scholarly journals The chemical structure and phosphorothioate content of hydrophobically modified siRNAs impact extrahepatic distribution and efficacy

2020 ◽  
Vol 48 (14) ◽  
pp. 7665-7680
Author(s):  
Annabelle Biscans ◽  
Jillian Caiazzi ◽  
Sarah Davis ◽  
Nicholas McHugh ◽  
Jacquelyn Sousa ◽  
...  
Keyword(s):  
Chemical Structure ◽  
Clinical Stage ◽  
Sirna Delivery ◽  
Fine Tuning ◽  
Endosomal Escape ◽  
Systematic Evaluation ◽  
Small Interfering Rnas ◽  
Tissue Accumulation ◽  
The Impact

Abstract Small interfering RNAs (siRNAs) have revolutionized the treatment of liver diseases. However, robust siRNA delivery to other tissues represents a major technological need. Conjugating lipids (e.g. docosanoic acid, DCA) to siRNA supports extrahepatic delivery, but tissue accumulation and gene silencing efficacy are lower than that achieved in liver by clinical-stage compounds. The chemical structure of conjugated siRNA may significantly impact invivo efficacy, particularly in tissues with lower compound accumulation. Here, we report the first systematic evaluation of the impact of siRNA scaffold—i.e. structure, phosphorothioate (PS) content, linker composition—on DCA-conjugated siRNA delivery and efficacy in vivo. We found that structural asymmetry (e.g. 5- or 2-nt overhang) has no impact on accumulation, but is a principal factor for enhancing activity in extrahepatic tissues. Similarly, linker chemistry (cleavable versus stable) altered activity, but not accumulation. In contrast, increasing PS content enhanced accumulation of asymmetric compounds, but negatively impacted efficacy. Our findings suggest that siRNA tissue accumulation does not fully define efficacy, and that the impact of siRNA chemical structure on activity is driven by intracellular re-distribution and endosomal escape. Fine-tuning siRNA chemical structure for optimal extrahepatic efficacy is a critical next step for the progression of therapeutic RNAi applications beyond liver.

scholarly journals Hydrophobicity drives the systemic distribution of lipid-conjugated siRNAs via lipid transport pathways

2018 ◽  
Author(s):  
Maire F. Osborn ◽  
Andrew H. Coles ◽  
Annabelle Biscans ◽  
Reka A. Haraszti ◽  
Loic Roux ◽  
...  
Keyword(s):  
Sirna Delivery ◽  
Lipid Transport ◽  
Small Interfering Rnas ◽  
Transport Pathways ◽  
Efficient Delivery ◽  
Systemic Distribution ◽  
Lipoprotein Binding ◽  
The Impact ◽  
Plasma Half Life

AbstractEfficient delivery of therapeutic RNA is the fundamental obstacle preventing its clinical utility. Lipid conjugation improves plasma half-life, tissue accumulation, and cellular uptake of small interfering RNAs (siRNAs). However, the impact of conjugate structure and hydrophobicity on siRNA pharmacokinetics is unclear, impeding the design of clinically relevant lipid-siRNAs. Using a panel of biologically-occurring lipids, we show that lipid conjugation modulates siRNA hydrophobicity and governs spontaneous partitioning into distinct plasma lipoprotein classes in vivo. Lipoprotein binding influences siRNA distribution by delaying renal excretion and promoting uptake into lipoprotein receptor-enriched tissues. Lipid-siRNAs elicit mRNA silencing without causing toxicity in a tissue-specific manner. Lipid-siRNA internalization occurs independently of lipoprotein endocytosis, and is mediated by siRNA phosphorothioate modifications. Although biomimetic lipoprotein nanoparticles have been considered for the enhancement of siRNA delivery, our findings suggest that hydrophobic modifications can be leveraged to incorporate therapeutic siRNA into endogenous lipid transport pathways without the requirement for synthetic formulation.

scholarly journals Lipid and Polymer-Based Nanoparticle siRNA Delivery Systems for Cancer Therapy

Molecules ◽  
2020 ◽  
Vol 25 (11) ◽  
pp. 2692 ◽  
Author(s):  
Francesco Mainini ◽  
Michael R. Eccles
Keyword(s):  
Cancer Therapy ◽  
Gene Silencing ◽  
Sirna Delivery ◽  
Cancer Therapeutics ◽  
Delivery Systems ◽  
Fine Tuning ◽  
Host Cells ◽  
Specific Cell ◽  
Small Interfering Rnas

RNA interference (RNAi) uses small interfering RNAs (siRNAs) to mediate gene-silencing in cells and represents an emerging strategy for cancer therapy. Successful RNAi-mediated gene silencing requires overcoming multiple physiological barriers to achieve efficient delivery of siRNAs into cells in vivo, including into tumor and/or host cells in the tumor micro-environment (TME). Consequently, lipid and polymer-based nanoparticle siRNA delivery systems have been developed to surmount these physiological barriers. In this article, we review the strategies that have been developed to facilitate siRNA survival in the circulatory system, siRNA movement from the blood into tissues and the TME, targeted siRNA delivery to the tumor or specific cell types, cellular uptake, and escape from endosomal degradation. We also discuss the use of various types of lipid and polymer-based carriers for cancer therapy, including a section on anti-tumor nanovaccines enhanced by siRNAs. Finally, we review current and recent clinical trials using NPs loaded with siRNAs for cancer therapy. The siRNA cancer therapeutics field is rapidly evolving, and it is conceivable that precision cancer therapy could, in the relatively near future, benefit from the combined use of cancer therapies, for example immune checkpoint blockade together with gene-targeting siRNAs, personalized for enhancing and fine-tuning a patient’s therapeutic response.

scholarly journals Modelling co-translational dimerisation for programmable nonlinearity in synthetic biology

2020 ◽  
Author(s):  
Ruud Stoof ◽  
Ángel Goñi-Moreno
Keyword(s):  
Nonlinear Dynamics ◽  
Biological Networks ◽  
Rational Design ◽  
Fine Tuning ◽  
Genetic Circuits ◽  
On Demand ◽  
Regulatory Circuits ◽  
Protein Dimers ◽  
The Impact

AbstractNonlinearity plays a fundamental role in the performance of both natural and synthetic biological networks. Key functional motifs in living microbial systems, such as the emergence of bistability or oscillations, rely on nonlinear molecular dynamics. Despite its core importance, the rational design of nonlinearity remains an unmet challenge. This is largely due to a lack of mathematical modelling that accounts for the mechanistic basics of nonlinearity. We introduce a model for gene regulatory circuits that explicitly simulates protein dimerization—a well-known source of nonlinear dynamics. Specifically, our approach focusses on modelling co-translational dimerization: the formation of protein dimers during—and not after—translation. This is in contrast to the prevailing assumption that dimer generation is only viable between freely diffusing monomers (i.e., post-translational dimerization). We provide a method for fine-tuning nonlinearity on demand by balancing the impact of co- versus post-translational dimerization. Furthermore, we suggest design rules, such as protein length or physical separation between genes, that may be used to adjust dimerization dynamics in-vivo. The design, build and test of genetic circuits with on-demand nonlinear dynamics will greatly improve the programmability of synthetic biological systems.

scholarly journals A highly selective fluorogenic probe for the detection and in vivo imaging of Cu/Zn superoxide dismutase

2016 ◽  
Vol 52 (58) ◽  
pp. 9093-9096 ◽  
Author(s):  
Liyun Zhang ◽  
Jun Cheng Er ◽  
Hao Jiang ◽  
Xin Li ◽  
Zhaofeng Luo ◽  
...  
Keyword(s):  
Superoxide Dismutase ◽  
In Vivo Imaging ◽  
Chemical Structure ◽  
Fine Tuning ◽  
Fluorogenic Probe

Fine-tuning the BODIPY chemical structure to develop a highly selective fluorophore for Cu/Zn SOD.

scholarly journals Non-Viral Delivery and Therapeutic Application of Small Interfering RNAs

Acta Naturae ◽  
2013 ◽  
Vol 5 (3) ◽  
pp. 35-53 ◽  
Author(s):  
N. A. Nikitenko ◽  
V. S. Prassolov
Keyword(s):  
Rna Interference ◽  
Gene Expression Regulation ◽  
Sirna Delivery ◽  
Target Cells ◽  
Powerful Method ◽  
Small Interfering Rnas ◽  
Therapeutic Application ◽  
Rnai Technology ◽  
In Vivo Degradation

RNA interference (RNAi) is a powerful method used for gene expression regulation. The increasing knowledge about the molecular mechanism of this phenomenon creates new avenues for the application of the RNAi technology in the treatment of various human diseases. However, delivery of RNA interference mediators, small interfering RNAs (siRNAs), to target cells is a major hurdle. Effective and safe pharmacological use of siRNAs requires carriers that can deliver siRNA to its target site and the development of methods for protection of these fragile molecules from in vivo degradation. This review summarizes various strategies for siRNA delivery, including chemical modification and non-viral approaches, such as the polymer-based, peptide-based, lipid-based techniques, and inorganic nanosystems. The advantages, disadvantages, and prospects for the therapeutic application of these methods are also examined in this paper.

scholarly journals mTOR inhibition enhances delivery and activity of antisense oligonucleotides in uveal melanoma cells

2021 ◽  
Author(s):  
Shanna Dewaele ◽  
Louis Delhaye ◽  
Boel De Paepe ◽  
Bram Bogaert ◽  
Ramiro Martinez ◽  
...  
Keyword(s):  
Cell Viability ◽  
Uveal Melanoma ◽  
Clinical Stage ◽  
Small Interfering Rnas ◽  
Mtor Inhibition ◽  
Non Coding Rna ◽  
Uveal Melanoma Cell ◽  
Lysosomal Accumulation

AbstractUveal melanoma (UM) is the most common primary intraocular malignancy in adults. Due to a lack of effective treatments, patients with metastatic disease have a median survival time of 6-12 months. We recently demonstrated that the SAMMSON long non-coding RNA (lncRNA) is essential for uveal melanoma cell survival and that antisense oligonucleotide (ASO)-mediated silencing of SAMMSON impaired cell viability and tumor growth in vitro and in vivo. By screening a library of 2911 clinical stage compounds, we identified the mTOR inhibitor GDC-0349 to synergize with SAMMSON inhibition in UM. Mechanistic studies revealed that mTOR inhibition enhanced uptake and reduced lysosomal accumulation of lipid complexed SAMMSON ASOs, improving SAMMSON knockdown and further decreasing UM cell viability. We found mTOR inhibition to also enhance target knockdown in other cancer cell lines as well as normal cells when combined with lipid nanoparticle complexed or encapsulated ASOs or small interfering RNAs (siRNAs). Our results are relevant to nucleic acid treatment in general and highlight the potential of mTOR inhibition to enhance ASO and siRNA mediated target knockdown.

scholarly journals Processing of eukaryotic Okazaki fragments by redundant nucleases can be uncoupled from ongoing DNA replicationin vivo

2018 ◽  
Author(s):  
Malik Kahli ◽  
Joseph S. Osmundson ◽  
Rani Yeung ◽  
Duncan J. Smith
Keyword(s):  
Dna Polymerase ◽  
Systematic Evaluation ◽  
Additional Contribution ◽  
Strand Displacement ◽  
Dna Polymerase Delta ◽  
Okazaki Fragment ◽  
Okazaki Fragments ◽  
The Impact ◽  
Lagging Strand

ABSTRACTPrior to ligation, each Okazaki fragment synthesized on the lagging strand in eukaryotes must be nucleolytically processed. Nuclease cleavage takes place in the context of 5’ flap structures generated via strand-displacement synthesis by DNA polymerase delta. At least three DNA nucleases: Rad27 (Fen1), Dna2, and Exo1, have been implicated in processing Okazaki fragment flaps. However, neither the contributions of individual nucleases to lagging-strand synthesis nor the structure of the DNA intermediates formed in their absence have been clearly definedin vivo.By conditionally depleting lagging-strand nucleases and directly analyzing Okazaki fragments synthesizedin vivoinS. cerevisiae, we conduct a systematic evaluation of the impact of Rad27, Dna2 and Exo1 on lagging-strand synthesis. We find that Rad27 processes the majority of lagging-strand flaps, with a significant additional contribution from Exo1 but not from Dna2. When nuclease cleavage is impaired, we observe a reduction in strand-displacement synthesis as opposed to the widespread generation of long Okazaki fragment 5’ flaps, as predicted by some models. Further, using cell cycle-restricted constructs, we demonstrate that both the nucleolytic processing and the ligation of Okazaki fragments can be uncoupled from DNA replication and delayed until after synthesis of the majority of the genome is complete.

scholarly journals Non-cationic RGD-containing protein carrier for tumor-targeted siRNA delivery

2021 ◽  
Author(s):  
Xiaolin Yu ◽  
Lu Xue ◽  
Jingjing Zhao ◽  
Shuhua Zhao ◽  
Daqing Wu ◽  
...  
Keyword(s):  
Targeted Delivery ◽  
Sirna Delivery ◽  
Integrin Αvβ3 ◽  
Cationic Liposome ◽  
Genetically Engineered ◽  
Endosomal Escape ◽  
Widespread Application ◽  
Rgd Peptides

Abstract Despite the recent successes in siRNA therapeutics, targeted delivery beyond the liver remains the major hurdle for the widespread application of siRNA in vivo. Current cationic liposome or polymer-based delivery agents are restricted to the liver and suffer from off-target effect, poor clearance, low serum stability, and high toxicity. In this study, we have genetically engineered a non-cationic tumor-targeted universal siRNA nanocarrier. This protein nanocarrier consists of three function domains: dsRNA binding domain (dsRBD) (from human protein kinase R) for any siRNA binding, 18-histidines for endosome escape, and two RGD peptides at N-and C-termini for targeting tumor and tumor neovasculature. We showed that cloned dual-RGD-dsRBD-18his (dual-RGD) protein protects siRNA against RNases, induces effective siRNA endosomal escape, specific targets on integrin αvβ3 expressing cells in vitro, and homes siRNA to tumor in vivo. The delivered siRNA leads target gene knockdown in the cell lines and tumor xenografts with low toxicity. This multifunctional, biomimetic, charge-neutral siRNA carrier is biodegradable, low toxic, suitable for mass production by fermentation, and serum stable, holding great potential to provide a widely applicable siRNA carrier for tumor-targeted siRNA delivery.

scholarly journals Investigations into the Effects of Linker Length Elongation on the Behaviour of Calcium-responsive MRI Probes

2019 ◽  
Author(s):  
Liam Connah ◽  
Vincent Truffault ◽  
Goran Angelovski
Keyword(s):  
Chemical Structure ◽  
Fine Tuning ◽  
Resonance Imaging ◽  
Nmr Studies ◽  
Coordination Behaviour ◽  
Magnetic Resonance Imaging Contrast ◽  
Paramagnetic Metal ◽  
Nmr Diffusion ◽  
The Impact ◽  
The Relationship

Understanding the relationship between chemical structure and the effectiveness of bioresponsive magnetic resonance imaging contrast agents can offer help to identify key components required for the future development of such probes. Here, we report the development and characteristion of two novel monomeric bifunctional chelators, whose paramagnetic metal complexes can serve as calcium-responsive smart contrast agent (SCA). Specifically, relaxometric titrations, luminescence lifetime measurements, NMR studies and NMR diffusion experiments were carried out to assess the behaviour of each system. Overall, our findings demonstrate the impact of subtle changes to the structure of such probes, affecting a range of properties and their coordination behaviour. Through the understanding of such changes, fine tuning of future SCA designs which show optimal changes in relaxivity can be achieved.

scholarly journals EPIDEMIOLOGICAL, TOXICOLOGICAL AND MOLEСULAR-GENETIC ASPECTS OF ENDOCRINE DISRUPTING CHEMICALS IN THE CHEMICAL SAFETY PROBLEM

2018 ◽  
Vol 97 (3) ◽  
pp. 197-203
Author(s):  
Oksana O. Sinitsyna ◽  
Yu. A. Rakhmanin ◽  
Z. I. Zholdakova ◽  
M. G. Aksenova ◽  
A. V. Kirillov ◽  
...  
Keyword(s):  
Chemical Structure ◽  
Endocrine Disrupting Chemicals ◽  
Endocrine System ◽  
Structural Features ◽  
The Body ◽  
Target Cells ◽  
Chemical Safety ◽  
Endocrine Disrupting ◽  
The Impact

The literature review has shown the problem of endocrine disrupting chemicals (EDC) to be associated with their wide distribution in the environment, the abundance, and variety of the chemical structure. Three leading mechanisms of EDCs action are identified as follows: imitation of the naturally occurring hormones action, blocking of receptors within the target cells of hormones, the impact of their kinetics in the body. Epidemiological studies indicate an increase in diseases caused by a disorder of the hormonal system. They are associated with the effect of EDCs. Substances that are completely dissimilar in chemical structure can cause the same effects. According to WHO [6], it is impossible, based on the chemical structure, to determine whether a substance is a disruptor of the endocrine system. However, some structural features determine the estrogenic, thyreogenic and glucocorticoid activity of chemicals. Hence, the need to differentiate the specific (primary) effect of a chemical substance on the endocrine system and the indirect (secondary) effect on it via other mechanisms comes to the fore. In own research, specific mechanisms were shown to be determined in the experiment when studying the complexity of effects, taking into account the processes of adaptation and decompensation, and identifying the effects manifested with the lowest doses. One of the methodological approaches can be the developed “structure-biotransformation-activity” prediction system aimed at revealing the primary types of effects: using quantum-chemical calculations and the plausible reasoning class (called the JSM-reasoning in honour of John Stuart Mill) logico-combinatorial method, it was possible to identify structural fragments of substances responsible for the manifestation of carcinogenic, allergenic effects, methemoglobin formation, etc. The results of clinical studies show the use of pharmacological drugs as models for in vivo study of the effects of EDC to allow not only studying atypical mechanisms of the impact of EDCs from the point of view of molecular genetics but also to predict the individual susceptibility to them taking into account polymorphism of candidate genes. The EDCs problem poses the need for a complex of interdisciplinary research, including three main relationships: exposure assessment-biomonitoring data-the prevalence of endocrine-dependent diseases, taking into account the qualitative and quantitative contribution of individual endocrine disrupters to the development of an ecologically dependent endocrine pathology using molecular genetic methods.

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