Polycationic catalysts for phosphodiester bond cleavage on the basis of 1,4-diazabicyclo[2.2.2]octane

A number of tetracationic compounds capable of phosphodiester bond cleavage within a 21-membered ribooligonucleotide were designed and synthesized. The artificial ribonucleases represent two residues of quaternized 1,4-diazabicyclo[2.2.2]octane bearing alkyl substituents of various lengths and connected with a rigid linker. The efficiency of cleavage of phosphodiester bonds in an RNA target depends on the linker structure and the length of alkyl substituent.     

Chemical ribonucleases: VII. Effect of positively charged RNA-binding domains and hydrophobic fragments of the conjugates based on 1,4-diazabicyclo[2.2.2]octane and imidazole on their ribonuclease activity

The effect of the total positive charge in the RNA-binding domain of chemical ribonucleases that are conjugates of bisquaternary salts of 1,4-diazabicylo[2.2.2]octane and imidazole on the cleavage of an HIV-1 RNA fragment was studied. An increase in the positive charge from +2 to +4 was shown to result in a significant growth in the ribonuclease activity. Possible mechanisms of the interactions between structural moieties of chemical ribonucleases and RNA that enable an effective catalysis of the cleavage of phosphodiester bonds are discussed.     

Chemical ribonucleases: VII. Effect of positively charged RNA-binding domains and hydrophobic fragments of the conjugates based on 1,4-diazabicyclo[2.2.2]octane and imidazol on their ribonuclease activity

The effect of the total positive charge in the RNA-binding domain of chemical ribonucleases that are conjugates of bisquaternary salts of diazabicyclo[2.2.2]octane and imidazol on the cleavage of an HIV-1 RNA fragment was studied. An increase in the positive charge from +2 to +4 was shown to result in a significant growth in the ribonuclease activity. Possible mechanisms of the interactions between structural moieties of chemical ribonucleases and RNA that enable an effective catalysis of the cleavage of phosphodiester bonds are discussed.     

Toward the development of metal-free synthetic nucleases: cleavage of a model substrates by 1,4-diazabicyclo[2.2.2]octane derivatives

Artificial ribonucleases of A(n)BCL series were synthesized by solid-phase method. They consist of a hydrophobic alkyl radical A (n = 3-12 carbon atoms), an "RNA-binding domain" B (bisquaternary salt of 1,4-diazabicyclo[2.2.2]octane), a "catalytic domain" C (histidine residue) and a "linker" L that joins the domains B and C. The effect of the alkyl radical on the catalytic properties of the chemical catalyst was studied using three activated phosphate ester substrates: p-nitrophenyl phosphate, bis-p-nitrophenyl phosphate, and thymidine-3'-p-nitrophenyl phosphate.     

Biological evaluation of tetracationic compounds based on two 1,4-diazabicyclo[2.2.2]octane moieties connected by different linkers

A series of 1,4-diazabicyclo[2.2.2]octane derivatives differing by linker moiety was evaluated for activity against several strains of both Gram-positive and Gram-negative bacteria including drug-resistant strains, one strain of fungus and influenza virus A/Puerto Rico/8/34 (H1N1). All compounds exhibited high antibacterial activity against all bacteria except Proteus vulgaris. The minimum inhibitory concentrations (MICs) of compound 1c with an o-phenylenebismethyl linker and compound 1e with a propylene aliphatic linker were found to be low and were comparable or better to the reference drug ciprofloxacin for Pseudomonas aeruginosa and Staphylococcus aureus. Additionally, a time-kill assay was performed to examine the bactericidal kinetics. Compounds 1c and 1e displayed rapid killing effects against St. aureus and Ps. aeruginosa after 2 h. Furthermore, compounds 1a–c with aromatic linkers and compound 1e showed the highest antiviral activity.     

Polycations. 18. The synthesis of polycationic lipid materials based on the diamine 1,4-diazabicyclo[2.2.2]octane

Herein is reported the preparation of several series of polyammonium salts that serve as cationic lipids or precursors thereof, and are structurally based on the parent diamine 1,4-diazabicyclo[2.2.2]octane (dabco). Through selective alkylation of dabco a variety of di- and tetracationic lipid species and precursors thereof have been prepared. The resultant materials are of significant interest for a variety of purposes, including serving as antimicrobial agents and antihydrophobic species, the details of which are provided in separate reports.     

An RNA sequence determines the speed of its cleavage by artificial ribonucleases

Phosphodiester bonds in RNA situated between similar nucleotides but in different sequences (context) were cleaved under the action of artificial and natural ribonucleases with different speeds, and the reason for this phenomenon has not yet been fully revealed. In this study, the influence of one-nucleotide substitution on the sensitivity to cleavage of the phosphodiester bonds in linear and structured RNA with homologous sequences is studied for the first time. It is indicated that the introduction of one-nucleotide substitution in the RNA sequence significantly (up to 10 times) changes the speed of the cleavage of the bonds that are separated from the substitution point not only by 1–3, but also 6–8 nucleotides, by artificial ribonucleases. The observed regularities may be explained by the fact that the introduction of a one-nucleotide substitution significantly changes the stacking interactions and the net of hydrogen bonds in the RNA molecule. The applied value of this study consists of the ability of using low-molecular artificial ribonucleases with the aim of choosing the region of the binding of the oligonucleotide in the construction of a conjugate for the site-directed cutting of RNA, because the choice of a phosphodiester bond (motif) easily subjected to cleavage significantly determines the efficacy of artificial ribonucleases of directed action.     

Towards artificial ribonucleases: the sequence-specific cleavage of RNA in a duplex.

Lanthanide complexes covalently attached to oligonucleotides have been shown to cleave RNA in a sequence-specific manner. Efficient cleavage, however, is at present limited to single-stranded RNA regions, as RNA in a duplex is considerably more resistant to strand scission. To overcome this limitation, we have designed and synthesised artificial nucleases comprising lanthanide complexes covalently linked to oligodeoxyribonucleotides which cleave a partially complementary RNA at a bulged site, in the duplex region. Strand scission occurs at or near the bulge. Cleavage of the RNA target by the metal complex can be addressed via the major or the minor groove. In an example of a competitive situation, where the cleavage moiety has access to both a bulge and a single-strand region, transesterification at the bulge is favoured. Such artificial ribonucleases may find application as antisense agents and as tools in molecular biology. In addition, the results may have importance for the design of artificial ribonucleases which are able to act with catalytic turnover.     

Catalysis of singlet oxygen production in the reaction of hydrogen peroxide and hypochlorous acid by 1,4-diazabicyclo[2.2.2]octane (DABCO)

The kinetics of the singlet oxygen production in the hydrogen peroxide plus hypochlorous acid reaction were studied by measuring the time course of the singlet oxygen emission at 1268 nm. The addition of 1,4-diazabicyclo[2.2.2]octane (DABCO) increased the peak intensity of the chemiluminescence, but decreased its duration. The increased rate of singlet oxygen production likely accounts for the enhancement of singlet oxygen dimol emission reported in 1976 by Deneke and Krinsky (J. Am. Chem. Soc. 98, 3041-3042). This phenomenon was not seen when singlet oxygen was generated with the reaction of hypobromous acid and hydrogen peroxide. Thus, the enhancement of red chemiluminescence by DABCO should not be regarded as a general test for the production of singlet oxygen in complex biochemical systems.     

Copper(I)-mediated quaternisation of 1,4-diazabicyclo[2.2.2]octane (DABCO). Crystal structure of bis{(1-chloromethyl-4-aza-1-azoniabicyclo[2.2.2]octane)-μ-chloro-chlorocopper(I)}

Copper(I)-mediated quaternisation of 1,4-diazabicyclo[2.2.2]octane (DABCO) in dichloromethane solvent affords the dichloromethylated ligand, which has been isolated as the copper(I) complex bis{(1-chloromethyl-4-aza-1-azoniabicyclo[2.2.2]octane)-μ-chloro-chlorocopper(I)}. The crystal structure of the product, a discrete dimer [Cu₂(μ-Cl)₂Cl₂(N(C₂H₄)₃NCH₂Cl)₂], has been determined. A similar reaction in a mixture of diiodomethane and dichloromethane yields [C₆H₁₂N₂(CH₂I)]₂(I₃)I, the identity of which was also established by means of crystal-structure determination. The dimeric units of [Cu₂(μ-Cl)₂Cl₂(N(C₂H₄)₃NCH₂Cl)₂] are interconnected by short Cl?H interactions of 2.6 Å to form layers. This Cl?H interaction, which is the sole intermolecular contact of this magnitude, involves the terminal chloride bonded to copper(I).     

Synthesis, crystal structures, and characterization of three mercury(II) halides inorganic-organic hybrid compounds with 1,4-diazabicyclo[2.2.2]octane ligand

Three new hybrid mercury halides compounds with 1,4-diazabicyclo[2.2.2]octan (DABCO) ligand, namely, Hg₂(μ₂-I)₂I₃(H-DABCO) (1), {[Hg₅(μ₂-I)₆I₄(μ₂-DABCO)₂][Hg₂I₄(μ₂-DABCO)]}_n (2) and {[Hg₂(μ₂-Br)₂Br₂(μ₂-DABCO)]·2(HgBr₂)}_n (3), have been synthesized. Compound 1 crystallizes in a P2₁ chiral space group and is a discrete dinuclear mercury(II) compound with inorganic Hg₂(μ₂-I)₂I₃ unit. Compound 2 consists of 1D neutral [Hg₅(μ₂-I)₆I₄(μ₂-DABCO)₂]_n broad polymeric array containing uncommon inorganic decanuclear [Hg₁₀(μ₂-I)₁₂I₈]_n clusters, and neutral guest Hg₂(μ₂-DABCO)I₄ molecules. Compound 3 is composed of a neutral [Hg₂(μ₂-Br)₂Br₂(μ₂-DABCO)]_n polymeric chain and guest inorganic HgBr₂ molecules. In all cases, the halide ions participate in the framework connectivity as bridging ligands. A variety of coordination geometries displayed by the metal sites such as linear, trigonal and tetrahedral are observed in these compounds. Of the three compounds, only compound 3 displays photoluminescence with a emission maximum at 528 nm upon excitation at 468 nm. In addition, these compounds are characterized by IR, elemental analysis, and thermogravimetric analysis.     

The role of metal ions in RNA catalysis

Understanding the catalytic mechanisms of RNA enzymes remains an important and intriguing challenge - one that has grown in importance since the recent demonstration that the ribosome is a ribozyme. At first, it seemed that all RNA enzymes compensate for the limited chemical versatility of ribonucleotide functional groups by recruiting obligatory metal ion cofactors to carry out catalytic chemistry. Mechanistic studies of the large self-splicing and pre-tRNA-processing ribozymes continue to support this idea, yielding increasingly detailed views of RNA active sites as scaffolds for positioning catalytic metal ions. Re-evaluation of the methodologies used to distinguish catalytic and structural roles for metal ions, however, has challenged this notion in the case of the small self-cleaving RNAs. Recent studies of the small ribozymes blur the distinction between catalytic and structural roles for metal ions, and suggest that RNA nucleobases have a previously unrecognized capacity for mediating catalytic chemistry.     

Metal ion catalysis of RNA cleavage by the influenza virus endonuclease

The influenza virus RNA-dependent RNA polymerase protein complex contains an associated RNA endonuclease activity, which cleaves host mRNA precursors in the cell nucleus at defined positions 9-15 nucleotides downstream of the cap structure. This reaction provides capped oligoribonucleotides, which function as primers for the initiation of viral mRNA synthesis. The endonuclease reaction is dependent on the presence of divalent metal ions. We have used a number of divalent and trivalent metal ions alone and in combination to probe the mechanism of RNA cleavage by the influenza virus endonuclease. Virus-specific cleavage was observed with various metal ions, and maximum cleavage activity was obtained with 100 microM Mn2+ or 100 microM Co2+. This activity was about 2-fold higher than that observed with Mg2+ at the optimal concentration of 1 mM. Activity dependence on metal ion concentration was cooperative with Hill coefficients close to or larger than 2. Synergistic activation of cleavage activity was observed with combinations of different metal ions at varying concentrations. These results support a two-metal ion mechanism of RNA cleavage for the influenza virus cap-dependent endonuclease. The findings are also consistent with a structural model of the polymerase, in which the specific endonuclease active site is spatially separated from the nucleotidyl transferase active site of the polymerase module.     

The role of hydrophobic interactions in ankyrin-spectrin complex formation

Spectrin and ankyrin are the key components of the erythrocyte cytoskeleton. The recently published crystal structure of the spectrin-ankyrin complex has indicated that their binding involves complementary charge interactions as well as hydrophobic interactions. However, only the former is supported by biochemical evidence. We now show that nonpolar interactions are important for high affinity complex formation, excluding the possibility that the binding is exclusively mediated by association of distinctly charged surfaces. Along these lines we report that substitution of a single hydrophobic residue, F917S in ankyrin, disrupts the structure of the binding site and leads to complete loss of spectrin affinity. Finally, we present data showing that minimal ankyrin binding site in spectrin is formed by helix 14C together with the loop between helices 15 B/C.     

Design,RNA cleavage and antiviral activity of new artificial ribonucleases derived from mono-, di- and tripeptides connected by linkers of different hydrophobicity

A novel series of metal-free artificial ribonucleases (aRNases) was designed, synthesized and assessed in terms of ribonuclease activity and ability to inactivate influenza virus WSN/A33/H1N1 in vitro. The compounds were built of two short peptide fragments, which include Lys, Ser, Arg, Glu and imidazole residues in various combinations, connected by linkers of different hydrophobicity (1,12-diaminododecane or 4,9-dioxa-1,12-diaminododecane). These compounds efficiently cleaved different RNA substrates under physiological conditions at rates three to five times higher than that of artificial ribonucleases described earlier and displayed RNase A-like cleavage specificity. aRNases with the hydrophobic 1,12-diaminododecane linker displayed ribonuclease activity 3–40 times higher than aRNases with the 4,9-dioxa-1,12-diaminododecane linker. The assumed mechanism of RNA cleavage was typical for natural ribonucleases, that is, general acid-base catalysis via the formation of acid/base pairs by functional groups of amino acids present in the aRNases; the pH profile of cleavage confirmed this mechanism. The most active aRNases under study exhibited high antiviral activity and entirely inactivated influenza virus A/WSN/33/(H1N1) after a short incubation period of viral suspension under physiological conditions.