Oligonucleotides are synthesized, polymeric sequences of nucleotides (RNA, DNA, and their analogs) that are utilized extensively as PCR and microarray-based reagents in life science research, as primer and probe reagents in DNA-based diagnostic test kits, and increasingly they are being developed as direct therapeutic agents against a wide range of disease conditions. The research on its application as a drug candidate began about 30 years ago, beginning with antisense oligonucleotides (ASOs) and aptamers and followed about 15 years ago by siRNAs. During that long period of time, numerous clinical trials have been performed and thousands of trial participants accrued onto studies. Until now, a total of fifteen FDA approved oligonucleotide drugs are on the market, but well over 100 are in the clinical pipeline and many more are in pre-clinical development.
Oligonucleotides as therapeutic drugs come in a variety of forms from antisense oligonucleotides (ASOs), small interfering RNAs (siRNAs), small hairpin RNAs (shRNAs), and anti-micro RNAs (anti-miRs)—which all affect "gene silencing" to aptamers, which are short nucleic acid sequences that fold into unique, three-dimensional shapes and bind to proteins/disease targets like small molecule drugs; to messenger RNAs (mRNAs), which are long gene transcript sequences that can augment gene expression; to CRISPR/Cas9 constructs that enable gene editing and hold tremendous promise.
FDA Approved Oligonucleotide Drugs
In 1998, Novartis Pharmaceutical's Vitravene (fomiversen), an antisense oligonucleotide, became the first oligonucleotide drug to be approved by the FDA. Vitravene was developed for the local treatment of cytomegalovirus (CMV) retinitis afflicting HIV patients. Ultimately, Vitravene was discontinued in 2004 because HIV treatment led to a reduction in the number of cases of CMV in HIV patients. Macugen (peaptanib sodium), an aptamer, was approved in 2004 for the treatment of wet age-related macular degeneration (AMD).
Over a decade after the approval of Vitravene, FDA approval came for Kynamro (mipomersen sodium) in 2013. This approval was followed by a flurry of activity that resulted in FDA approvals for more oligonucleotides.
|ASO||Fomivirsen||1998 (Withdrawn)||Ionis/Novartis||Cytomegalovirus retinitis in immunocompromised patients|
|Mipomersen||2013 (Withdrawn)||Kastle||Homozygous familial hypercholesterolemia|
|Nusinersen||2016||Ionis/Biogen||Spinal muscular atrophy|
|Eteplirsen||2016||Sarepta||Duchenne muscular dystrophy|
|Defibrotide||2016||Jazz Pharmaceuticals||Veno-occlusive disease|
|Inotersen||2018||Ionis||Hereditary transthyretin-mediated amyloidosis|
|Golodirsen||2019||Sarepta||Duchenne muscular dystrophy|
|Viltolarsen||2020||Nippon Shinyaku||Duchenne muscular dystrophy|
|Casimersen||2021||Sarepta||Duchenne muscular dystrophy|
|siRNA||Patisiran||2018||Alnylam||Hereditary transthyretin-mediated amyloidosis|
|Givosiran||2019||Alnylam||Acute hepatic porphyria|
|Lumasiran||2020||Alnylam||Primary hyperoxaluria type 1|
|Vutrisiran||2022||Alnylam||Hereditary transthyretin-mediated amyloidosis|
|Aptamer||Pegaptanib||2004 (Withdrawn)||Pfizer/Eyetech||Neovascular (Wet) Age-Related Macular Degeneration|
FDA-approved oligonucleotide drugs
Therapeutic Importance of Oligonucleotides
Oligonucleotides have been utilized for the last two decades for their therapeutic properties. Majorly these are used either for inhibition of genes or protein expression. Following are a few areas in which these can be used:
- • Neurodegenerative disorders: Oligonucleotides can be used as an effective therapy for the treatment of Huntington's disease (HD) because it is an autosomal disease caused by a mutation on a single allele. Oligonucleotides target the altered messenger RNA (mRNA) and decrease the synthesis of the causative protein-Huntingtin. ASO can also be used as a therapy for the treatment of spinal muscular atrophy (SMA), amyotrophic lateral sclerosis (ALS) and spinocerebellar ataxias.
- • Respiratory disorders: Oligonucleotides can be administered as an inhalation for the treatment of asthma and COPD. They have fewer side effects as these molecules are directly targeted to the lungs. In addition, their uptake is usually enhanced at the target site which leads to their prolonged duration of action.
- • Cancer: Antisense oligonucleotides have emerged as a new therapeutical approach for the treatment of various types of cancers whereby, they attach with mRNA and inhibit gene translation. However, non-specific protein binding and efficient delivery appear to be the major hurdles for their use in cancer treatment.
- • Diabetic retinopathy: Antisense oligonucleotides (e.g., iCo-007) are currently under trials for the treatment of diabetic retinopathy. These act by downregulating the signaling pathway of multiple growth factors that are involved in the ocular angiogenesis and vascular leakage. They provide several advantages namely, increased half-life, lesser degradation and improved safety profile. It is interesting to note that the only oligonucleotide currently approved is Vitravene® (Novartis, New York, NY, USA), which is used for cytomegalovirus retinitis, where the drug is directly administered to the site of disease (intravitreal).
Challenges of Oligonucleotide Therapies
Oligonucleotide-based drugs have attracted considerable attention as promising therapeutic agents for the treatment of various human diseases; however, several issues must be overcome in the development of oligonucleotide-based drugs. These issues include the instability of oligonucleotides against enzymatic degradation and rapid renal clearance. In an attempt to stabilize oligonucleotides, many modifications on their sugar motif and/or the phosphate backbone have been reported; however, these modifications often cause unwanted bioactivities such as toxicity. Considering toxicities, Polyethylene glycol (PEG) is very useful because it is categorized as “Generally Regarded As Safe (GRAS)” by the FDA. PEGylation increases nuclease resistance and the circulating half-lives of oligonucleotides. Accordingly, stabilization of oligonucleotides with PEG is a promising method for use in the development of therapeutic oligonucleotides. In fact, one of the therapeutic oligonucleotides, Macugen (Pegaptanib), consists of PEGylated oligonucleotides. In this aptamer drug, the oligonucleotide is modified with branched PEG (40 kDa) at the 50 terminus. This modification increases the nuclease resistance of PEG-aptamer conjugates. The extent of stabilization is dependent on the length of PEG. High-molecular-weight PEG stabilizes molecules better than low-molecular-weight PEG.
Although the development of oligonucleotide therapies is still difficult, it is believed that with the continuous development, improvement and progress of related technologies, oligonucleotide therapies represented by antisense oligonucleotide and small interfering RNA will surely set off a new wave in the pharmaceutical industry. And it will become an indispensable backbone force in the third-generation pharmaceutical industry revolution oriented by gene expression regulation.
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2. Pharmacology of Antisense Drugs. Annu Rev Pharmacol Toxicol 2017 Jan;57 81-105.
3. Molecular Mechanisms of Antisense Oligonucleotides. Nucleic Acid Ther. 2017 April 1; 27 (2): 70–77.
4.Nusinersen, an antisense oligonucleotide drug for spinal muscular atrophy. Nature Neuroscience 20, 497–499 (2017) doi:10.1038/nn.4508