Antisense molecules

Zamecnik P 1978

Antisense oligonucleotides are chemically modified and thus synthetic, short-chain single-stranded nucleic acids that contain the complementary (and thus "contrary to the original sense" = anti-sense opposite) genetic information of a gene. They bind firmly to the messenger RNA of the gene, which means that translation thus influences or even prevents the conversion of the mRNA into a protein in the ribosomes and thus the biosynthesis of proteins (Benimetskaya L et al. 1997; Bennett CF et al. 2017).

Antisense oligonucleotides are spontaneously taken up by cells in small amounts. By using certain carriers (e.g. certain carrier lipids), an improvement in their uptake into the cell (transfection) and a better intracellular distribution can be achieved. The therapeutic effect of antisense oligonucleotides (ASO) has now been well documented in a wide range of clinical pictures (Askari FK et al. 1996). Perhaps their most significant advantage over other therapeutics is that knowledge of the gene target sequence directly provides knowledge of possible complementary oligonucleotide therapeutics. Thus, the concept of a targeted modulation of disease-causing proteins with antisense oligonucleotides has shown positive results in various clinical studies in viral, inflammatory and oncological diseases. In the last 5 years, more than 100 therapeutic approaches based on antisense oligonucleotides have been tested in Phase I clinical studies, of which about 25% have reached Phase II / III.

A good example of a positive therapeutic effect of this substance group is the antisense compound milases, which is tailored to the gene mutation in Batten disease, a rare genetic defect that leads to neurological deficits.

Furthermore, Exondys51® , an antisense oligonucleotide, is available for the treatment of Duchenne muscular atrophy.

Since July 2017, nusinersen (Spinraza®), a causal, disease-modifying therapy for the treatment of 5q-associated spinal muscular atrophy (SMA), has been available on the German market for the first time. This gene modulator increases the production of complete and functional SMN protein, binds to SMN2 pre-mRNA and thus promotes the inclusion of exon 7 in the mRNA. This allows functional SMN protein to be formed. The half-life in CSF is 135 to 177 days (Finkel RS et al. 2017).

Of note are fomivirsen and mipomersen, which have been approved for the treatment of cytomegalovirus retinitis and in familial hypercholsterinemia, respectively (Adams BD et al. 2017). For example, in the pivotal trials, treatment with mipomersen (Kynamro®) an antisense oligonucleotide (blocks messenger RNA for the synthesis of apolipoprotein B in the liver) as an add-on therapy to statins at the primary efficacy time point (PET, PET) resulted in a statistically significant reduction in LDL-C levels of 24.7% in patients with homozygous familial hypercholesterolemia (HoFH) and 35.9% in patients with severe heterozygous familial hypercholesterolemia (HeFH) compared to their respective baseline levels, which can be considered clinically relevant. The FDA voted in favor of approval of this antisense oligonucleotide in 2012 while the EMA voted against it in 2013.

Fomivirsen(Vitravene®) is a 21mer antisense DNA phosphorothioate oligonucleotide that has been used since 1996 as a virostatic agent for the treatment of cytomegalovirus (CMV) infections in immunodeficiency (e.g. AIDS). Fomivirsen has a complementary sequence to the mRNA, the major immediate-early (MIE) transcriptional unit of the human cytomegalovirus (CMV). Binding of the aRNA to the complementary mRNA blocks translation of this viral mRNA (Anderson KP et al. 1996). No protein synthesis takes place. Due to the double strand formation, the cell's own enzyme ribonuclease H becomes active and cleaves the mRNA in this region. The oligonucleotide is thus released again and can bind to another mRNA.

The orally administrable antisense oligonucleotide (mongersen) has been used in several clinical trials in patients with Crohn's disease. Mongersen inhibits SMAD7, a molecule that blocks the release ofTGF-ß1 (Monteleone G et al. 2015). SMAD7 is overexpressed in Crohn's disease, among other diseases. This overexpression leads to disturbances in the "TGF-beta" signaling pathway whose undisturbed function has an anti-inflammatory effect. Blockage of TGF-beta signaling by overexpressed SMAD7 (or by CYLD) suppresses the function of regulatory T cells and leads to inflammatory responses, a mechanism thought to have pathogenetic significance in Crohn's disease. Approval of mongersen is anticipated.

Antisense oligonucleotides in tumor diseases: In tumor diseases, several proliferation-promoting proteins (oncogenes) usually contribute to growth at the same time. Therefore, inhibition of single oncogenic proteins is not very promising. However, certain protein kinases play a predominant role in the regulation of proliferation and differentiation of cells. For example, in leukemia cell lines, inhibition of protein kinase A1 (PKA1) with an antisense oligonucleotide leads to an equilibrium shift in favor of protein kinase A2 (PKA2) expression.

Inhibition of Bcl-2 protein: Oblimersen (Genasense®; also known as Augmerosen or bcl-2 antisense oligodeoxynucleotide G3139) is a synthetic single-stranded phosphorothioate 18-base DNA oligonucleotide designed to downregulate bcl-2 mRNA expression (Klasa et al. 2002). Oblimersen selectively hybridizes to the first 6 codons of the open reading frame encoding the Bcl-2 protein and ultimately prevents translation of the Bcl-2 protein. Bcl-2- is a key molecule that is overexpressed by many tumor cells. This shifts the balance between survival and apoptosis toward tumor cell survival. Thus, in many tumor entities, neoplastic cells can survive by protecting themselves from programmed cell death (apoptosis). Oblimersen can enhance the effect of cytostatic therapy against a number of tumor entities through complete Bcl-2 blockade, including chronic lymphocytic leukemia, B-cell lymphoma, breast carcinoma in bronchial carcinoma, and malignant melanoma (Ott PA et al. 2013; Herbst RS et al. 2004). However, later studies failed to demonstrate the efficacy of this therapeutic principle in metastatic malignant melanoma (Bedikian AY et al. 2014).

Non-antisense-mediated effects" of oligonucleotides: In addition to the targeted antisense-mediated inhibition of a target protein, additional effects of antisense oligonucleotides can be demonstrated that occur independently of the specific antisense effect. These so-called "non-antisense-mediated effects" of oligonucleotides are based on their direct binding to proteins (Hartmann G et al. 1997). Such effects can induce, among others, antiviral, antiadhesive or even immunostimulatory effects.

Thus, in therapeutic terms, the non-antisense-mediated immune stimulation of oligonucleotides is of interest. This effect is due to general differences in the base composition of bacterial DNA and vertebrate DNA. In bacterial DNA, the two-base sequence cytidine base followed by guanidine base (CpG dinucleotide) is common. In vertebrate DNA, this two-terminal sequence is less frequent and is modified by the addition of a methyl group to the cytidine base (in contrast to non-methylated bacterial DNA). Vertebrates recognize this difference in the base composition of DNA via a mechanism that has not yet been elucidated. In vertebrates, the recognition of bacterial DNA leads to the physiological activation of a non-specific immune response. The immunostimulatory property of bacterial DNA can be mimicked by synthetic oligonucleotides. A phosphorothioate modification of these oligonucleotides additionally enhances their immunostimulatory effect. Monocytes, macrophages and dendritic cells are also directly activated. In these cells, there is an increased synthesis of the cytokines tumor necrosis factor-alpha and interleukin-12. However, bacterial DNA or oligonucleotides with CpG dinucleotides do not exert a direct influence on T lymphocytes.

In inflammatory (including oncological and viral) processes, proteins are known to contribute significantly to the pathogenesis of the respective disease. Thus, in inflammatory diseases, inhibition of the formation of proinflammatory cytokines and leukocytic/endothelial adhesion molecules lead to a reduction in undesirable inflammatory responses. In acute and chronic inflammatory diseases, proinflammatory tumor necrosis factor-alpha (TNFa) assumes a central mediator function. The synthesis of TNF-alpha can be specifically inhibited in cell cultures with antisense oligonucleotides.

The continuous improvement of innovative RNA modifications as well as the improvement of release mechanisms (e.g. as nanoparticles) will open up the development of future RNA-based therapeutics for a broader spectrum of chronic diseases (Adams BD et al. 2017).

1. Adams BD et al (2017) Targeting noncoding RNAs in disease. The Journal of clinical investigation 127: 761-771
2. Anderson KP et al (1996): Inhibition of human cytomegalovirus immediate-early gene expression by an antisense oligonucleotide complementary to immediate-early RNA. Antimicrob agents Chemother 40: 2004-2011.
3. Askari FK et al (1996) Antisense oligonucleotide therapy. New Engl J Med 334: 316-320.Bedikian AY et al. (2014) Dacarbazine with or without oblimersen (a Bcl-2 antisense oligonucleotides) in chemotherapy-naive patients with advanced melanoma and low-normal serum lactate dehydrogenase: 'The AGENDA trial'. Melanoma research 24:237-243.
4. Benimetskaya L et al (1997) Mac-1 (cdllb/cd18) is a protein binding to oligodeoxynucleotides. Nat Med 1997; 3: 414-420.
5. Bennett CF et al (2017) Pharmacology of Antisense Drugs. Annual review of pharmacology and toxicology 57: 81-105.
6. Bennet CF (2019) Therapeutic Antisense Oligonucleotides are coming of age. Annu Rev Med 70:307-321
7. Finkel RS et al (2017) Treatment of infantile-onset spinal muscular atrophy with nusinersen: a phase 2, open-label, dose-escalation study. Lancet 388: 3017-3026
8. Hartmann G et al (1997) Playground of oligonucleotides: extrapolation from in vitro to in vivo? Nat Med 1997 (letter); 3: 702
9. Herbst RS et al (2004) Oblimersen sodium (Genasense bcl-2 antisense oligonucleotides): a rational therapeutic to enhance apoptosis in therapy of lung cancer. Clinical cancer research: an official journal of the American Association for Cancer Research 10: 4245-4248.
10. Li D et al (2018) Precision Medicine through Antisense Oligonucleotide-Mediated Exon Skipping. Trends in pharmacological sciences 39: 982-994.
11. Mercuri E et al (2018) Nusinersen versus sham control in later-onset spinal muscular atrophy. N Engl J Med 378:625-635
12. Monteleone G et al (2015) Mongersen, on Oral SMAD7 Antisense Oligonucleotides, and Crohn's Disease. N Engl J Med 372:1104-1113
13. Ott PA et al (2013) Oblimers in combination with temozolomide and albumin-bound paclitaxel in patients with advanced melanoma: a phase I trial. Cancer chemotherapy and pharmacology 71:183-191