Towards genomic drug therapy with antisense oligonucleotides

Antisense oligonucleotides represent a novel class of potential drugs for highly selective blocking of genes. The basic concept of antisense strategy is simple: an antisense molecule recognizes a complementary mRNA (or DNA) by sequence-specific base pairing, and hence prevents translation (or transcription), resulting in a selective inhibition of protein synthesis. Because of these properties, antisense oligonucleotides have great potential as therapeutic agents in several human diseases, such as viral diseases, malignancies and dominant hereditary diseases. However, technical difficulties have slowed down their use as drugs: structural modifications are needed to increase the stability and potency of synthetic oligonucleotides, specific delivery systems are required to facilitate their entry into target cells, and more information is needed to their mechanism of action. Much of the current research on antisense oligonucleotides takes place at the interface of chemistry and biomedical sciences, a multidisciplinary field where finding a common language is sometimes difficult. The aim of this review is to present an overview of the antisense strategy in terms which should be understandable for chemists, biologists and physicians.

The use of intracellular single-chain antibody fragments to inhibit specifically the expression of cell surface molecules

One possible method to inhibit specifically the function of a protein inside a cell is to express an intracellular antibody combining site that can block function or prevent expression of the targeted molecule. In this report the parameters involved in the production and expression of functional, endoplasmic reticulum-retained, single chain Fv antibody fragments (scFv) were investigated. These intracellular scFv constructs were tested for their ability to inhibit specifically the expression of a CHO cell line pretransfected with the relevant cell surface antigen CD2. No scFv was detected in the cell supernatant although functional scFv, as assayed by ELISA, was detected in an NP-40 soluble fraction if an N-linked glycosylation site had been introduced into the antibody construct. This demonstrates that functional antibody combining sites can be produced even though they are not secreted. Inhibition of CD2 was obtained but was not complete and differed between clones. Levels of scFv could be increased by gene amplification but the level of functional binding activity remained constant and no further inhibition of CD2 expression was obtained. Immunofluorescence analysis at the single-cell level of the permeabilised transfected cell lines showed that less than 8% of cells expressed detectable levels of intracellular scFv, indicating selection against cells producing high levels of single-chain antibody. This selection was not seen when comparable single-chain TCR constructs, known to be retained intracellularly, were used. Thus, production of scFv with binding activity is not sufficient for good inhibition of gene expression although introduction of an N-linked glycosylation site is beneficial. The best strategy is probably to screen a panel of scFv constructs and use those that are secreted rather than those that are retained intracellularly.

RNA enzymes as tools for gene ablation

Ribozymes have the potential to ablate the expression of any gene in a sequence-specific manner and, therefore, may be useful as therapeutic molecules or as tools for the analysis of gene function. Although a number of reports have described ribozymes that are effective in inhibiting gene expression, few studies have attempted, systematically, to analyze the features of ribozymes that affect their potency within cells. Experimental observations suggest that emerging rules governing ribozyme potency in cells can be understood in terms of the competitive interactions between RNA-binding proteins, complementary RNAs and their internal secondary structure.

Gene therapy for infectious diseases: the AIDS model

Genetic manipulation of somatic cells may be of therapeutic value in a variety of infectious diseases, particularly in human immunodeficiency virus (HIV) infection. Stable insertion of custom-designed 'resistance genes' into cells susceptible to HIV could reduce the viral burden in infected individuals and potentially retard the characteristic progressive immune dysfunction. Alternatively, ectopic expression of genes that encode viral antigens might induce potent antiviral immune responses and form the basis for novel prophylactic and therapeutic vaccines. While laboratory studies have proved that the approach works in principle, preclinical and clinical studies will be necessary to evaluate the therapeutic benefit of such gene-based therapies.

Suppression of simian immunodeficiency virus replication in primary peripheral mononuclear cells by antisense RNA

It has been demonstrated that human immunodeficiency virus (HIV) replication can be effectively blocked by an antisense sequence that was introduced into the lymphoid cell line through retroviral-mediated gene transfer. In this study, it is demonstrated that antisense RNA can also inhibit simian immunodeficiency virus (SIV) replication in the peripheral blood mononuclear cells (MNCs) of healthy donors. MNCs were transduced with amphotropic recombinant virus encoding either sense or antisense constructs of SIV DNA fragments. After challenge with SIV, the viral replication was suppressed in the antisense-recombinant virus-transduced MNCs compared to sense-recombinant virus-transduced and untransduced MNCs. These data indicate that amphotropic retroviral vectors can be used to introduce antiviral factors (antisense sequence) into human primary MNCs and render them resistant to viral replication.

Antisense strategies for the control of aberrant gene expression

Antisense nucleic acids have been shown to be potent and specific inhibitors of gene expression and viral replication in cells from various species, including mammals. Their potential applicability in vivo has been demonstrated by the use of antisense oligonucleotides and antisense RNA transcribed from recombinant antisense genes, respectively. It is conceivable that both classes of antisense nucleic acids can be used to correct pathogenic cellular or viral gene expression, thereby extending the range of therapeutic options from new techniques developed in the field of molecular biology. Possible improvements in the inhibitory potential of antisense nucleic acids and selected points to consider concerning their design, their function, and their application are discussed.

Picornavirus inhibitors

Picornaviruses are among the best understood animal viruses in molecular terms. A number of important human and animal pathogens are members of the Picornaviridae family. The genome organization, the different steps of picornavirus growth and numerous compounds that have been reported as inhibitors of picornavirus functions are reviewed. The picornavirus particles and several agents that interact with them have been solved at atomic resolution, leading to computer-assisted drug design. Picornavirus inhibitors are useful in aiding a better understanding of picornavirus biology. In addition, some of them are promising therapeutic agents. Clinical efficacy of agents that bind to picornavirus particles has already been demonstrated.

The structure and function of the HSV DNA replication proteins: defining novel antiviral targets

The absolute dependence of herpes simplex virus (HSV) replication on HSV DNA polymerase and six other viral-encoded replication proteins implies that specific inhibitors of these proteins' functions would be potent antiviral agents. The only currently licensed anti-herpes simplex drug, acyclovir, is an inhibitor of HSV DNA polymerase and is widely held to block viral replication primarily by specifically inhibiting viral DNA replication. In spite of the substantial advance in HSV therapy in recent years through the introduction of acyclovir, this anti-HSV compound and most of the other compounds under pharmaceutical development are substrate analogs. Since antiviral drug resistance has become an issue of increasing clinical importance, the need for structurally unrelated agents which incorporate novel mechanisms of viral inhibition is apparent. Understanding the structure and function of herpesvirus DNA polymerase and its interaction with the other six essential replication proteins at the replication origin should assist us in designing the next generation of therapeutic agents. The sequences of these proteins have been deduced and the proteins themselves have been expressed and purified in a variety of systems. The current challenge, therefore, is to use the available information about these proteins to identify and develop new, exquisitely specific antiviral therapeutics. In this review, we have summarized the current approaches and the results of structure/function studies of the herpes virus proteins essential for DNA replication, with the goal of more precisely defining novel antiviral targets.

Computer-aided search for effective antisense RNA target sequences of the human immunodeficiency virus type 1

For the biological and therapeutic application of antisense nucleic acids, there is a need to identify effective local target regions of given cellular target mRNAs or viral single-stranded nucleic acids. One critical parameter for the effectiveness of antisense nucleic acids could be the potential of intramolecular folding of a given sequence element of the target strand and the antisense strand, respectively. The folding potential of such subsequences was calculated by using an established secondary structure prediction algorithm. For the genomic RNA and the complementary RNA strand of the human immunodeficiency virus type 1 (HIV-1), an energy profile was calculated that monitors the local folding potential of each sequence position surrounded by a window of given length ranging from 50 to 400 nucleotides. The resulting energy profile was compared to the effectiveness of HIV-1-directed antisense RNAs. It was found that significant minima of the local folding potential (high delta G values) correlated with antisense RNA target regions involved in strong inhibition of HIV-1 replication that had been measured independently in two earlier studies by using different experimental approaches. Conversely, antisense RNAs directed against local subregions with a high folding potential (low delta G values) showed weak or no antiviral effect in human cells. The results indicate that analyses of the local folding potential of a given target RNA can support the selection of effective target sequences for antisense RNA.