Ribozyme mimics as catalytic antisense reagents

Hydrolysis of 5',5'-tri- or tetraphosphate-mRNA 5'-cap analogs promoted by Cu2+ or Zn2+ metal ions

Kinetics of the hydrolysis of a P(1)-(7-methylguanosinyl-5') P(3)-(guanosinyl-5') triphosphate (m(7)GpppG), P(1)-(7-methylguanosinyl-5') P(4)- (guanosinyl-5') tetraphosphate (m(7)GppppG), diadenosine-5',5'''-P(1),P(3)-triphosphate (ApppA), and diadenosine-5',5'''-P(1),P(4)-tetraphosphate (AppppA) promoted by Cu(2+) or Zn(2+) has been investigated. Time-dependent products distributions at various metal ion concentrations have been determined by CZE and HPLC-RP. The results show that in acidic conditions, in the presence of metal ion, the predominant hydrolytic reaction is the cleavage of 5',5'-oligophosphate bridge. The 5',5'-oligophosphate bridge of the dinucleotides studied is hydrolyzed by Cu(2+) more efficiently than by Zn(2+). At the catalyst concentration of 2 mM the cleavage of the 5',5'-triphosphate bridge of m(7)GpppG was ∼3.6 times faster, and that of the tetraphosphate bridge of m(7)GppppG ∼2.3-fold faster in the presence of Cu(2+) compared to the Zn(2+) ion, applied as catalysts. Dependence of the rates of hydrolysis on the catalyst concentration was in some instances not linear, interpreted as evidence for participation of more than one metal ion in the transition complex.

RNA hydrolysis and inhibition of translation by a Co(III)-cyclen complex

Metal ion-chelator catalysts based on main-group, lanthanide, or transition metal complexes have been developed as nonenzymatic alternatives for the hydrolysis of the phosphodiester bonds in DNA and RNA. Cobalt (III), with its high-charge density, is known for its ability to hydrolyze phosphodiesters with rate constants as high as 2 x 10(-4) s(-1). We have developed a kinetically inert Co(III)-cyclen-based complex, Co(III)-cycmmb that is very potent in inhibiting the translation of RNA into protein. Contact time as short as 10 min is sufficient to achieve the complete inhibition of the translation of a concentrated luciferase RNA solution into the enzyme in a cell-free translation system. The inhibition appears to proceed through two pathways. The first pathway involves the kinetic or substitutional inertness of Co(III) for the RNA template at short contact times. This interaction is mediated through the kinetic inertness of Co(III) for the phosphate groups of the nucleotides, as well as coordination of Co(III) to the nitrogenous bases. The second pathway occurs at longer contact times and is mediated by the hydrolysis of the phosphodiester backbone. This report represents the first demonstrated use of a metal-chelate complex to achieve the inhibition of the translation of RNA into protein. This Co(III) system can be useful in its present nonsequence-specific form as a novel viral decontamination agent. When functionalized to recognize specific nucleic acid sequences, such a system could potentially be used in gene-silencing applications as an alternative to standard antisense or RNAi technologies.

Oligonucleotide conjugates as potential antisense drugs with improved uptake, biodistribution, targeted delivery, and mechanism of action

This review summarizes the effect of conjugating small molecules and large biomacromolecules to antisense oligonucleotides to improve their therapeutic potential. In many cases, favorable changes in pharmacokinetic and pharmacodynamic properties were observed. Opportunities exist to change the terminating mechanism of antisense action or to enhance the RNase H mode of action via conjugate formation.

Prospects for gene therapy for inherited cardiomyopathies

Over the last few years the genes responsible for a number of genetic diseases of the cardiovascular system have been identified. These have included X-linked and autosomal dominant dilated cardiomyopathy, and hypertrophic cardiomyopathy. Genetic heterogeneity has been described in both of these diseases but a commonality of function has been apparent: defects in cytoskeletal proteins cause dilated cardiomyopathy and mutations in sarcomeric proteins cause hypertrophic cardiomyopathy. This led us to develop a 'final common pathway' hypothesis as a framework for selecting candidate genes for mutation screening in families with these diseases. The characterization of gene mutations has led to the development of therapies specifically targeting the defective protein or the pathway in which it is involved. These have included the use of pharmaceutical agents to replace or to antagonize the mutated protein, and replacement of the defective gene with a functional one (gene therapy). While early studies using gene therapy vectors were promising, translating studies in animals to viable therapeutic options for humans has remained problematic. There have been many publications describing the use of vectors to transduce target cells for the correction of gene defects, including recombinant retroviruses, adenoviruses, and adeno-associated viruses, as well as non-viral vectors. In this review we will discuss the identification of gene defects associated with cardiomyopathies, and the potential of gene therapy for the treatment of these diseases, as well as addressing some concerns related to the use of adenovirus-based vectors, a virus known to be an etiologic agent of acquired dilated cardiomyopathy.

Modulation of RNase H activity by modified DNA probes: major groove vs minor groove effects

We have previously prepared ribozyme mimics and chemical nucleases from modified DNA containing pendant bipyridine and terpyridine groups. The ability of these modified DNA probes to support RNase H cleavage of complementary RNA is described. DNA/RNA duplexes were formed using DNA probes designed to deliver metal complexes via either the major groove or the minor groove of the duplex. The duplexes were treated with Escherichia coli RNase H. Modifications in the major groove produced the same RNA cleavage pattern as unmodified DNA probes. However, minor groove substituents inhibited RNA cleavage over a four-base region. Comparison was made with a DNA probe containing a 2'-OMe modification. Our results support enzyme binding in the minor groove of a DNA/RNA duplex. We do not observe cleavage directly across from the modified nucleoside. The RNA cleavage efficiency effected by RNase H and a DNA probe decreases as follows: unmodified DNA > or = C-5 modified DNA >> c2'-modified DNA > C1'-modified DNA. Results with 28-mer RNA substrates roughly parallel those obtained with a 159-mer RNA target. The differences observed between low and high MW RNA substrates can be explained by a much higher enzyme-substrate binding constant for the high MW target.

On the failure of de novo-designed peptides as biocatalysts

While the elegance and efficiency of enzymatic catalysis have long tempted chemists and biochemists with reductionist leanings to try to mimic the functions of natural enzymes in much smaller peptides, such efforts have only rarely produced catalysts with biologically interesting properties. However, the advent of genetic engineering and hybridoma technology and the discovery of catalytic RNA have led to new and very promising alternative means of biocatalyst development. Synthetic chemists have also had some success in creating nonpeptide catalysts with certain enzyme-like characteristics, although their rates and specificities are generally much poorer than those exhibited by the best novel biocatalysts based on natural structures. A comparison of the various approaches from theoretical and practical viewpoints is presented. It is suggested that, given our current level of understanding, the most fruitful methods may incorporate both iterative selection strategies and rationally chosen small perturbations, superimposed on frameworks designed by nature.