Biotechnological Evolution of siRNA Molecules: From Bench Tool to the Refined Drug
Abstract
:1. History of Interference RNA: Discovery and Mechanism of Action
1.1. Discovery
1.2. Mechanism of Action
2. siRNA Design and Delivery to Human Cells
3. siRNA Therapy in Clinical Studies and the Progress of Biopharmaceutical Companies
4. Pros and Cons for the Broader Use of siRNAs into Clinics
- (1)
- siRNA has a high degree of safety, as it acts on the post-translational stage of gene expression, and therefore, does not interact with DNA, thereby avoiding mutation and teratogenic risks common to gene therapy. Based on clinical studies, siRNA therapeutics were relatively well tolerated, and cytokine release and infusion-related adverse events were manageable with supportive treatments, such as dexamethasone, acetaminophen, diphenhydramine, and ranitidine [46].
- (2)
- siRNA is highly efficacious in a precision therapeutic arsenal, once genes can be silenced by over 90%. Based on this feature, siRNA has innate advantages in comparison with small molecule therapeutics and monoclonal antibodies, because siRNA executes its function by complete Watson–Crick base pairing with mRNA, whereas small molecule and monoclonal antibody drugs need to recognize the 3D spatial conformation of proteins.
- (3)
- siRNA can cause dramatic suppression of gene expression in a single cell with just a few copies.
- (4)
- It has high specificity; in some cases, a single point mutation can abrogate silencing effect [47]. To take advantage of the sequence specificity of siRNA, a prerequisite to achieving allele-specific gene silencing is to identify the most significant difference between two alleles, which may be as little as a single nucleotide change stemming from mutation or polymorphism [48].
- (5)
- siRNA presents versatility because interfering RNA can be designed against virtually any gene.
- (6)
- Ease of synthesis, with lower production costs compared to protein or antibodies, and no need for a cellular expression system and complex protein purification.
- (1)
- Blood circulation: siRNA is not stable under physiological conditions because it is susceptible to serum nuclease-catalyzed degradation. The phosphodiester bond of siRNA is vulnerable to RNases and phosphatases. Once it is intravenously administered, endonucleases or exonucleases throughout the body will degrade siRNA, thus preventing the accumulation of intact therapeutic siRNA in the target tissue. The half-life of naked or unmodified siRNA in serum ranges from several minutes to 1hour. Consequently, siRNAs present poor pharmacokinetic behavior. Regarding chemical modifications, the most common strategy involves modification of the ribose 2′-OH group, as this functional group is critical to the mechanism of many serum RNAses [10]. Among the most effective backbone modifications for serum stability improvement is the substitution of the ribose 2′ hydroxyl with 2′-fluorine or 2′-methoxy groups. However, siRNA modification alone may not be enough to achieve the therapeutic activity. In this way, physical encapsulation of siRNA promotes stability to proper therapeutic activity. Concerning delivery systems, non-specific interactions with serum proteins result in nanocarrier degradation, dissociation, or aggregation. In addition to degradation by circulating nuclease, another barrier to in vivo delivery of siRNA is the uptake by the reticuloendothelial system. The reticuloendothelial system is composed of phagocytic cells, including circulating monocytes and tissue macrophages, which act to clear foreign pathogens and to remove cellular debris and apoptotic cells. Tissue macrophages, called Kupffer cells, are most abundant in the liver and spleen, tissues that receive high blood flow. Among nanocarrier options, PEGylated nanoparticles were highly efficient in delivering siRNA to the tumor with low liver uptake by evasion of the reticuloendothelial system [58].
- (2)
- Tissue carriage and internalization: The major concern about siRNA, besides degradation, is the transport from the bloodstream to the desired tissue. siRNA is ~7–8 nm in length and 2–3 nm in diameter. Therefore, these molecules are too large to cross cell membranes but small enough to be freely cleared by glomeruli, as molecules with a size smaller than 8 nm are easily filtered by the renal system. Hence, once siRNAs leave the bloodstream, they will accumulate in the bladder and be excreted from the body quickly. Additionally, chemical properties of siRNAs also interfere with the ability to cross the cell membrane, more specifically their relatively high molecular weight (~13–16 kD) and negative charge. These observations reinforce the notion that siRNAs should be encapsulated in order to overcome clearance, degradation and enable cell penetration.
- (3)
- Extracellular stability: In comparison with the pH values in the blood and healthy tissues (pH 7.4), the pH values in the tumor microenvironment, for example, have been found to range from 6.0 to 7.2 [59]. These differences in the pH, together with enzymes or ions of the tissue microenvironment could injure the nanocarrier, causing dissociation and releasing of the cargo before cellular entry.
- (4)
- Cell specificity: The rational is to coat the nanocarrier with a receptor, specific for the cell type to be targeted and, therefore, taken up by the targeted cells only. Presently, nanoparticles are frequently used for specific siRNA delivery in clinical trials due to the stringent specificity possessed by them. Davis et al. [55] conducted the first-in-human phase I clinical trial involving the systemic administration of siRNA to patients with solid cancers using a targeted, nanoparticle delivery system. The authors developed a nanoparticle coated with a human transferrin protein targeting ligand, displayed on the exterior of the nanoparticle, to engage Tf receptors on the surface of the cancer melanoma cells. The same strategy was used in Patisiran therapy, to target receptors that transport low-density lipoproteins (LDLs) into the cell.
- (5)
- Innate immune system: High levels of siRNA have been known to result in the activation of innate immune responses, immunostimulation, immunosuppression, and the production of cytokines both in vitro and in vivo [60]. Toll-like receptors (TLRs) 3, 7, and 8 are involved in the recognition of siRNA. siRNA has been found to activate TLR3, signaling in a sequence-independent manner. However, TLR7 and TLR8 mediate the recognition of siRNA in a sequence dependent manner that could be activated by sense or antisense strand. Thus, the importance of the sequence in siRNA-mediated immune stimulation requires more investigation [61].
- (6)
- Intracellular trafficking: Although it is commonly accepted that siRNA enters into cells via endocytosis, this broad statement masks the complexities inherent to the multiple pathways of internalization and subsequent intracellular trafficking, and this complexity is based on the chemical composition of the nanocarrier [62]. Subcellular membrane bound compartments include early and recycling endosomes, late endosomes, lysosomes, the Golgi apparatus, and the endoplasmic reticulum. Trafficking is not a random process, but rather, it is a carefully orchestrated pathway that allows the cell to transport endogenous and exogenous materials to the most appropriate place. The main point of concern regarding siRNA and intracellular trafficking is that siRNA needs to escape from vesicles to reach the cytoplasm, in order to find the siRNA machinery and avoid degradation induced by low pH into the vesicles.
- (7)
- Off-target: An siRNA duplex may target more than one mRNA molecules, due to sequence homologies. It is now widely observed that most siRNAs can tolerate one mismatch to the mRNA target and, at the same time, retain good silencing capacity [62,63,64]. Off-target effects of siRNA lead to unanticipated phenotypes that complicate the interpretation of the therapeutic benefits. RISCs can potentially downregulate any mRNAs with perfect base-pairing complementarity to the guide-strand seed region. This limitation could be circumvented in the siRNA design step. It is extremely important to use, for example, the NCBI BLAST tool to avoid matching to other non-desired sequences. Another critical issue with siRNA therapeutic development in cancer is an off-target accumulation of the delivery vehicle and its cargo, which depends on the chemical material used to produce it.
5. Immune System Activation and Escape by siRNA
5.1. Immune Activation
5.2. Immune Evasion Strategies
6. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Drug | Target | Delivery System | Administration | Disease | Company | Status | Phase | Study Start | NCT Number * |
---|---|---|---|---|---|---|---|---|---|
Patisiran (ONPATTRO ™) ALN-TTR02 | TTR | Lipid Nanoparticle | IV infusion | TTR-mediated amyloidosis | Alnylam Pharmaceuticals | Completed | Phase 3 | 2013 | NCT01960348 |
Phase 3 | 2019 | NCT03862807 | |||||||
Active, not recruiting | Phase 3 | 2015 | NCT02510261 | ||||||
Phase 3 | 2019 | NCT03759379 | |||||||
Approved for marketing | 2016 | NCT02939820 | |||||||
Active, not recruiting | Phase 4 | 2019 | NCT04201418 | ||||||
Phase 3 | 2019 | NCT03997383 | |||||||
Givosiran (Givlaari ™) ALN-AS1 | ALAS1 | GalNAc conjugate | SC injection | AHP | Alnylam Pharmaceuticals | Completed | Phase 3 | 2017 | NCT03338816 |
Approved for marketing | 2019 | NCT04056481 | |||||||
Recruiting | 2021 | NCT04883905 | |||||||
Lumasiran (Oxlumo ™) ALN-GO1 | HAO1 | GalNAc conjugate | SC injection | PH1 | Alnylam Pharmaceuticals | Active, not recruiting | Phase 3 | 2018 | NCT03681184 |
Phase 3 | 2019 | NCT03905694 | |||||||
Phase 3 | 2020 | NCT04152200 | |||||||
Recruiting | 2021 | NCT04982393 | |||||||
Approved for marketing | NCT04125472 | ||||||||
Inclisiran (Leqvio ™) ALN-PCSsc | PCSK9 | GalNAc conjugate | SC injection | ASCV and Elevated Cholesterol | Novartis | Completed | Phase 3 | 2017 | NCT03399370 |
Phase 3 | 2017 | NCT03400800 | |||||||
Enrolling by invitation | Phase 3 | 2019 | NCT03814187 | ||||||
Atherosclerotic Cardiovascular Disease | Recruiting | Phase 3 | 2018 | NCT03705234 | |||||
Phase 3 | 2021 | NCT04929249 | |||||||
Phase 3 | 2021 | NCT04807400 | |||||||
Not yet recruiting | Phase 3 | 2021 | NCT05030428 | ||||||
Hypercholesterolemia | Recruiting | Phase 3 | 2021 | NCT04652726 | |||||
Phase 3 | 2021 | NCT04659863 | |||||||
Phase 3 | 2021 | NCT04765657 | |||||||
Completed | Phase 3 | 2017 | NCT03397121 | ||||||
Active, not recruiting | Phase 3 | 2019 | NCT03851705 | ||||||
Not yet recruiting | Phase 3 | 2021 | NCT05004675 | ||||||
2021 | NCT05118230 | ||||||||
ACS | Recruiting | Phase 3 | 2021 | NCT04873934 | |||||
Fitusiran ALN-AT3SC | AT | GalNAc conjugate | SC injection | Hemophilia | Genzyme | Active, not recruiting | Phase 3 | 2018 | NCT03549871 |
Completed | Phase 3 | 2018 | NCT03417245 | ||||||
Phase 3 | 2018 | NCT03417102 | |||||||
Recruiting | Phase 3 | 2019 | NCT03754790 | ||||||
Vutrisiran ALN-TTRSC02 | TTR | GalNAc conjugate | SC injection | ATTR | Alnylam Pharmaceuticals | Active, not recruiting | Phase 3 | 2019 | NCT04153149 |
Phase 3 | 2019 | NCT03759379 | |||||||
Teprasiran QPI-1002 | p53 | None | IV injection | Delayed Graft Function | Quark Pharmaceuticals | Completed | Phase 3 | 2016 | NCT02610296 |
Cardiac Surgery | Terminated | Phase 3 | 2018 | NCT03510897 | |||||
QPI-1007 | Caspase-2 | None | Intravitreal | NAION | Quark Pharmaceuticals | Completed | Phase 2 | 2013 | NCT01965106 |
Tivanisiran SYL1001 | TRPV1 | None | Ophthalmic solution | Dry Eye Disease | Sylentis, S.A. | Completed | Phase 3 | 2017 | NCT03108664 |
Recruiting | Phase 3 | 2021 | NCT04819269 | ||||||
Nedosiran DCR-PHXC | HAO1 | GalNAc conjugate | SC injection | Primary Hyperoxaluria | Dicerna Pharmaceuticals | Enrolling by invitation | Phase 3 | 2019 | NCT04042402 |
Cemdisiran ALN-CC5 | C5 | GalNAc conjugate | SC injection | gMG | Alnylam Pharmaceuticals | Not yet recruiting | Phase 3 | 2021 | NCT05070858 |
Paroxysmal Nocturnal Hemoglobinuria | Phase 3 | 2022 | NCT05133531 | ||||||
Phase 3 | 2022 | NCT05131204 |
Pharmaceuticals Companies | Pathology |
---|---|
DTx pharma | Eye, neuromuscular, neurodegenerative, cardiovascular, immune, and oncology |
Alnylam Pharmaceuticals, Inc. | Genetic medicines, cardio metabolic diseases, infectious diseases, ocular diseases, CNS (central nervous system diseases) |
Phio Pharmaceuticals | Oncology |
Silence Therapeutics | Rare diseases, cardiovascular disease |
Aphios Corporation | Oncology, anti-infectives, CNS diseases such as Alzheimer’s Disease, Cognition, Depression, and Pain. |
Dicerna Pharmaceuticals | Metabolic and cardio metabolic diseases, complement-mediated, hepatitis B |
Avidity Biosciences | Muscular diseases |
Sirnaomics, Inc | Oncology, fibrosis, antiviral |
ARIZ Biopharma | Oncology |
Atalanta Therapeutics | Neurodegenerative diseases |
Entos pharmaceutics | Oncology, Age-related diseases |
Arbutusus Biopharma | Products for HBV infection |
Arrowhead | Products for cancer, viral infections, metabolic and rare diseases |
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de Brito e Cunha, D.; Frederico, A.B.T.; Azamor, T.; Melgaço, J.G.; da Costa Neves, P.C.; Bom, A.P.D.A.; Tilli, T.M.; Missailidis, S. Biotechnological Evolution of siRNA Molecules: From Bench Tool to the Refined Drug. Pharmaceuticals 2022, 15, 575. https://doi.org/10.3390/ph15050575
de Brito e Cunha D, Frederico ABT, Azamor T, Melgaço JG, da Costa Neves PC, Bom APDA, Tilli TM, Missailidis S. Biotechnological Evolution of siRNA Molecules: From Bench Tool to the Refined Drug. Pharmaceuticals. 2022; 15(5):575. https://doi.org/10.3390/ph15050575
Chicago/Turabian Stylede Brito e Cunha, Danielle, Ana Beatriz Teixeira Frederico, Tamiris Azamor, Juliana Gil Melgaço, Patricia Cristina da Costa Neves, Ana Paula Dinis Ano Bom, Tatiana Martins Tilli, and Sotiris Missailidis. 2022. "Biotechnological Evolution of siRNA Molecules: From Bench Tool to the Refined Drug" Pharmaceuticals 15, no. 5: 575. https://doi.org/10.3390/ph15050575
APA Stylede Brito e Cunha, D., Frederico, A. B. T., Azamor, T., Melgaço, J. G., da Costa Neves, P. C., Bom, A. P. D. A., Tilli, T. M., & Missailidis, S. (2022). Biotechnological Evolution of siRNA Molecules: From Bench Tool to the Refined Drug. Pharmaceuticals, 15(5), 575. https://doi.org/10.3390/ph15050575