Gapmer

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Gapmers are short DNA antisense oligonucleotide structures with RNA-like segments on both sides of the sequence. [1] These linear pieces of genetic information are designed to hybridize to a target piece of RNA and silence the gene through the induction of RNase H cleavage. Binding of the gapmer to the target has a higher affinity due to the modified RNA flanking regions, as well as resistance to degradation by nucleases. [2] [3] Gapmers are currently being developed as therapeutics for a variety of cancers, viruses, and other chronic genetic disorders. [4]

Contents

Gapmer Structure Gapmer molecular structure.png
Gapmer Structure

Chemical Structure

Gapmers are composed of short DNA strands flanked by strands of RNA mimics. The mimics are typically composed of locked nucleic acids (LNA), 2'-OMe, or 2'-F modified bases. [2] LNA sequences are RNA analogues "locked" into an ideal Watson-Crick base pairing conformation. Gapmers often utilize nucleotides modified with phosphorothioate (PS) groups. [4] [3]

Mechanism of Action

The mechanism of therapeutic gene-silencing action relies on degradation through the action of RNase H. [1] [5] Nearly all organisms utilize this family of enzymes to degrade DNA-RNA hybrids as a defense against viral infection. [6] In protein synthesis, DNA is first transcribed into mRNA, and then translated in an amino acid sequence. Gapmers take advantage of this biological pathway by binding to the mRNA target. [7] In humans, the gapmer DNA-mRNA duplex is degraded by RNase H1. [1] [5] The degradation of the mRNA prevents protein synthesis [7] [8]

Gapmer Mechanism of Action Gapmer mechanism of action updated.png
Gapmer Mechanism of Action

Advantages

The gapmer chemical structure is designed to increase resistance to nuclease degradation and enhance stability in vivo. [1] [2] LNAs, 2'-OMe, or 2'-F modified bases are chemical analogs of natural RNA nucleic acids. These modifications allow for an increase in nuclease resistance, reduced immunogenicity, and a decrease in toxicity. [1] Gapmers can also have a high binding affinity to the target mRNA. [1] This high binding affinity reduces off-target effects, non-specific binding, and unwanted gene silencing [2]

Therapeutics

Mipomersen (Kynamro)

Kynamro was approved by the FDA in January 2013 for the treatment of homozygous familial hypercholesterolemia (HoFH). [9] The drug, developed by Ionis Pharmaceuticals and marketed by Genzyme Corporation, is administered via subcutaneous injection in the form of a mipomersen sodium solution. The chemical structure is composed of a 20-nucleotide (20-mer) chain with phosphorothioate (PS) backbone modifications and 2'-O-Methoxyethyl (MOE) ribose substitutions. [4] Kynamro targets the mRNA product of the APOB gene, which codes for the Apolipoprotein B-100 protein, a component of low-density lipoprotein (LDL). [2] The binding of mipomersen to the APOB mRNA effectively blocks the translation of ApoB-100, and the gapmer-RNA hybrid is then degraded by the RNase H enzyme. Kynamro is reported to have an elimination half-life of approximately 1–2 months [9]

Inotersen (Tegsedi)

Tegsedi, developed and marketed by Ionis Pharmaceuticals, was approved by the FDA in October 2018 for the treatment of hereditary transthyretin amyloidosis (hATTR). [10] The chemical structure is a 20-mer oligonucleotide with PS backbone modifications and 2'-MOE ribose substitutions. [4] Tegsedi, in the form of an inotersen sodium solution, is administered subcutaneously on a weekly interval. Inotersen binds to the mRNA coding for the transthyretin protein, [11] which blocks translation of the mRNA and recruits RNase enzymes to degrade the gapmer-RNA hybrid. This effectively reduces the level of transthyretin in blood serum, which has been shown to treat polyneuropathy symptoms in patients with hATTR [11]

Safety

Gapmer antisense oligonucleotides (ASOs) have the potential to cause unintended, off-target effects. These off-target effects are produced when the gapmer binds to mRNA with a sufficient degree of complementarity to the target mRNA, blocking or down-regulating the translation of unintended proteins. [12] The functional consequences of gapmer off-target effects can vary widely, depending on the proteins affected and the extent of the down-regulation. Gapmer-based therapeutics also have the potential for side effects. For example, Kynamro has been shown to induce injection site reactions, nausea, headaches, flu-like symptoms, and hepatotoxic reactions. [9] Side effects of Inotersen include thrombocytopenia, glomerulonephritis, injection site reactions, nausea, headache, fatigue, and fever [10]

See also

References

  1. 1 2 3 4 5 6 Crooke, Stanley T.; Baker, Brenda F.; Crooke, Rosanne M.; Liang, Xue-hai (2021-03-24). "Antisense technology: an overview and prospectus" . Nature Reviews Drug Discovery. 20 (6): 427–453. doi:10.1038/s41573-021-00162-z. ISSN   1474-1784. PMID   33762737. S2CID   232354935. Archived from the original on 2021-11-15. Retrieved 2021-04-30.
  2. 1 2 3 4 5 Dhuri, Karishma; Bechtold, Clara; Quijano, Elias; Pham, Ha; Gupta, Anisha; Vikram, Ajit; Bahal, Raman (2020-06-26). "Antisense Oligonucleotides: An Emerging Area in Drug Discovery and Development". Journal of Clinical Medicine. 9 (6): 2004. doi: 10.3390/jcm9062004 . ISSN   2077-0383. PMC   7355792 . PMID   32604776.
  3. 1 2 QIAGEN. (2017). Antisense LNA GapmeRs Handbook: LNA-optimized oligonucleotides for strand-specific knockdown of mRNA and IncRNA. Germantown, MD: Author
  4. 1 2 3 4 Roberts, Thomas C.; Langer, Robert; Wood, Matthew J. A. (October 2020). "Advances in oligonucleotide drug delivery". Nature Reviews Drug Discovery. 19 (10): 673–694. doi:10.1038/s41573-020-0075-7. ISSN   1474-1784. PMC   7419031 . PMID   32782413. S2CID   221097649.
  5. 1 2 Kasuya, Takeshi; Hori, Shin-ichiro; Watanabe, Ayahisa; Nakajima, Mado; Gahara, Yoshinari; Rokushima, Masatomo; Yanagimoto, Toru; Kugimiya, Akira (2016-07-27). "Ribonuclease H1-dependent hepatotoxicity caused by locked nucleic acid-modified gapmer antisense oligonucleotides". Scientific Reports. 6 (1): 30377. Bibcode:2016NatSR...630377K. doi:10.1038/srep30377. ISSN   2045-2322. PMC   4961955 . PMID   27461380.
  6. ↑ Cerritelli, Susana M.; Crouch, Robert J. (March 2009). "Ribonuclease H: the enzymes in Eukaryotes". The FEBS Journal. 276 (6): 1494–1505. doi:10.1111/j.1742-4658.2009.06908.x. ISSN   1742-464X. PMC   2746905 . PMID   19228196.
  7. 1 2 Amodio, Nicola; Stamato, Maria Angelica; Juli, Giada; Morelli, Eugenio; Fulciniti, Mariateresa; Manzoni, Martina; Taiana, Elisa; Agnelli, Luca; Cantafio, Maria Eugenia Gallo; Romeo, Enrica; Raimondi, Lavinia (September 2018). "Drugging the lncRNA MALAT1 via LNA gapmeR ASO inhibits gene expression of proteasome subunits and triggers anti-multiple myeloma activity". Leukemia. 32 (9): 1948–1957. doi:10.1038/s41375-018-0067-3. ISSN   1476-5551. PMC   6127082 . PMID   29487387.
  8. ↑ Cheng, Xinwei; Liu, Qibing; Li, Hong; Kang, Chen; Liu, Yang; Guo, Tianqi; Shang, Ke; Yan, Chengyun; Cheng, Guang; Lee, Robert J. (2017-02-01). "Lipid Nanoparticles Loaded with an Antisense Oligonucleotide Gapmer Against Bcl-2 for Treatment of Lung Cancer" . Pharmaceutical Research. 34 (2): 310–320. doi:10.1007/s11095-016-2063-5. ISSN   1573-904X. PMID   27896589. S2CID   7147120. Archived from the original on 2024-03-14. Retrieved 2021-04-30.
  9. 1 2 3 Mipomersen [package insert]. Cambridge, MA: Genzyme Corporation; 2013.
  10. 1 2 Inotersen [package insert]. Carlsbad, CA: Ionis Pharmaceuticals, Inc.; 2018.
  11. 1 2 "Drug Information Portal - U.S. National Library of Medicine - Quick Access to Quality Drug Information". druginfo.nlm.nih.gov. Archived from the original on 2021-05-05. Retrieved 2021-04-29.
  12. ↑ Yoshida, Tokuyuki; Naito, Yuki; Yasuhara, Hidenori; Sasaki, Kiyomi; Kawaji, Hideya; Kawai, Jun; Naito, Mikihiko; Okuda, Haruhiro; Obika, Satoshi; Inoue, Takao (2019). "Evaluation of off-target effects of gapmer antisense oligonucleotides using human cells". Genes to Cells. 24 (12): 827–835. doi:10.1111/gtc.12730. ISSN   1365-2443. PMC   6915909 . PMID   31637814.
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