2-OH-naphthylidene)-1,2-cyclohexanediamine have been measured. Comparative analysis of the NMR and IR spectra of the complexes with those of the corresponding ligands has shown that the complexation of the di-Schiff bases leads to changes in the conformation of the ligands and the charge redistribution. The asymmetric structure and non-planar structure of the complexes have been suggested.     

1,3-Dipolar cycloaddition of diazomethane and diazocyclopropane to 2-fluoro-3-methylbutadiene and thermal transformations of fluorine-containing vinylpyrazolines and vinylcyclopropanes

Reactions of 2-fluoro-3-methylbuta-1,3-diene with diazomethane in ether at 15 °C and with diazocyclopropane generated in situ by decomposition of N-cyclopropyl-N-nitrosourea in the presence of K₂CO₃ in CH₂Cl₂ at –10 °C selectively involve the double bond at the methyl group to give 3-(1-fluorovinyl)-3-methylpyrazolines. Thermal dediazotization of the latter at 250 °C yields 1-(1-fluorovinyl)-1-methylcyclopropane and -spiropentane 5, which are capable of isomerizing, under more severe conditions (400—600 °C), into 1-fluoro-2-methylcyclopent-1-ene and 5-fluoro-4-methylspiro[2.4]hept-4-ene (7), respectively. Spiropentane derivative 5 partially isomerizes into 1-fluoro-2-methyl-3-methylidenecyclohex-1-ene. In a similar way, thermolysis of 6-(2,3,3-trifluorocyclobut-1-enyl)-4,5-diazaspiro[2.4]hept-4-ene at 400 °C gives a mixture of 1-(spiropentyl)-2,3,3-trifluorocyclobut-1-ene and 2,3,3-trifluoro-1-(2-methylidenecyclobutyl)cyclobut-1-ene. Thermolysis of 1-cyclopropyl-2,3,3-trifluorocyclobut-1-ene at 550—620 °C affords a mixture of 1-(trifluorovinyl)cyclopentene and 2,3-difluorotoluene.     

Formation and reactions of substituted diazocyclopropanes and cyclopropyldiazonium ions

Decomposition of N-nitroso-N-cyclopropylureas at 5—7 °C on treatment with K₂CO₃ containing 15—20% H₂O allows simultaneous generation of both substituted diazocyclopropanes and cyclopropyldiazonium ions, which can react according to 1,3-dipolar cycloaddition or azo-coupling pattern with appropriate substrates. The nature of substituents in the cyclopropyl ring have a pronounced influence on the product ratio (and, probably, on the equilibrium between the diazo compound and the diazonium ion). Thus, on treatment with a base in the presence of equimolar amounts of methyl metacrylate as a trap for the diazo compound and 2-naphthol as a trap for the diazonium ion, N-cyclopropyl- and N-(2,2-dimethylcyclopropyl)-N-nitrosourea azo coupling products predominate. Conversely, N-(2,2-dichlorocyclopropyl)-N-nitrosourea is transformed predominantly into 1,3-cycloaddition products. A rationalization for the experimental data is proposed.     

Synthesis and properties of oligodeoxyribonucleotides containing 2’-<Emphasis Type="Italic">O</Emphasis>-(2,3-dihydroxypropyl)- and 2’-<Emphasis Type="Italic">O</Emphasis>-(2-oxoethyl)arabinouridine residues

2’-O-(2,3-Dihydroxypropyl)arabinouridine-containing oligodeoxyribonucleotides were synthesized starting from a new modified nucleoside, viz., 2’-O-(2,3-dihydroxypropyl)arabinouridine, and the corresponding 3’-phosphoramidite. Oxidation of these oligodeoxyribonucleotides with sodium periodate afforded oligonucleotides containing 2’-O-(2-oxoethyl)arabinouridine residues. Subsequent modification of the aldehyde-containing oligonucleotides involved the reactions with 9-hydrazinoacridine and N-aminooxyacetyl peptide and reductive amination by 4-(1-pyrenyl)butyrohydrazide and biotin hydrazide. Thermal stabilities of duplexes of modified oligodeoxyribonucleotides with complementary oligodeoxyribonucleotides are slightly lower than those of natural duplexes. Duplexes with complementary oligoribonucleotides are substantially destabilized.__________Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 1, pp. 233–241, January, 2005.     

Bis-Amiridines as Acetylcholinesterase and Butyrylcholinesterase Inhibitors: N-Functionalization Determines the Multitarget Anti-Alzheimer’s Activity Profile

Using two ways of functionalizing amiridine—acylation with chloroacetic acid chloride and reaction with thiophosgene—we have synthesized new homobivalent bis-amiridines joined by two different spacers—bis-N-acyl-alkylene (3) and bis-N-thiourea-alkylene (5) —as potential multifunctional agents for the treatment of Alzheimer’s disease (AD). All compounds exhibited high inhibitory activity against acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) with selectivity for BChE. These new agents displayed negligible carboxylesterase inhibition, suggesting a probable lack of untoward drug–drug interactions arising from hydrolytic biotransformation. Compounds 3 with bis-N-acyl-alkylene spacers were more potent inhibitors of both cholinesterases compared to compounds 5 and the parent amiridine. The lead compounds 3a–c exhibited an IC₅₀(AChE) = 2.9–1.4 µM, IC₅₀(BChE) = 0.13–0.067 µM, and 14–18% propidium displacement at 20 μM. Kinetic studies of compounds 3a and 5d indicated mixed-type reversible inhibition. Molecular docking revealed favorable poses in both catalytic and peripheral AChE sites. Propidium displacement from the peripheral site by the hybrids suggests their potential to hinder AChE-assisted Aβ₄₂ aggregation. Conjugates 3 had no effect on Aβ₄₂ self-aggregation, whereas compounds 5c–e (m = 4, 5, 6) showed mild (13–17%) inhibition. The greatest difference between conjugates 3 and 5 was their antioxidant activity. Bis-amiridines 3 with N-acylalkylene spacers were nearly inactive in ABTS and FRAP tests, whereas compounds 5 with thiourea in the spacers demonstrated high antioxidant activity, especially in the ABTS test (TEAC = 1.2–2.1), in agreement with their significantly lower HOMO-LUMO gap values. Calculated ADMET parameters for all conjugates predicted favorable blood–brain barrier permeability and intestinal absorption, as well as a low propensity for cardiac toxicity. Thus, it was possible to obtain amiridine derivatives whose potencies against AChE and BChE equaled (5) or exceeded (3) that of the parent compound, amiridine. Overall, based on their expanded and balanced pharmacological profiles, conjugates 5c–e appear promising for future optimization and development as multitarget anti-AD agents.     

Molecular recognition capability and rheological behavior in solution of novel lactone-based glycopolymers

Novel glycopolymers have been prepared from ethylene–vinyl alcohol copolymers, EVOH. For that purpose, three distinct aminosaccharides (N-(4-aminobutyl)-d-gluconamide (NABG), N-(4-aminobutyl)-O-β-d-galactopyranosyl-(1 → 4)-d-gluconamide (NABL) and N-(4-aminobutyl)-O-β-d-glucopyranosyl-(1 → 4)-d-gluconamide (NABM) have been synthesized. The previous functionalization of these EVOH copolymers is mandatory to activate their hydroxyl reactivity before the subsequent coupling reaction with the aminosaccharides. The activation with carboxylic acid groups by reaction with phthalic anhydride has been chosen in the current investigation because of its almost quantitative yield and the subsequent high modification extent reached (>60%). The glycopolymers that turned out water-soluble (i.e., those based on NABL and NABM) have shown a reversible network formation unusually described in glycopolymers. In addition, their capability to interact with lectins, particularly Concanavalin A and Ricinus communis Agglutinin, has confirmed the specificity of lectin recognition in these glycopolymers.     

Synthesis,Neuroprotection, and Antioxidant Activity of 1,1′-Biphenylnitrones as α-Phenyl-N-tert-butylnitrone Analogues in In Vitro Ischemia Models

Herein, we report the neuroprotective and antioxidant activity of 1,1′-biphenyl nitrones (BPNs) 1–5 as α-phenyl-N-tert-butylnitrone analogues prepared from commercially available [1,1′-biphenyl]-4-carbaldehyde and [1,1′-biphenyl]-4,4′-dicarbaldehyde. The neuroprotection of BPNs 1-5 has been measured against oligomycin A/rotenone and in an oxygen–glucose deprivation in vitro ischemia model in human neuroblastoma SH-SY5Y cells. Our results indicate that BPNs 1–5 have better neuroprotective and antioxidant properties than α-phenyl-N-tert-butylnitrone (PBN), and they are quite similar to N-acetyl-L-cysteine (NAC), which is a well-known antioxidant agent. Among the nitrones studied, homo-bis-nitrone BPHBN5, bearing two N-tert-Bu radicals at the nitrone motif, has the best neuroprotective capacity (EC₅₀ = 13.16 ± 1.65 and 25.5 ± 3.93 μM, against the reduction in metabolic activity induced by respiratory chain blockers and oxygen–glucose deprivation in an in vitro ischemia model, respectively) as well as anti-necrotic, anti-apoptotic, and antioxidant activities (EC₅₀ = 11.2 ± 3.94 μM), which were measured by its capacity to reduce superoxide production in human neuroblastoma SH-SY5Y cell cultures, followed by mononitrone BPMN3, with one N-Bn radical, and BPMN2, with only one N-tert-Bu substituent. The antioxidant activity of BPNs 1-5 has also been analyzed for their capacity to scavenge hydroxyl free radicals (82% at 100 μM), lipoxygenase inhibition, and the inhibition of lipid peroxidation (68% at 100 μM). Results showed that although the number of nitrone groups improves the neuroprotection profile of these BPNs, the final effect is also dependent on the substitutent that is being incorporated. Thus, BPNs bearing N-tert-Bu and N-Bn groups show better neuroprotective and antioxidant properties than those substituted with Me. All these results led us to propose homo-bis-nitrone BPHBN5 as the most balanced and interesting nitrone based on its neuroprotective capacity in different neuronal models of oxidative stress and in vitro ischemia as well as its antioxidant activity.     

Transformations of the chiral diphosphine rhodium catalyst [(1,5-COD)Rh(—)R,R-DIOP]+CF3SO3– under conditions of hydrogenation

Transformation products of the cationic rhodium complex [(1,5-COD)Rh(—)R,R-DIOP]⁺CF₃SO₃ ^– (1) (COD is cycloocta-1,5-diene and DIOP is (±)-2,3-O-isopropylidene-2,3-dihydroxy-1,4-bis(diphenylphosphino)butane), which were obtained in its reactions with molecular hydrogen, base (NEt₃), and solvents in the absence of a substrate, were investigated by ¹H and ³¹P NMR spectroscopy. The solvate complexes [(Solv)₂Rh(—)R,R-DIOP]⁺CF₃SO₃ ^–, which were generated from complex 1 in its reaction with molecular hydrogen, underwent destruction of the diphosphine ligand with elimination of benzene and were subjected to oxidation by traces of moisture and oxygen to form the DIOP dioxide complex with Rh^I. In the absence of hydrogen, complex 1 in solutions produced the diphosphine dioxide rhodium(i) complex and mono- and binuclear rhodium(i) solvate complexes. The scheme of deactivation of the complex in the absence of the substrate was proposed. The catalytic activity of the solvate complexes [(ArH)Rh(—)R,R-DIOP]⁺CF₃SO₃ ^–, which contain benzene, p-xylene, and mesitylene in the coordination sphere, was studied in hydrogenation of Z--acetamidocinnamic acid.     

New results in the ammonolysis of hexafluoro-cyclo-triphosphazene: Crystal structure of P3N3F5–NH–P3N3F4NH2

The reaction of hexafluoro-cyclo-triphosphazene P₃N₃F₆ with ammonia in acetonitrile has been studied. New compounds, (2-imino-2,4,4,6,6-pentafluoro-2λ⁵,4λ⁵,6λ⁵-cyclo-triphosphaza-1,3,5-trienyl)-2-amino-4,4,6,6-tetrafluoro-2λ⁵,4λ⁵,6λ⁵-cyclo-triphosphaza-1,3,5-triene, P₃N₃F₅–NH–P₃N₃F₄NH₂ (2) and cis and trans isomers of non-gem-2,4-diamino-2,4,6,6-tetrafluoro-2λ⁵,4λ⁵,6λ⁵-cyclo-triphosphaza-1,3,5-triene, P₃N₃F₄(NH₂)₂ (4, 5)_, were detected by GC/MS, and ³¹P NMR spectroscopy in reaction mixtures. X-ray diffraction analysis of P₃N₃F₅–NH–P₃N₃F₄NH₂ (2) revealed two conformational polymorphs, 2A and 2B, the latter being built up of two different conformers that were further denoted as 2B_a (the same as the single conformer in 2A) and 2B_b. The compound 2 was characterized by spectroscopic methods and its 2D potential energy surface (PES) was described by density functional theory computations depending on two dihedral angles. The calculated PES spans over 30 kJ/mol in energy including 8 local minima and all first and second order saddle points. The occurrence of the two experimentally observed conformers 2B_a and 2B_b seems to be governed by crystal packing effects.     

Generation and reactions of diazo-3,3-dideuterio-2-methylidenecyclopropane and isomerization of 3",3"-dideuterio-2"-methylidenespiro[4,5-dihydropyrazole-5,1"-cyclopropanes] into isopropenylpyrazoles

N-(1,3,3-Trideuterio-2-methylidenecyclopropyl)-N-nitrosourea was synthesized and its decomposition on treatment with K₂CO₃ in the presence of acrylonitrile and ethyl acrylate or on treatment with MeONa in the absence of unsaturated substrates was studied. The rate of decomposition of the nitrosourea is much lower than that of the nondeuterated analog. The use of acrylates for trapping the intermediate 3,3-dideuterio-1-diazo-2-methylidenecyclopropane results in the corresponding 2"-methylidenespiro[4,5-dihydropyrazole-5,1"-cyclopropanes] containing two deuterium atoms in the cyclopropane fragment. The resulting dihydropyrazoles are isomerized almost entirely over a period of 1—3 days to give a mixture (1 : 1) of isopropenylpyrazoles in which both deuterium atoms occur either in the methyl or in the methylidene groups of the isopropenyl substituent. A possible mechanism of this transformation is considered.     

Synthesis of 2′-O-[2-[(N,N-dialkylamino)oxy]ethyl]-modified oligonucleotides: hybridization affinity, resistance to nuclease, and protein binding characteristics

Synthesis of a series of 2′-O-[2-[(N,N-dialkylamino)oxy]ethyl]-modified 5-methyluridine nucleoside phosphoramidites and solid supports are described. Using these monomers, modified oligonucleotides containing phosphodiester linkages were synthesized in high yields. These modified oligonucleotides showed enhanced binding affinity to the complementary RNA (and not to DNA) and excellent nuclease stability with t_1/2>24 h. The human serum albumin binding properties of modified oligonucleotides have been evaluated to assess their transport and toxicity properties.     

The synthesis, structure and reactivity of aldehyde substituted η-allylic complexes of molybdenum

Reaction of cis-[Mo(NCMe)₂(CO)₂(η⁵-L)][BF₄] (L=C₅H₅ or C₅Me₅) with 1-acetoxybuta-1,3-diene gives the cationic complexes [Mo{η⁴-syn-s-cis-CH₂CHCHCH(OAc)}(CO)₂(η⁵-L)][BF₄], which, on reaction with aqueous NaHCO₃/CH₂Cl₂, afford good yields of the anti-aldehyde substituted complexes [Mo{η³-exo-anti-CH₂CHCH(CHO)}(CO)₂(η⁵-L)] 2 (L=C₅Me₅), 4 (L=C₅H₅)]. The corresponding η⁵-indenyl substituted complex 5 was prepared by protonation (HBF₄·OEt₂) of [Mo(η³-C₃H₅)(CO)₂(η⁵-C₉H₇)] followed by addition of CH₂=CHCH=CH(OAc) and hydrolysis (aq. NaHCO₃/CH₂Cl₂). An X-ray crystallographic study of complex 2 confirmed the structure and showed that there is a contribution from a zwitterionic form involving donation of electron density from the molybdenum to the aldehyde carbonyl group. Treatment of 2 and 4, in methanol solution, with NaBH₄ afforded the alcohols [Mo{η³-exo-anti-CH₂CHCHCH₂(OH)}(CO)₂(η⁵-L)] [6 (L=C₅H₅), 8 (L=C₅Me₅)]; however, prolonged (30 h) reaction with NaBH₄/MeOH surprisingly gave good yields of the methoxy-substituted complexes [Mo{η³-exo-anti-CH₂CHCHCH₂(OMe)}(CO)₂(η⁵-L)] [7 (L=C₅H₅), 9 (L=C₅Me₅)], the structure of 7 being confirmed by single crystal X-ray crystallography. This methoxylation reaction can be explained by coordination of the hydroxyl group present in 6 and 8 onto B₂H₆ to form the potential leaving group HOBH₃⁻, which on ionisation affords [Mo(η⁴-exo-buta-1-3-diene)(CO)₂(η⁵-L)]⁺ which is captured by reaction with OMe⁻. Complex 8 is also formed in good yield on reaction of 2 with HBF₄·OEt₂ followed by treatment of the resulting cation [Mo{η⁴-exo-s-cis-syn-CH₂CHCHCH(OH)}(CO)₂(η⁵-C₅Me₅)][BF₄] with Na[BH₃CN]. Reaction of 4 with the Grignard reagents MeMgI, EtMgBr or PhMgCl afforded moderate yields of the alcohols [Mo{η³-exo-anti-CH₂CHCHCH(OH)R}(CO)₂(η⁵-C₅H₅)] [11 (R=Me), 12 (R=Et), 13 (R=Ph)]. Similarly, treatment of 2 with MeLi gave the corresponding alcohol 14. An attempt to carry out the Oppenauer oxidation [Al(OPr′)₃/Me₂CO] of 11 resulted in an elimination reaction and the formation of the η³-s-pentadienyl complex [Mo{η³-exo-anti-CH₂CHCH(CHCH₂)}(CO)₂(η⁵-C₅H₅)], which was structurally identified by X-ray crystallography. Interestingly, oxidation of 6 with [Bu₄ⁿN][RuO₄]/morpholine-N-oxide affords the aldehyde complex, 4 in good yield. Finally, reaction of 11 with [NO][BF₄] followed by addition of Na₂CO₃ affords the fur-3-ene complex [Mo{η²-

(H)Me}(CO)(NO)(η⁵-C₅H₅)].     

Crystal and molecular structure of a 1:1 complex of a chiral α-d-glucosido-benzo-18-crown-6 and potassium thiocyanate

C₂₈H₃₆O₁₀. KSCN is monoclinic, space groupP2₁ withZ=2,a=10.390(3),b=8.959(7),c=16.377(7) Å, =92.49(5)°. FinalR=0.053 for 1437 reflections measured at room temperature. The K^– ion lies on the least-squares plane formed by the six oxygen atoms in the macrocyclic ring. The SCN^– ion was found on the same face of the macrocycle as the chiral glucopyranoside moiety.Methyl-4,6-O-benzylidene-2,3-O-(1,2-bis(ethoxyethoxy)benzenediyl)--d-glucopyranoside.     

2′-O-Lysylaminohexyladenosine modified oligonucleotides

Abstract  

Development of therapeutically active oligonucleotides for sequence-specific gene knockdown relies on chemical modifications that confer high stability and target affinity and ideally enable cellular uptake. 2′-O-Lysylaminohexyluridine-containing antisense and siRNA oligonucleotides have been shown to be well suited for gene knockdown. They are highly resistant to enzymatic degradation while having good affinity for the targeted RNA strand and efficiently down-regulate their target in cell culture tumor models. The 2′-O-lysylaminohexyl modification was expanded to adenosine nucleosides. The corresponding phosphoramidite building block was prepared in a straightforward procedure comprising six steps starting from adenosine. After 2′-O-alkylation with N-(6-bromohexyl)phthalimide and removal of the N-protecting group, the protected lysine was specifically attached to the alkylamino group. Incorporation of 2′-O-lysylaminohexyladenosine nucleotides in a test sequence confirmed that the cationic chains lead only to minor duplex destabilization and do not disturb the duplex structure. Results further emphasize the advantageous properties of 2′-O-lysylaminohexyl modified oligonucleotides for therapeutic applications.     

Lipase-mediated deracemization of secondary 1-phenyl-substituted propargylic alcohols of different topology

Acetylation of (±)-1-phenylnon-2-yn-1-ol, (±)-1-phenylhept-1-yn-3-ol, and (±)-1-phenylundec-4-yn-3-ol ((±)-5) in the presence of lipase from Candida cylindracea (CCL) proceeds slowly to give products with ee 20%. The acetates of these alcohols are hydrolyzed in the presence of porcine pancreatic lipase (PPL) equally unsatisfactorily. The (⁶-arene)tricarbonylchromium complex of alcohol (±)-5 is acetylated in the presence of CCL up to 22% conversion to give (R)-acetate whose oxidative decomplexation followed by saponification results in alcohol (R)-(–)-5 with ee 95%. The configuration of alcohols (–)-5 and (+)-5 was determined by NMR spectroscopy of their esters with (R)- and (S)-Mosher"s acids.     

Improved Synthesis of Phosphoramidite-Protected N6-Methyladenosine via BOP-Mediated SNAr Reaction

N⁶-methyladenosine(m⁶A) is the most abundant modification in mRNA. Studies on proteins that introduce and bind m⁶A require the efficient synthesis of oligonucleotides containing m⁶A. We report an improved five-step synthesis of the m⁶A phosphoramidite starting from inosine, utilising a 1-H-benzotriazol-1-yloxytris(dimethylamino)phosphoniumhexafluorophosphate (BOP)_-mediated S_NAr reaction in the key step. The route manifests a substantial increase in overall yield compared to reported routes, and is useful for the synthesis of phosphoramidites of other adenosine derivatives, such as ethanoadenosine, an RNA analogue of the DNA adduct formed by the important anticancer drug Carmustine.