Increased potency of an aptameric G-rich oligonucleotide is associated with novel functional properties of phosphorothioate linkages

Discovery and development of the G-rich oligonucleotide AS1411 as a novel treatment for cancer

Certain guanine-rich (G-rich) DNA and RNA molecules can associate intermolecularly or intramolecularly to form four stranded or "quadruplex" structures, which have unusual biophysical and biological properties. Several synthetic G-rich quadruplex-forming oligodeoxynucleotides have recently been investigated as therapeutic agents for various human diseases. We refer to these biologically active G-rich oligonucleotides as aptamers because their activities arise from binding to protein targets via shape-specific recognition (analogous to antibody-antigen binding). As therapeutic agents, the G-rich aptamers may have some advantages over monoclonal antibodies and other oligonucleotide-based approaches. For example, quadruplex oligonucleotides are non-immunogenic, heat stable and they have increased resistance to serum nucleases and enhanced cellular uptake compared to unstructured sequences. In this review, we describe the characteristics and activities of G-rich oligonucleotides. We also give a personal perspective on the discovery and development of AS1411, an antiproliferative G-rich phosphodiester oligonucleotide that is currently being tested as an anticancer agent in Phase II clinical trials. This molecule functions as an aptamer to nucleolin, a multifunctional protein that is highly expressed by cancer cells, both intracellularly and on the cell surface. Thus, the serendipitous discovery of the G-rich oligonucleotides also led to the identification of nucleolin as a new molecular target for cancer therapy.

Use of antisense oligonucleotides in functional genomics and target validation

With the completion of sequencing of the human genome, a great deal of interest has been shifted toward functional genomics-based research for identification of novel drug targets for treatment of various diseases. The major challenge facing the pharmaceutical industry is to identify disease-causing genes and elucidate additional roles for genes of known functions. Gene functionalization and target validation are probably the most important steps involved in identifying novel potential drug targets. This review focuses on recent advances in antisense technology and its use for rapid identification and validation of new drug targets. The significance and applicability of this technology as a beginning of the drug discovery process are underscored by relevant cell culture-based assays and positive correlation in specific animal disease models. Some of the antisense inhibitors used to validate gene targets are themselves being developed as drugs. The current clinical trials based on such leads that were identified in a very short time further substantiate the importance of antisense technology-based functional genomics as an integral part of target validation and drug target identification.

CpG motifs in bacterial DNA and their immune effects

Unmethylated CpG motifs are prevalent in bacterial but not vertebrate genomic DNAs. Oligodeoxynucleotides (ODN) containing CpG motifs activate host defense mechanisms leading to innate and acquired immune responses. The recognition of CpG motifs requires Toll-like receptor (TLR) 9, which triggers alterations in cellular redox balance and the induction of cell signaling pathways including the mitogen activated protein kinases (MAPKs) and NF kappa B. Cells that express TLR-9, which include plasmacytoid dendritic cells (PDCs) and B cells, produce Th1-like proinflammatory cytokines, interferons, and chemokines. Certain CpG motifs (CpG-A) are especially potent at activating NK cells and inducing IFN-alpha production by PDCs, while other motifs (CpG-B) are especially potent B cell activators. CpG-induced activation of innate immunity protects against lethal challenge with a wide variety of pathogens, and has therapeutic activity in murine models of cancer and allergy. CpG ODN also enhance the development of acquired immune responses for prophylactic and therapeutic vaccination.

Evaluation of the binding between potential anti-HIV DNA-based drugs and viral envelope glycoprotein gp120 by capillary electrophoresis with laser-induced fluorescence detection

The fusion of the human immunodeficiency virus (HIV) with the target cell was assisted by the interaction between the viral envelope glycoprotein HIV-1 gp120 and a chemokine receptor. Studies have shown that the efficiency of the binding depends on the presence of the V3 loop of the gp120 which is known to interact with polyanions, such as phosphorothioate oligodeoxynucleotides (Sd, potential anti-HIV drugs). In this study, capillary electrophoresis with laser-induced fluorescence detection (CE-LIF) was used to systematically evaluate binding between Sd and HIV-1 gp120. A 25-mer fluorescently tagged phosphorothioate oligodeoxynucleotide (GEM) was employed as a probe to study this interaction. The dissociation constant (K(d)) between GEM and gp120 was determined to be 0.98 nM by Scatchard analysis. The competition constants (K(c)) of a set of Sd that compete with GEM for binding to gp120 were also determined. The results showed that the interaction had a strong dependence on the sulfur phosphorothioate backbone. Chain length and the sequence of Sd also affect the ability of binding to gp120. The ability to study the protein-drug binding in the solution with minimal sample consumption makes CE-LIF very attractive for biological studies.

Inhibition of CD28 Expression by Oligonucleotide Decoys to the Regulatory Element in Exon 1 of the CD28 Gene

Ligation of CD28 provides a costimulatory signal essential for Ag-mediated T cell activation via the TCR. Previously we demonstrated that inhibition of human and murine CD28 expression by a guanosine (G)-rich oligonucleotide (ODN), GR1, led to immunosuppression in vitro and in vivo. The bioactivity of GR1 was dependent on a G-rich DNA sequence motif consisting of two G tetrads separated by four nucleotides, (G4N4G4). We have shown recently that a G-rich region, designated CD28GR, in exon 1 of the CD28 gene is such a motif and is a positive regulatory element that binds the transcription factors Sp1 and EGR-1. Here we showed that the bioactivity of GR1 and the related GR2 correlated with the sequence-specific formation of distinct nuclear protein complexes and a high degree of ODN secondary structure. In addition, these ODN blocked transcription factor binding to CD28GR (also in a sequence-specific manner) and prevented CD28GR from driving transcription of a reporter gene. Interestingly, GR1 potently inhibited CD28, but not the expression of other Sp1- and EGR-1-regulated genes, an effect associated with lower Sp1 protein binding affinity of GR1 and GR2 compared with that of canonical Sp1 sites. These data show that DNA sequences that contain the G-rich sequence motif, G4N4G4, such as GR1 and GR2, can functionally mimic the regulatory protein binding ability of CD28GR. Thus, GR1 and GR2 act as molecular decoys to selectively interfere with transcriptional regulation of the CD28 gene.