A Status Update of Modified Oligonucleotides for Chemotherapeutics Applications

Abstract

This unit presents an update of recent developments and clinical progress in chemically modified oliogonucleotides useful for therapeutic applications. During the last decade, the number of therapeutic oligonucleotides in clinical trials has nearly tripled. This is primarily due to advances in the synthesis protocols, better understanding of the biology, improved delivery, and better formulation technologies. Currently, over 100 clinical trials with oligonucleotide-based drugs are ongoing in the United States for potential treatment of a variety of life-threatening diseases. Among various oligonucleotides, antisense technology has been at the forefront, with one product on the market. Antisense technologies represent about half of the active clinical trials. Similarly, siRNA, aptamers, spiegelmers microRNA, shRNA, IMO, and CpG have been other active classes of oligonucleotides that are also undergoing clinical trials. This review attempts to summarize the current status of synthesis, chemical modifications, purification, and analysis in light of the rapid progress with multitude of oligonucleotides pursued as therapeutic modality.

Organic Solvent Nanofiltration (OSN): A New Technology Platform for Liquid-Phase Oligonucleotide Synthesis (LPOS)

“…It is possible that the chain extension did not reach completion because the 5'-mGmG dinucleotide is the most hindered inter-nucleotide linkage to form. Even so, it can be seen that upon purification of the 9-mer using ion exchange chromatography, the purity can be increased up to acceptable standards (> 90%) 6 .…”

“…The first two operate through anti-sense mechanisms, while the last is an aptamer. Following on from these successful market entries, over 100 oligobased drugs are now going through different phases of clinical trials 6 .…”

“…Secondly, the intensity of SPOS is restricted by sub-maximal loading of the polymeric support to minimize interference between neighboring chains (particularly when preparing longer oligos), and thus maintain coupling efficiency 15 . Thirdly, the SPOS process is highly mass intensive at large scale 6 . For instance, to produce 1kg of 20-mer phosphorothioate oligos, approximately 4,000 kg of solvents, reagents, and water are needed 16 .…”

“…Thus, product assay is again conducted only once the entire synthesis is complete, and in the event of one poor step the whole batch must be extensively purified, or even discarded. Despite the drawbacks, many significant breakthroughs have been made in SPOS scale-up recently, as reviewed by Sanghvi 6 .…”

RNA-Based Therapeutics: Current Progress and Future Prospects

“…Such modifications in short synthetic ONs include changes in the sugar, base, or backbone and may increase target affinity and specificity, decrease susceptibility to nuclease degradation, improve PK, and improve RNAi silencing efficiency. Recent advances in the process of synthesizing modified RNA and DNA molecules have increased the efficiency and reliability of manufacturing while also reducing production costs [6]. While dozens of different sugar, base, and backbone modifications are available by ON synthesis, the variety of chemical modifications for RNA-derived ONs destined for the clinic include phosphorothioate (PS) backbone modification; 2’- O -methyl (2’-OMe), 2’-fluoro (2’-F), 2’- O -methoxyethyl (2’-MOE) sugar substitutions; 2’- O , 4’- C -methylene linked bicyclic ribonucleotides known as a locked nucleic acid (LNA); and L-RNA (enantiomer of natural RNA) ONs known as spiegelmers (Figure 1) [7].…”