1
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Li Q, Dong M, Chen P. Advances in structural-guided modifications of siRNA. Bioorg Med Chem 2024; 110:117825. [PMID: 38954918 DOI: 10.1016/j.bmc.2024.117825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 06/27/2024] [Accepted: 06/27/2024] [Indexed: 07/04/2024]
Abstract
To date, the US Food and Drug Administration (FDA) has approved six small interfering RNA (siRNA) drugs: patisiran, givosiran, lumasiran, inclisiran, vutrisiran, and nedosiran, serving as compelling evidence of the promising potential of RNA interference (RNAi) therapeutics. The successful implementation of siRNA therapeutics is improved through a combination of various chemical modifications and diverse delivery approaches. The utilization of chemically modified siRNA at specific sites on either the sense strand (SS) or antisense strand (AS) has the potential to enhance resistance to ribozyme degradation, improve stability and specificity, and prolong the efficacy of drugs. Herein, we provide comprehensive analyses concerning the correlation between chemical modifications and structure-guided siRNA design. Various modifications, such as 2'-modifications, 2',4'-dual modifications, non-canonical sugar modifications, and phosphonate mimics, are crucial for the activity of siRNA. We also emphasize the essential strategies for enhancing overhang stability, improving RISC loading efficacy and strand selection, reducing off-target effects, and discussing the future of targeted delivery.
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Affiliation(s)
- Qiang Li
- Department of Medicinal Chemistry, School of Pharmacy, Qingdao University, Qingdao 266021, China; Research and Development Department, NanoPeptide (Qingdao) Biotechnology Ltd., Qingdao, China.
| | - Mingxin Dong
- Department of Medicinal Chemistry, School of Pharmacy, Qingdao University, Qingdao 266021, China.
| | - Pu Chen
- Research and Development Department, NanoPeptide (Qingdao) Biotechnology Ltd., Qingdao, China; Department of Chemical Engineering and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, Canada.
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2
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Pal C, Richter M, Rozners E. Synthesis and Properties of RNA Modified with Cationic Amine Internucleoside Linkage. ACS Chem Biol 2024; 19:249-253. [PMID: 38314716 PMCID: PMC11058646 DOI: 10.1021/acschembio.3c00784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Chemical modifications of RNA are important tools for the development of RNA therapeutics. The present study reports a novel RNA backbone modification that replaces the negatively charged phosphate with a positively charged amine linkage. Despite being thermally destabilizing in RNA duplexes, the amine linkage caused a relatively modest decrease of activity of a modified short interfering RNA (siRNA). At position 2 of the guide strand, the amine modification strongly enhanced the specificity of siRNA while causing an ∼5-fold drop of on-target activity. These results support the future development of amines as cationic RNA modifications and novel tools to modulate protein-RNA interactions.
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Affiliation(s)
- Chandan Pal
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
| | - Michael Richter
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
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3
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Osawa T, Akino T, Obika S. Synthesis, Duplex-Forming Ability, and Enzymatic Stability of Oligonucleotides Modified with Amide-Linked Dinucleotides Containing a 3',4'-Tetrahydropyran-Bridged Nucleic Acid. J Org Chem 2024; 89:269-280. [PMID: 38064209 DOI: 10.1021/acs.joc.3c02019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
Replacement of a phosphodiester linkage with an amide linkage can improve the binding affinity of oligonucleotides to complementary RNA and their stability toward nucleases. In addition, restricting the conformation of the sugar moiety and the phosphate backbone in oligonucleotides effectively improves duplex stability. In this study, we designed amide-linked dinucleotides containing a 3',4'-tetrahydropyran-bridged nucleic acid (3',4'-tpBNA) with a constrained sugar conformation as well as a torsion angle ε. Phosphoramidites of the designed dinucleotides were synthesized and incorporated into oligonucleotides. Conformational analysis of the synthesized dinucleotides showed that the sugar conformation of the S-isomer of the amide-linked dinucleotide containing 3',4'-tpBNA was N-type, which has the same conformation as that of the RNA duplex, while that of another R-isomer was S-type. Tm analysis indicated that the oligonucleotides containing the synthesized S-isomer showed RNA-selective hybridizing ability, although their duplex-forming ability was slightly inferior to that of natural oligonucleotides. Interestingly, the stability of the oligonucleotides toward endonucleases was significantly improved by modification with the two types of amide-linked dinucleotides developed in this study.
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Affiliation(s)
- Takashi Osawa
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Taiki Akino
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Yamadaoka 1-3, Suita, Osaka 565-0871, Japan
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4
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Skiba J, Kowalczyk A, Gorski A, Dutkiewicz N, Gapińska M, Stróżek J, Woźniak K, Trzybiński D, Kowalski K. Replacement of the phosphodiester backbone between canonical nucleosides with a dirhenium carbonyl "click" linker-a new class of luminescent organometallic dinucleoside phosphate mimics. Dalton Trans 2023; 52:1551-1567. [PMID: 36655722 DOI: 10.1039/d2dt03995h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The first-in-class luminescent dinucleoside phosphate analogs with a [Re2(μ-Cl)2(CO)6(μ-pyridazine)] "click" linker as a replacement for the natural phosphate group are reported together with the synthesis of luminescent adenosine and thymidine derivatives having the [Re2(μ-Cl)2(CO)6(μ-pyridazine)] entity attached to positions 5' and 3', respectively. These compounds were synthesized by applying inverse-electron-demand Diels-Alder and copper(I)-catalyzed azide-alkyne 1,3-dipolar cycloaddition reactions in three or four steps. The obtained compounds exhibited orange emission (λPL ≈ 600 nm, ΦPL ≈ 0.10, and τ = 0.33-0.61 μs) and no toxicity (except for one nucleoside) to human HeLa cervical epithelioid and Ishikawa endometrial adenocarcinoma cancer cells in vitro. Furthermore, the compounds' ability to inhibit the growth of Gram-positive Staphylococcus aureus and Gram-negative Escherichia coli bacterial strains was moderate and only observed at a high concentration of 100 μM. Confocal microscopy imaging revealed that the "dirhenium carbonyl" dinucleosides and nucleosides localized mainly in the membranous structures of HeLa cells and uniformly inside S. aureus and E. coli bacterial cells. An interesting finding was that some of the tested compounds were also found in the nuclei of HeLa cells.
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Affiliation(s)
- Joanna Skiba
- Faculty of Chemistry, Department of Organic Chemistry, University of Łódź, Tamka 12, 91-403 Łódź, Poland.
| | - Aleksandra Kowalczyk
- Department of Molecular Microbiology, Institute of Microbiology, Biotechnology and Immunology, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 12/16, 90-237 Łódź, Poland
| | - Aleksander Gorski
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, Warsaw, Poland
| | - Natalia Dutkiewicz
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, Warsaw, Poland
| | - Magdalena Gapińska
- Faculty of Biology and Environmental Protection, Laboratory of Microscopic Imaging and Specialized Biological Techniques, University of Łódź, Banacha 12/16, 90-237 Łódź, Poland
| | - Józef Stróżek
- Faculty of Chemistry, Department of Organic Chemistry, University of Łódź, Tamka 12, 91-403 Łódź, Poland.
| | - Krzysztof Woźniak
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Damian Trzybiński
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Konrad Kowalski
- Faculty of Chemistry, Department of Organic Chemistry, University of Łódź, Tamka 12, 91-403 Łódź, Poland.
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5
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Abosalha AK, Ahmad W, Boyajian J, Islam P, Ghebretatios M, Schaly S, Thareja R, Arora K, Prakash S. A comprehensive update of siRNA delivery design strategies for targeted and effective gene silencing in gene therapy and other applications. Expert Opin Drug Discov 2023; 18:149-161. [PMID: 36514963 DOI: 10.1080/17460441.2022.2155630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
INTRODUCTION RNA interference (RNAi) using small interfering RNA (siRNA) is a promising strategy to control many genetic disorders by targeting the mRNA of underlying genes and degrade it. However, the delivery of siRNA to targeted organs is highly restricted by several intracellular and extracellular barriers. AREAS COVERED This review discusses various design strategies developed to overcome siRNA delivery obstacles. The applied techniques involve chemical modification, bioconjugation to specific ligands, and carrier-mediated strategies. Nanotechnology-based systems like liposomes, niosomes, solid lipid nanoparticles (SLNs), dendrimers, and polymeric nanoparticles (PNs) are also discussed. EXPERT OPINION Although the mechanism of siRNA as a gene silencer is well-established, only a few products are available as therapeutics. There is a great need to develop and establish siRNA delivery systems that protects siRNAs and delivers them efficiently to the desired sitesare efficient and capable of targeted delivery. Several diseases are reported to be controlled by siRNA at their early stages. However, their targeted delivery is a daunting challenge.
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Affiliation(s)
- Ahmed Khaled Abosalha
- Biomedical Technology and Cell Therapy Research Laboratory, Department of Biomedical Engineering, Faculty of Medicine, McGill University H3A 2B4, Montreal, Quebec, Canada.,Pharmaceutical Technology department, Faculty of Pharmacy, Tanta University, Tanta, Egypt
| | - Waqar Ahmad
- Biomedical Technology and Cell Therapy Research Laboratory, Department of Biomedical Engineering, Faculty of Medicine, McGill University H3A 2B4, Montreal, Quebec, Canada
| | - Jacqueline Boyajian
- Biomedical Technology and Cell Therapy Research Laboratory, Department of Biomedical Engineering, Faculty of Medicine, McGill University H3A 2B4, Montreal, Quebec, Canada
| | - Paromita Islam
- Biomedical Technology and Cell Therapy Research Laboratory, Department of Biomedical Engineering, Faculty of Medicine, McGill University H3A 2B4, Montreal, Quebec, Canada
| | - Merry Ghebretatios
- Biomedical Technology and Cell Therapy Research Laboratory, Department of Biomedical Engineering, Faculty of Medicine, McGill University H3A 2B4, Montreal, Quebec, Canada
| | - Sabrina Schaly
- Biomedical Technology and Cell Therapy Research Laboratory, Department of Biomedical Engineering, Faculty of Medicine, McGill University H3A 2B4, Montreal, Quebec, Canada
| | - Rahul Thareja
- Biomedical Technology and Cell Therapy Research Laboratory, Department of Biomedical Engineering, Faculty of Medicine, McGill University H3A 2B4, Montreal, Quebec, Canada
| | - Karan Arora
- Biomedical Technology and Cell Therapy Research Laboratory, Department of Biomedical Engineering, Faculty of Medicine, McGill University H3A 2B4, Montreal, Quebec, Canada
| | - Satya Prakash
- Biomedical Technology and Cell Therapy Research Laboratory, Department of Biomedical Engineering, Faculty of Medicine, McGill University H3A 2B4, Montreal, Quebec, Canada
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6
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Richter M, Viel JA, Kotikam V, Gajula PK, Coyle L, Pal C, Rozners E. Amide Modifications in the Seed Region of the Guide Strand Improve the On-Target Specificity of Short Interfering RNA. ACS Chem Biol 2023; 18:7-11. [PMID: 36580486 PMCID: PMC9894624 DOI: 10.1021/acschembio.2c00769] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
RNA interference (RNAi) is a well-established research tool and is also maturing as a novel therapeutic approach. For the latter, microRNA-like off-target activity of short interfering RNAs (siRNAs) remains as one of the main problems limiting RNAi drug development. In this communication, we report that replacement of a single internucleoside phosphodiester in the seed region (nucleotides 2 to 7) of the guide strand with an amide linkage suppressed the undesired microRNA-like off-target activity by at least an order of magnitude. For the specific siRNA targeting the PIK3CB gene, an amide modification between the third and fourth nucleotides of the guide strand showed the strongest enhancement of specificity (completely eliminated off-target silencing) while maintaining high on-target activity. These results are important because off-target activity is one of the main remaining roadblocks for RNA based drug development.
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Affiliation(s)
- Michael Richter
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
| | - Julien A. Viel
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
| | - Venubabu Kotikam
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
| | - Praveen Kumar Gajula
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
| | - Lamorna Coyle
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
| | - Chandan Pal
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
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7
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Lee JW, Choi J, Choi Y, Kim K, Yang Y, Kim SH, Yoon HY, Kwon IC. Molecularly engineered siRNA conjugates for tumor-targeted RNAi therapy. J Control Release 2022; 351:713-726. [DOI: 10.1016/j.jconrel.2022.09.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 09/16/2022] [Accepted: 09/18/2022] [Indexed: 11/28/2022]
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8
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An LNA-amide modification that enhances the cell uptake and activity of phosphorothioate exon-skipping oligonucleotides. Nat Commun 2022; 13:4036. [PMID: 35821218 PMCID: PMC9276774 DOI: 10.1038/s41467-022-31636-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 06/28/2022] [Indexed: 11/24/2022] Open
Abstract
Oligonucleotides that target mRNA have great promise as therapeutic agents for life-threatening conditions but suffer from poor bioavailability, hence high cost. As currently untreatable diseases come within the reach of oligonucleotide therapies, new analogues are urgently needed to address this. With this in mind we describe reduced-charge oligonucleotides containing artificial LNA-amide linkages with improved gymnotic cell uptake, RNA affinity, stability and potency. To construct such oligonucleotides, five LNA-amide monomers (A, T, C, 5mC and G), where the 3′-OH is replaced by an ethanoic acid group, are synthesised in good yield and used in solid-phase oligonucleotide synthesis to form amide linkages with high efficiency. The artificial backbone causes minimal structural deviation to the DNA:RNA duplex. These studies indicate that splice-switching oligonucleotides containing LNA-amide linkages and phosphorothioates display improved activity relative to oligonucleotides lacking amides, highlighting the therapeutic potential of this technology. Oligonucleotides targeting mRNA are promising therapeutic agents but suffer from poor bioavailability. Here, the authors develop reduced-charge oligonucleotides with artificial LNA-amide linkages with improved cell uptake and minimal structural deviation to the DNA:RNA duplex.
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9
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Rozners E. Chemical Modifications of CRISPR RNAs to Improve Gene-Editing Activity and Specificity. J Am Chem Soc 2022; 144:12584-12594. [PMID: 35796760 DOI: 10.1021/jacs.2c02633] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
CRISPR (clustered, regularly interspaced, short palindromic repeats) has become a cutting-edge research method and holds great potential to revolutionize biotechnology and medicine. However, like other nucleic acid technologies, CRISPR will greatly benefit from chemical innovation to improve activity and specificity for critical in vivo applications. Chemists have started optimizing various components of the CRISPR system; the present Perspective focuses on chemical modifications of CRISPR RNAs (crRNAs). As with other nucleic acid-based technologies, early efforts focused on well-established sugar and backbone modifications (2'-deoxy, 2'-F, 2'-OMe, and phosphorothioates). Some more significant alterations of crRNAs have been done using bicyclic (locked) riboses and phosphate backbone replacements (phosphonoacetates and amides); however, the range of chemical innovation applied to crRNAs remains limited to modifications that have been successful in RNA interference and antisense technologies. The encouraging results given by these tried-and-true modifications suggest that, going forward, chemists should take a bolder approach─research must aim to investigate what chemistry will have the most impact on maturing CRISPR as therapeutic and other in vivo technologies. With an eye to the future, this Perspective argues that the complexity of CRISPR presents rich unprecedented opportunities for chemists to synergize advances in synthetic methodology and structural biochemistry to rationally optimize crRNA-protein interactions.
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Affiliation(s)
- Eriks Rozners
- Department of Chemistry, Binghamton University, Binghamton, New York 13902, United States
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10
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Viel J, Pal C, Rozners E. Optimization of Automated Synthesis of Amide-Linked RNA. ACS OMEGA 2022; 7:20420-20427. [PMID: 35721988 PMCID: PMC9201902 DOI: 10.1021/acsomega.2c02742] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 05/16/2022] [Indexed: 05/16/2023]
Abstract
The recent FDA approval of several antisense and siRNA drugs illustrates the utility of nucleic acid chemical modifications, but numerous challenges remain for generalized nucleic acid therapeutics, urging the exploration of new modification strategies. Replacing backbone phosphates with amides has shown promise for enhancing siRNA activity, specificity, and nuclease resistance; however, amide-linked RNA has not been fully explored due to lengthy and low yielding manual amide coupling procedures. We have addressed this by automating the assembly of amide-linked RNA using an Expedite 8909 nucleic acid synthesizer and optimizing solid-phase synthesis conditions to achieve 91-95% yields in just 5 min of coupling time. The optimized protocol allowed synthesis of a 21-nucleotide-long siRNA guide strand having six consecutive amide linkages at the 3'-end with an overall yield of ∼1%. Our results show that the steric hindrance caused by bulky 2'-O protecting groups and steric hindrance of the solid support are the key optimization variables for improving the amide couplings.
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11
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Kotikam V, Gajula PK, Coyle L, Rozners E. Amide Internucleoside Linkages Are Well Tolerated in Protospacer Adjacent Motif-Distal Region of CRISPR RNAs. ACS Chem Biol 2022; 17:509-512. [PMID: 35225591 PMCID: PMC9636586 DOI: 10.1021/acschembio.1c00900] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The development of CRISPR-Cas9 mediated gene editing technology is revolutionizing molecular biology, biotechnology, and medicine. However, as with other nucleic acid technologies, CRISPR would greatly benefit from chemical modifications that optimize delivery, activity, and specificity of gene editing. Amide modifications at certain positions of short interfering RNAs have been previously shown to improve their RNAi activity and specificity, which motivated the current study on replacement of selected internucleoside phosphates of CRISPR RNAs with amide linkages. Herein, we show that amide modifications did not interfere with CRISPR-Cas9 activity when placed in the protospacer adjacent motif (PAM) distal region of CRISPR RNAs. In contrast, modification of the seed region led to a loss of DNA cleavage activity at most but not all positions. These results are encouraging for future studies on amides as backbone modifications in CRISPR RNAs.
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Affiliation(s)
- Venubabu Kotikam
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
| | - Praveen Kumar Gajula
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
| | - Lamorna Coyle
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
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12
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Liczner C, Duke K, Juneau G, Egli M, Wilds CJ. Beyond ribose and phosphate: Selected nucleic acid modifications for structure-function investigations and therapeutic applications. Beilstein J Org Chem 2021; 17:908-931. [PMID: 33981365 PMCID: PMC8093555 DOI: 10.3762/bjoc.17.76] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 04/14/2021] [Indexed: 12/16/2022] Open
Abstract
Over the past 25 years, the acceleration of achievements in the development of oligonucleotide-based therapeutics has resulted in numerous new drugs making it to the market for the treatment of various diseases. Oligonucleotides with alterations to their scaffold, prepared with modified nucleosides and solid-phase synthesis, have yielded molecules with interesting biophysical properties that bind to their targets and are tolerated by the cellular machinery to elicit a therapeutic outcome. Structural techniques, such as crystallography, have provided insights to rationalize numerous properties including binding affinity, nuclease stability, and trends observed in the gene silencing. In this review, we discuss the chemistry, biophysical, and structural properties of a number of chemically modified oligonucleotides that have been explored for gene silencing.
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Affiliation(s)
- Christopher Liczner
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - Kieran Duke
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - Gabrielle Juneau
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - Martin Egli
- Department of Biochemistry, Vanderbilt Institute of Chemical Biology, and Center for Structural Biology, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Christopher J Wilds
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada
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13
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Akabane-Nakata M, Erande ND, Kumar P, Degaonkar R, Gilbert JA, Qin J, Mendez M, Woods LB, Jiang Y, Janas M, O’Flaherty DK, Zlatev I, Schlegel M, Matsuda S, Egli M, Manoharan M. siRNAs containing 2'-fluorinated Northern-methanocarbacyclic (2'-F-NMC) nucleotides: in vitro and in vivo RNAi activity and inability of mitochondrial polymerases to incorporate 2'-F-NMC NTPs. Nucleic Acids Res 2021; 49:2435-2449. [PMID: 33577685 PMCID: PMC7969009 DOI: 10.1093/nar/gkab050] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 01/13/2021] [Accepted: 02/07/2021] [Indexed: 02/01/2023] Open
Abstract
We recently reported the synthesis of 2'-fluorinated Northern-methanocarbacyclic (2'-F-NMC) nucleotides, which are based on a bicyclo[3.1.0]hexane scaffold. Here, we analyzed RNAi-mediated gene silencing activity in cell culture and demonstrated that a single incorporation of 2'-F-NMC within the guide or passenger strand of the tri-N-acetylgalactosamine-conjugated siRNA targeting mouse Ttr was generally well tolerated. Exceptions were incorporation of 2'-F-NMC into the guide strand at positions 1 and 2, which resulted in a loss of the in vitro activity. Activity at position 1 was recovered when the guide strand was modified with a 5' phosphate, suggesting that the 2'-F-NMC is a poor substrate for 5' kinases. In mice, the 2'-F-NMC-modified siRNAs had comparable RNAi potencies to the parent siRNA. 2'-F-NMC residues in the guide seed region position 7 and at positions 10, 11 and 12 were well tolerated. Surprisingly, when the 5'-phosphate mimic 5'-(E)-vinylphosphonate was attached to the 2'-F-NMC at the position 1 of the guide strand, activity was considerably reduced. The steric constraints of the bicyclic 2'-F-NMC may impair formation of hydrogen-bonding interactions between the vinylphosphonate and the MID domain of Ago2. Molecular modeling studies explain the position- and conformation-dependent RNAi-mediated gene silencing activity of 2'-F-NMC. Finally, the 5'-triphosphate of 2'-F-NMC is not a substrate for mitochondrial RNA and DNA polymerases, indicating that metabolites should not be toxic.
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Affiliation(s)
| | - Namrata D Erande
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, MA 02142, USA
| | - Pawan Kumar
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, MA 02142, USA
| | - Rohan Degaonkar
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, MA 02142, USA
| | - Jason A Gilbert
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, MA 02142, USA
| | - June Qin
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, MA 02142, USA
| | - Martha Mendez
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, MA 02142, USA
| | - Lauren Blair Woods
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, MA 02142, USA
| | - Yongfeng Jiang
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, MA 02142, USA
| | - Maja M Janas
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, MA 02142, USA
| | - Derek K O’Flaherty
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, MA 02142, USA
| | - Ivan Zlatev
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, MA 02142, USA
| | - Mark K Schlegel
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, MA 02142, USA
| | - Shigeo Matsuda
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, MA 02142, USA
| | - Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA
| | - Muthiah Manoharan
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, MA 02142, USA
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14
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Subhan MA, Attia SA, Torchilin VP. Advances in siRNA delivery strategies for the treatment of MDR cancer. Life Sci 2021; 274:119337. [PMID: 33713664 DOI: 10.1016/j.lfs.2021.119337] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 03/02/2021] [Accepted: 03/04/2021] [Indexed: 12/18/2022]
Abstract
RNA interference (RNAi) represents a promising therapeutic method that uses siRNA for cancer treatment. Although the RNAi technique has been increasingly used for clinical trials, systemic siRNA delivery into targeted cells is still challenging. The barriers impeding siRNA therapeutics delivery and impacting the treatment outcome must overcome with negligible systemic toxicity for a desirable and successful delivery of siRNA to MDR cancer cells. Nano delivery strategies have been investigated for nanocarrier functionalization, cancer immunotherapy and cancer targeting. Lipid nanoparticles (LNPs), dynamic polyconjugates (DPC™), GalNAc-siRNA conjugates, exosome and RBC systems have shown potential for efficient delivery of siRNA to cancer cells. Delivery of siRNA to tumor cells, immune cells to regulate T cell functions for immunotherapy are promising approaches.
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Affiliation(s)
- Md Abdus Subhan
- Department of Chemistry, ShahJalal University of Science and Technology, Sylhet 3114, Bangladesh.
| | - Sara Aly Attia
- CPBN, Department of Pharmaceutical Sciences, Northeastern University, Boston, MA 02115, USA
| | - Vladimir P Torchilin
- CPBN, Department of Pharmaceutical Sciences, Northeastern University, Boston, MA 02115, USA; Department of Oncology, Radiotherapy and Plastic Surgery I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia.
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15
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Varley AJ, Desaulniers JP. Chemical strategies for strand selection in short-interfering RNAs. RSC Adv 2021; 11:2415-2426. [PMID: 35424193 PMCID: PMC8693850 DOI: 10.1039/d0ra07747j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 12/24/2020] [Indexed: 12/13/2022] Open
Abstract
Therapeutic small interfering RNAs (siRNAs) are double stranded RNAs capable of potent and specific gene silencing through activation of the RNA interference (RNAi) pathway. The potential of siRNA drugs has recently been highlighted by the approval of multiple siRNA therapeutics. These successes relied heavily on chemically modified nucleic acids and their impact on stability, delivery, potency, and off-target effects. Despite remarkable progress, clinical trials still face failure due to off-target effects such as off-target gene dysregulation. Each siRNA strand can downregulate numerous gene targets while also contributing towards saturation of the RNAi machinery, leading to the upregulation of miRNA-repressed genes. Eliminating sense strand uptake effectively reduces off-target gene silencing and helps limit the disruption to endogenous regulatory mechanisms. Therefore, our understanding of strand selection has a direct impact on the success of future siRNA therapeutics. In this review, the approaches used to improve strand uptake are discussed and effective methods are summarized.
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Affiliation(s)
- Andrew J Varley
- Faculty of Science, University of Ontario Institute of Technology Oshawa Ontario L1G 0C5 Canada +1 905 721 3304 +1 905 721 8668 (ext. 3621)
| | - Jean-Paul Desaulniers
- Faculty of Science, University of Ontario Institute of Technology Oshawa Ontario L1G 0C5 Canada +1 905 721 3304 +1 905 721 8668 (ext. 3621)
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16
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Epple S, Thorpe C, Baker YR, El-Sagheer AH, Brown T. Consecutive 5'- and 3'-amide linkages stabilise antisense oligonucleotides and elicit an efficient RNase H response. Chem Commun (Camb) 2021; 56:5496-5499. [PMID: 32292963 DOI: 10.1039/d0cc00444h] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Antisense oligonucleotides are now entering the clinic for hard-to-treat diseases. New chemical modifications are urgently required to enhance their drug-like properties. We combine amide coupling with standard oligonucleotide synthesis to assemble backbone chimera gapmers that trigger an efficient RNase H response while improving serum life time and cellular uptake.
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Affiliation(s)
- Sven Epple
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK.
| | - Cameron Thorpe
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK.
| | - Ysobel R Baker
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK.
| | - Afaf H El-Sagheer
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK. and Chemistry Branch, Department of Science and Mathematics, Faculty of Petroleum and Mining Engineering, Suez University, Suez 43721, Egypt
| | - Tom Brown
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK.
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17
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Sun Y, Lü H, Sun L, Wang D, Wang J. Synthesis of DNAs with succinamide internucleoside linkages and its application in discrimination of T-C mismatch. POLYMER 2021. [DOI: 10.1016/j.polymer.2020.123162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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18
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Kotikam V, Rozners E. Amide-Modified RNA: Using Protein Backbone to Modulate Function of Short Interfering RNAs. Acc Chem Res 2020; 53:1782-1790. [PMID: 32658452 DOI: 10.1021/acs.accounts.0c00249] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
RNA-based technologies to control gene expression, such as RNA interference (RNAi) and CRISPR-Cas9, have become powerful tools in molecular biology and genomics. The exciting potential that RNAi and CRISPR-Cas9 may also become new therapeutic approaches has reinvigorated interest in chemically modifying RNA to improve its properties for in vivo applications. Chemical modifications can improve enzymatic stability, in vivo delivery, cellular uptake, and sequence specificity as well as minimize off-target activity of short interfering RNAs (siRNAs) and CRISPR associated RNAs. While numerous good solutions for improving stability toward enzymatic degradation have emerged, optimization of the latter functional properties remains challenging. In this Account, we discuss synthesis, structure, and biological activity of novel nonionic analogues of RNA that have the phosphodiester backbone replaced by amide linkages (AM1). Our long-term goal is to use the amide backbone to improve the stability and specificity of siRNAs and other functional RNAs. Our work in this area was motivated by early discoveries that nonionic backbone modifications, including AM1, did not disturb the overall structure or thermal stability of RNA duplexes. We hypothesized that the reduced negative charge and hydrophobic nature of the AM1 backbone modification might be useful in optimizing functional applications through enhanced cellular uptake, and might suppress unwanted off-target effects of siRNAs. NMR and X-ray crystallography studies showed that AM1 was an excellent mimic of phosphodiester linkages in RNA. The local conformational changes caused by the amide linkages were easily accommodated by small adjustments in RNA's conformation. Further, the amide carbonyl group assumed an orientation that is similar to one of the nonbridging P-O bonds, which may enable amide/phosphate mimicry by conserving hydrogen bonding interactions. The crystal structure of a short amide-modified DNA-RNA hybrid in complex with RNase H indicated that the amide N-H could also act as an H-bond donor to stabilize RNA-protein interactions, which is an interaction mode not available to phosphate groups. Functional assays established that amides were well tolerated at internal positions in both strands of siRNAs. Surprisingly, amide modifications in the middle of the guide strand and at the 5'-end of the passenger strand increased RNAi activity compared to unmodified siRNA. Most importantly, an amide linkage between the first and second nucleosides of the passenger strand completely abolished its undesired off-target activity while enhancing the desired RNAi activity. These results suggest that RNAi may tolerate more substantial modifications of siRNAs than the chemistries tried so far. The findings are also important and timely because they demonstrate that amide modifications may reduce off-target activity of siRNAs, which remains an important roadblock for clinical use of RNAi. Taken together, our work suggests that amide linkages have underappreciated potential to optimize the biological and pharmacological properties of RNA. Expanded use of amide linkages in RNA to enhance CRISPR and other technologies requiring chemically stable, functional mimics of noncoding RNAs is expected.
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Affiliation(s)
- Venubabu Kotikam
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902, United States
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902, United States
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19
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Tsubaki K, Hammill ML, Varley AJ, Kitamura M, Okauchi T, Desaulniers JP. Synthesis and Evaluation of Neutral Phosphate Triester Backbone-Modified siRNAs. ACS Med Chem Lett 2020; 11:1457-1462. [PMID: 32676154 DOI: 10.1021/acsmedchemlett.0c00232] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 06/09/2020] [Indexed: 11/30/2022] Open
Abstract
Two unsymmetrical dinucleotide phosphate triesters were synthesized via transesterification from tris(2,2,2-trifluoroethyl) phosphate. The protected triesters were phosphytilated to generate phosphoramidites for solid-phase oligonucleotide synthesis. Neutral phenylethyl phosphate-modified short-interfering RNAs (siRNAs) were synthesized and evaluated for their gene-silencing ability, siRNA strand selection, and resistance to nucleases. These backbone-modified phosphate triester siRNAs offer many improvements compared to natural unmodified siRNAs.
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Affiliation(s)
- Kouta Tsubaki
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu Institute of Technology, 1-1 Sensui-cho, Tobata, Kitakyushu 804-8550, Japan
- Faculty of Science, University of Ontario Institute of Technology, 2000 Simcoe Street North, Oshawa, Ontario L1G 0C5, Canada
| | - Matthew L. Hammill
- Faculty of Science, University of Ontario Institute of Technology, 2000 Simcoe Street North, Oshawa, Ontario L1G 0C5, Canada
| | - Andrew J. Varley
- Faculty of Science, University of Ontario Institute of Technology, 2000 Simcoe Street North, Oshawa, Ontario L1G 0C5, Canada
| | - Mitsuru Kitamura
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu Institute of Technology, 1-1 Sensui-cho, Tobata, Kitakyushu 804-8550, Japan
| | - Tatsuo Okauchi
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu Institute of Technology, 1-1 Sensui-cho, Tobata, Kitakyushu 804-8550, Japan
| | - Jean-Paul Desaulniers
- Faculty of Science, University of Ontario Institute of Technology, 2000 Simcoe Street North, Oshawa, Ontario L1G 0C5, Canada
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20
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Kotikam V, Viel JA, Rozners E. Synthesis and Biological Activity of Short Interfering RNAs Having Several Consecutive Amide Internucleoside Linkages. Chemistry 2020; 26:685-690. [PMID: 31693228 PMCID: PMC6980941 DOI: 10.1002/chem.201903754] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 11/01/2019] [Indexed: 02/06/2023]
Abstract
The success of RNA interference (RNAi) as a research tool and potential therapeutic approach has reinvigorated interest in chemical modifications of RNA. Replacement of the negatively charged phosphates with neutral amides may be expected to improve bioavailability and cellular uptake of small interfering RNAs (siRNAs) critical for in vivo applications. In this study, we introduced up to seven consecutive amide linkages at the 3'-end of the guide strand of an siRNA duplex. Modified guide strands having four consecutive amide linkages retained high RNAi activity when paired with a passenger strand having one amide modification between its first and second nucleosides at the 5'-end. Further increase in the number of modifications decreased the RNAi activity; however, siRNAs with six and seven amide linkages still showed useful target silencing. While an siRNA duplex having nine amide linkages retained some silencing activity, the partial reduction of the negative charge did not enable passive uptake in HeLa cells. Our results suggest that further chemical modifications, in addition to amide linkages, are needed to enable cellular uptake of siRNAs in the absence of transfection agents.
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Affiliation(s)
- Venubabu Kotikam
- Department of Chemistry, Binghamton University, Binghamton, New York, 13902, USA
| | - Julien A Viel
- Department of Chemistry, Binghamton University, Binghamton, New York, 13902, USA
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, Binghamton, New York, 13902, USA
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21
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Chernikov IV, Vlassov VV, Chernolovskaya EL. Current Development of siRNA Bioconjugates: From Research to the Clinic. Front Pharmacol 2019; 10:444. [PMID: 31105570 PMCID: PMC6498891 DOI: 10.3389/fphar.2019.00444] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 04/08/2019] [Indexed: 12/12/2022] Open
Abstract
Small interfering RNAs (siRNAs) acting via RNA interference mechanisms are able to recognize a homologous mRNA sequence in the cell and induce its degradation. The main problems in the development of siRNA-based drugs for therapeutic use are the low efficiency of siRNA delivery to target cells and the degradation of siRNAs by nucleases in biological fluids. Various approaches have been proposed to solve the problem of siRNA delivery in vivo (e.g., viruses, cationic lipids, polymers, nanoparticles), but all have limitations for therapeutic use. One of the most promising approaches to solve the problem of siRNA delivery to target cells is bioconjugation; i.e., the covalent connection of siRNAs with biogenic molecules (lipophilic molecules, antibodies, aptamers, ligands, peptides, or polymers). Bioconjugates are "ideal nanoparticles" since they do not need a positive charge to form complexes, are less toxic, and are less effectively recognized by components of the immune system because of their small size. This review is focused on strategies and principles for constructing siRNA bioconjugates for in vivo use.
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Affiliation(s)
- Ivan V Chernikov
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Valentin V Vlassov
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Elena L Chernolovskaya
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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22
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Abstract
Efforts to chemically modify nucleic acids got underway merely a decade after the discovery of the DNA double helix and initially targeted nucleosides and nucleotides. The origins of three analogues that remain staples of modification strategies and figure prominently in FDA-approved nucleic acid therapeutics can be traced to the 1960s: 2'-deoxy-2'-fluoro-RNA (2'-F RNA), 2'- O-methyl-RNA (2'- OMe RNA), and the phosphorothioates (PS-DNA/RNA). Progress in nucleoside phosphoramidite-based solid phase oligonucleotide synthesis has gone hand in hand with the creation of second-generation (e.g., 2'- O-(2-methoxyethyl)-RNA, MOE-RNA) and third-generation (e.g., bicyclic nucleic acids, BNAs) analogues, giving rise to an expanding universe of modified nucleic acids. Thus, beyond site-specifically altered DNAs and RNAs with a modified base, sugar, and/or phosphate backbone moieties, nucleic acid chemists have created a host of conjugated oligonucleotides and artificial genetic polymers (XNAs). The search for oligonucleotides with therapeutic efficacy constitutes a significant driving force for these investigations. However, nanotechnology, diagnostics, synthetic biology and genetics, nucleic acid etiology, and basic research directed at the properties of native and artificial pairing systems have all stimulated the design of ever more diverse modifications. Modification of nucleic acids can affect pairing and chemical stability, conformation and interactions with a flurry of proteins and enzymes that play important roles in uptake, transport or processing of targets. Enhancement of metabolic stability is a central concern in the design of antisense, siRNA and aptamer oligonucleotides for therapeutic applications. In the antisense approach, uniformly modified oligonucleotides or so-called gapmers are used to target a specific RNA. The former may sterically block transcription or direct alternative splicing, whereas the latter feature a central PS window that elicits RNase H-mediated cleavage of the target. The key enzyme in RNA interference (RNAi) is Argonaute 2 (Ago2), a dynamic multidomain enzyme that binds multiple regions of the guide (antisense) and passenger (sense) siRNAs. The complexity of the individual interactions between Ago2 and the siRNA duplex provides significant challenges for chemical modification. Therefore, a uniform (the same modification throughout, e.g., antisense) or nearly uniform (e.g., aptamer) modification strategy is less useful in the pursuit of siRNA therapeutic leads. Instead, unique structural features and protein interactions of 5'-end (guide/Ago2MID domain), seed region, central region (cleavage site/Ago2 PIWI domain), and 3'-terminal nucleotides (guide/Ago2 PAZ domain) demand a more nuanced approach in the design of chemically modified siRNAs for therapeutic use. This Account summarizes current siRNA modification strategies with an emphasis on the regio-specific interactions between oligonucleotide and Ago2 and how these affect the choice of modification and optimization of siRNA efficacy. In addition to standard assays applied to measure the effects of modification on the stability of pairing and resistance against nuclease degradation, structural insights based on crystallographic data for modified RNAs alone and in complex with Ago2 from molecular modeling studies are a valuable guide in the design of siRNA therapeutics. Thus, this comprehensive approach is expected to result in accelerated generation of new siRNA-based therapies against various diseases, now that the first siRNA has obtained approval by the US FDA for treatment of hereditary hATTR amyloidosis.
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Affiliation(s)
- Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Muthiah Manoharan
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, Massachusetts 02142, United States
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23
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Pal C, Velusamy A, Sunkari YK, Chakraborty TK. Studies on sugar puckering and glycosidic stabilities of 3'-amino-5'-carboxymethyl-3',5'-dideoxy nucleoside mimics. Org Biomol Chem 2019; 16:6735-6740. [PMID: 30187064 DOI: 10.1039/c8ob01788c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The synthesis of nucleoside amino acid monomers and dimers has been carried out to evaluate and characterize the impact of the neutral amide backbone on key attributes like puckering of the sugar rings and glycosidic bond strengths of these analogs. The conformational analysis suggests that amide-linked nucleotides have a high predilection towards N-type conformers. The glycosidic bond strength was found to be slightly weaker compared to ribonucleosides under acidic conditions at high temperatures. The results will be helpful to explore in future the development of fully amide-linked oligonucleotides for therapeutic purposes.
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Affiliation(s)
- Chandan Pal
- Department of Organic Chemistry, Indian Institute of Science, Bengaluru 560 012, India.
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24
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Hardcastle T, Novosjolova I, Kotikam V, Cheruiyot SK, Mutisya D, Kennedy SD, Egli M, Kelley ML, van Brabant Smith A, Rozners E. A Single Amide Linkage in the Passenger Strand Suppresses Its Activity and Enhances Guide Strand Targeting of siRNAs. ACS Chem Biol 2018; 13:533-536. [PMID: 29298376 PMCID: PMC7755457 DOI: 10.1021/acschembio.7b01012] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Potential in vivo applications of RNA interference (RNAi) require suppression of various off-target activities. Herein, we report that replacement of a single phosphate linkage between the first and second nucleosides of the passenger strand with an amide linkage almost completely abolished its undesired activity and restored the desired activity of guide strands that had been compromised by unfavorable amide modifications. Molecular modeling suggested that the observed effect was most likely due to suppressed loading of the amide-modified strand into Ago2 caused by inability of amide to adopt the conformation required for the backbone twist that docks the first nucleotide of the guide strand in the MID domain of Ago2. Eliminating off-target activity of the passenger strand will be important for improving therapeutic potential of RNAi.
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Affiliation(s)
| | - Irina Novosjolova
- Department of Chemistry, Binghamton University, Binghamton, New York 13902, USA
| | - Venubabu Kotikam
- Department of Chemistry, Binghamton University, Binghamton, New York 13902, USA
| | - Samwel K. Cheruiyot
- Department of Chemistry, Binghamton University, Binghamton, New York 13902, USA
| | - Daniel Mutisya
- Department of Chemistry, Binghamton University, Binghamton, New York 13902, USA
| | - Scott D. Kennedy
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
| | - Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, USA
| | | | | | - Eriks Rozners
- Department of Chemistry, Binghamton University, Binghamton, New York 13902, USA
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25
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Dzowo YK, Wolfbrandt C, Resendiz MJE, Wang H. Modeling of canonical and C2′- O-thiophenylmethyl modified hexamers of RNA. Insights into the nature of structural changes and thermal stability. NEW J CHEM 2018. [DOI: 10.1039/c8nj01739e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Modification of the C2′-O-position with thiophenylmethyl groups on both strands leads to thermal stabilization of the duplex. Predicting the effects that modifications will have on structure of RNA is of importance in the development of new RNA technologies.
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Affiliation(s)
| | | | | | - Haobin Wang
- Department of Chemistry
- University of Colorado Denver
- Denver
- USA
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26
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Vlaho D, Fakhoury JF, Damha MJ. Structural Studies and Gene Silencing Activity of siRNAs Containing Cationic Phosphoramidate Linkages. Nucleic Acid Ther 2017; 28:34-43. [PMID: 29195060 DOI: 10.1089/nat.2017.0702] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
A series of siRNA duplexes containing cationic non-bridging 3',5'-linked phosphoramidate (PN) linkages was designed and synthesized using a combination of phosphoramidite and H-phosphonate chemistries. Modified oligonucleotides were assayed for their thermal stability, helical structure, and ability to modulate the expression of firefly luciferase. We demonstrate that PN modifications of siRNAs are, in general, minimally destabilizing with respect to duplex thermal stability; destabilization can be mitigated through the incorporation of 2'-modified RNA-like residues or PN conjugates containing ionizable pendant moieties. We also demonstrate that single cationic dimethylethylenediamine PN linkages have little effect on siRNA potency, whether located in the passenger or guide strand of the duplex. Highly modified siRNA passenger strands were further modified with up to four cationic PN linkages, with little effect on duplex potency or helical structure. We envision that PN modifications could be useful in the production of therapeutic siRNAs with optimal biological properties.
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Affiliation(s)
- Danielle Vlaho
- Department of Chemistry, McGill University , Montreal, Canada
| | | | - Masad J Damha
- Department of Chemistry, McGill University , Montreal, Canada
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