1
|
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.
Collapse
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.
| |
Collapse
|
2
|
Gafur SH, Ghosh S, Richter M, Rozners E. Synthesis and Properties of RNA Modified with Thioamide Internucleoside Linkage. Chembiochem 2024:e202400364. [PMID: 38819607 DOI: 10.1002/cbic.202400364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Revised: 05/23/2024] [Accepted: 05/31/2024] [Indexed: 06/01/2024]
Abstract
Recent success of RNA therapeutics has reinvigorated interest in chemical modifications of RNA. As exemplified by the phosphorothioates, modifications of sugar-phosphate backbone have been remarkably impactful but relatively underexplored in therapeutic RNAs. The present study reports synthesis, thermal stability, and RNA interference activity of RNAs modified with thioamide linkages. Compared to the previously studied amide-modified RNA, thioamide linkages strongly destabilized a short self-complementary RNA model duplex. However, in short interfering RNAs amides and thioamides had a similar effect on duplex stability and target RNA cleavage activity and specificity. Hence, the thioamide may be added to the toolbox of chemical biologist as a useful backbone modification well tolerated by the RNA interference machinery.
Collapse
Affiliation(s)
- Sayed Habibul Gafur
- Department of Chemistry, Binghamton University, Binghamton, New York, 13902, USA
| | - Samir Ghosh
- Department of Chemistry, Binghamton University, Binghamton, New York, 13902, USA
| | - Michael Richter
- Department of Chemistry, Binghamton University, Binghamton, New York, 13902, USA
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, Binghamton, New York, 13902, USA
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Kowalski K. Synthesis and chemical transformations of glycol nucleic acid (GNA) nucleosides. Bioorg Chem 2023; 141:106921. [PMID: 37871392 DOI: 10.1016/j.bioorg.2023.106921] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/09/2023] [Accepted: 10/16/2023] [Indexed: 10/25/2023]
Abstract
Xeno nucleic acids (XNA) are an increasingly important class of hypermodified nucleic acids with great potential in bioorganic chemistry and synthetic biology. Glycol nucleic acid (GNA) is constructed from a three-carbon 1,2-propanediol (propylene glycol) backbone attached to a nucleobase entity, representing the simplest known XNA. This review is intended to present GNA nucleosides from a synthetic chemistry perspective-a perspective that serves as a starting point for biological studies. Therefore this account focuses on synthetic methods for GNA nucleoside synthesis, as well as their postsynthetic chemical transformations. The properties and biological activity of GNA constituents are also highlighted. A literature survey shows four major approaches toward GNA nucleoside scaffold synthesis. These approaches pertain to glycidol ring-opening, Mitsunobu, SN2, and dihydroxylation reactions. The general arsenal of reactions used in GNA chemistry is versatile and encompasses the Sonogashira reaction, Michael addition, silyl-Hilbert-Johnson reaction, halogenation, alkylation, cyclization, Rh-catalyzed N-allylation, Sharpless catalytic dihydroxylation, and Yb(OTf)3-catalyzed etherification. Additionally, various phosphorylation reactions have enabled the synthesis of diverse types of GNA nucleotides, dinucleoside phosphates, phosphordiamidites, and oligos. Furthermore, recent advances in GNA chemistry have resulted in the synthesis of previously unknown redox-active (ferrocenyl) and luminescent (pyrenyl and phenanthrenyl) GNA nucleosides, which are also covered in this review.
Collapse
Affiliation(s)
- Konrad Kowalski
- University of Lodz, Faculty of Chemistry, Department of Organic Chemistry, Tamka 12, PL-91403 Lodz, Poland.
| |
Collapse
|
6
|
Datta D, Theile CS, Wassarman K, Qin J, Racie T, Schmidt K, Jiang Y, Sigel R, Janas MM, Egli M, Manoharan M. Rational optimization of siRNA to ensure strand bias in the interaction with the RNA-induced silencing complex. Chem Commun (Camb) 2023; 59:6347-6350. [PMID: 37144553 DOI: 10.1039/d3cc01143g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
To ensure specificity of small interfering RNAs (siRNAs), the antisense strand must be selected by the RNA-induced silencing complex (RISC). We have previously demonstrated that a 5'-morpholino-modified nucleotide at the 5'-end of the sense strand inhibits its interaction with RISC ensuring selection of the desired antisense strand. To improve this antagonizing binding property even further, a new set of morpholino-based analogues, Mo2 and Mo3, and a piperidine analogue, Pip, were designed based on the known structure of Argonaute2, the slicer enzyme component of RISC. Sense strands of siRNAs were modified with these new analogues, and the siRNAs were evaluated in vitro and in mice for RNAi activity. Our data demonstrated that Mo2 is the best RISC inhibitor among the modifications tested and that it effectively mitigates sense strand-based off-target activity of siRNA.
Collapse
Affiliation(s)
- Dhrubajyoti Datta
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, USA.
| | - Christopher S Theile
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, USA.
| | - Kelly Wassarman
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, USA.
| | - June Qin
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, USA.
| | - Tim Racie
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, USA.
| | - Karyn Schmidt
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, USA.
| | - Yongfeng Jiang
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, USA.
| | - Rachel Sigel
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, USA.
| | - Maja M Janas
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, USA.
| | - Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, USA
| | - Muthiah Manoharan
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, USA.
| |
Collapse
|
7
|
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.
Collapse
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.
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
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.
Collapse
|
10
|
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.
Collapse
|
11
|
Hammill ML, Tsubaki K, Salim L, Varley AJ, Giorgees I, Kitamura M, Okauchi T, Desaulniers JP. SiRNAs with Neutral Phosphate Triester Hydrocarbon Tails Exhibit Carrier-Free Gene-Silencing Activity. ACS Med Chem Lett 2022; 13:695-700. [PMID: 35450364 PMCID: PMC9014433 DOI: 10.1021/acsmedchemlett.2c00027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 03/08/2022] [Indexed: 12/23/2022] Open
Abstract
Short interfering RNAs (siRNAs) show promise as gene-silencing therapeutics, but their cellular uptake remains a challenge. We have recently shown the synthesis of siRNAs bearing a single neutral phenylethyl phosphotriester linkage within the sense strand. Here, we report the synthesis of siRNAs bearing three different hydrophobic phosphate triester linkages at key positions within the sense strand and assess their gene silencing in the absence of a transfection carrier. The best siRNAs bearing hydrophobic phosphate triester tails were not aromatic and exhibited effective gene silencing (IC50 ≈ 56-141 nM), whereas the aromatic derivative with three hydrophobic tails did not exhibit carrier-free gene silencing.
Collapse
Affiliation(s)
- Matthew L. Hammill
- Faculty of Science, University of Ontario Institute of Technology, 2000 Simcoe Street North, Oshawa, Ontario L1G 0C5, Canada
| | - Kouta Tsubaki
- Faculty of Science, University of Ontario Institute of Technology, 2000 Simcoe Street North, Oshawa, Ontario L1G 0C5, Canada
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu Institute of Technology, 1-1 Sensui-cho, Tobata, Kitakyushu 804-8550, Japan
| | - Lidya Salim
- 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
| | - Ifrodet Giorgees
- 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
| |
Collapse
|
12
|
Guo Y, Xie Y, Luo Y. The Role of Long Non-Coding RNAs in the Tumor Immune Microenvironment. Front Immunol 2022; 13:851004. [PMID: 35222443 PMCID: PMC8863945 DOI: 10.3389/fimmu.2022.851004] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 01/24/2022] [Indexed: 02/05/2023] Open
Abstract
Tumorigenesis is a complicated process caused by successive genetic and epigenetic alterations. The past decades demonstrated that the immune system affects tumorigenesis, tumor progression, and metastasis. Although increasing immunotherapies are revealed, only a tiny proportion of them are effective. Long non-coding RNAs (lncRNAs) are a class of single-stranded RNA molecules larger than 200 nucleotides and are essential in the molecular network of oncology and immunology. Increasing researches have focused on the connection between lncRNAs and cancer immunotherapy. However, the in-depth mechanisms are still elusive. In this review, we outline the latest studies on the functions of lncRNAs in the tumor immune microenvironment. Via participating in various biological processes such as neutrophil recruitment, macrophage polarization, NK cells cytotoxicity, and T cells functions, lncRNAs regulate tumorigenesis, tumor invasion, epithelial-mesenchymal transition (EMT), and angiogenesis. In addition, we reviewed the current understanding of the relevant strategies for targeting lncRNAs. LncRNAs-based therapeutics may represent promising approaches in serving as prognostic biomarkers or potential therapeutic targets in cancer, providing ideas for future research and clinical application on cancer diagnosis and therapies.
Collapse
Affiliation(s)
- Yingli Guo
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Yajuan Xie
- Department of Orthodontics, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Yao Luo
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
| |
Collapse
|
13
|
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.
Collapse
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
| |
Collapse
|
14
|
miRNAs in Cancer (Review of Literature). Int J Mol Sci 2022; 23:ijms23052805. [PMID: 35269947 PMCID: PMC8910953 DOI: 10.3390/ijms23052805] [Citation(s) in RCA: 73] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 02/27/2022] [Accepted: 03/02/2022] [Indexed: 02/07/2023] Open
Abstract
MicroRNAs (miRNAs) are short, noncoding, single-stranded RNA molecules that regulate gene expression at the post-transcriptional level by binding to mRNAs. miRNAs affect the course of processes of fundamental importance for the proper functioning of the organism. These processes include cell division, proliferation, differentiation, cell apoptosis and the formation of blood vessels. Altered expression of individual miRNAs has been shown in numerous cancers, which may indicate the oncogenic or suppressor potential of the molecules in question. This paper discusses the current knowledge about the possibility of using miRNA as a diagnostic marker and a potential target in modern anticancer therapies.
Collapse
|
15
|
Liu P, Hu B, Li Y, Ji GC, Ma MY, Bi S, Jiang YY. Double-Regiodetermining-Stages Mechanistic Model Explaining the Regioselectivity of Pd-Catalyzed Hydroaminocarbonylation of Alkenes with Carbon Monoxide and Ammonium Chloride. J Org Chem 2021; 86:12988-13000. [PMID: 34459187 DOI: 10.1021/acs.joc.1c01672] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Pd-catalyzed hydroaminocarbonylation (HAC) of alkenes with CO and NH4Cl enables atom-economic and regiodivergent synthesis of primary amides, but the origin of regioselectivity was incorrectly interpreted in previous computational studies. A density functional theory study was performed herein to investigate the mechanism. Different from the previous proposals, both alkene insertion and aminolysis were found to be potential regioselectivity-determining stages. In the alkene insertion stage, 2,1-insertion is generally faster than 1,2-insertion irrespective of neutral or cationic pathways for both P(tBu)3 and xantphos. Such selectivity results from the unconventional proton-like hydrogen of the Pd-H bond in alkene insertion transition states. For less bulky alkenes, aminolysis with P(tBu)3 shows low selectivity, while linear selectivity dominates in this stage with xantphos due to a stronger repulsion between xantphos and branched acyl ligands. It was further revealed that the less-mentioned CO concentration and solvents also influence the regioselectivity by adjusting the relative feasibilities of CO-involved steps and NH3 release from ammonium chloride, respectively. The presented double-regiodetermining-stages mechanistic model associated with the effects of ligands, CO concentration, and solvents well reproduced the experimental selectivity to prove its validity and illuminated new perspectives for the regioselectivity control of HAC reactions.
Collapse
Affiliation(s)
- Peng Liu
- School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, People's Republic of China
| | - Bing Hu
- School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, People's Republic of China
| | - Yu Li
- School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, People's Republic of China
| | - Guo-Cui Ji
- School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, People's Republic of China
| | - Ming-Yu Ma
- School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, People's Republic of China
| | - Siwei Bi
- School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, People's Republic of China
| | - Yuan-Ye Jiang
- School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, People's Republic of China
| |
Collapse
|
16
|
Song P, Zhang R, He C, Chen T. Transcription, Reverse Transcription, and Amplification of Backbone-Modified Nucleic Acids with Laboratory-Evolved Thermophilic DNA Polymerases. Curr Protoc 2021; 1:e188. [PMID: 34232574 DOI: 10.1002/cpz1.188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Backbone-modified nucleic acids are usually more stable enzymatically than their natural counterparts, enabling their broad application as potential diagnostic or therapeutic agents. Moreover, the development of nucleic acids with unnatural backbones has expanded the pool of genetic information carriers and paved the way toward synthetic xenobiology. However, synthesizing these molecules remains very challenging due to the requirement for harsh reaction conditions and the low coupling efficiency during their traditional solid-phase synthesis. Although enzymatic synthesis provides an attractive alternative that also allows the replication and artificial evolution of these molecules, it is crucially dependent on the availability of polymerases capable of synthesizing these backbone-modified nucleotides. Previously, a series of thermostable polymerases that can efficiently synthesize or even amplify backbone-modified DNA or RNA have been evolved through a polymerase evolution method based on phage display. Herein we summarize protocols to use these evolved polymerase mutants to transcribe, reverse transcribe, and PCR amplify backbone-modified nucleic acids. We also outline the polymerase chain transcription method, developed later for the rapid production of RNA or backbone-modified RNA with one of these evolved polymerases, SFM4-3. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Transcription/synthesis of modified DNA/RNA from DNA templates with evolved polymerases SFM4-3 or SFM4-6 Basic Protocol 2: Reverse transcription of modified DNA/RNA with evolved polymerase SFM4-9 Basic Protocol 3: PCR amplification of modified DNA with evolved polymerase SFM4-3 Basic Protocol 4: Polymerase chain transcription for the production of RNA/modified RNA oligonucleotides with evolved polymerase SFM4-3.
Collapse
Affiliation(s)
- Ping Song
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, P. R. China
| | - Rujie Zhang
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, P. R. China
| | - Chuanping He
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, P. R. China
| | - Tingjian Chen
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, P. R. China
| |
Collapse
|
17
|
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.
Collapse
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
| |
Collapse
|
18
|
Portet A, Galinier R, Lassalle D, Faille A, Gourbal B, Duval D. Hemocyte siRNA uptake is increased by 5' cholesterol-TEG addition in Biomphalaria glabrata, snail vector of schistosome. PeerJ 2021; 9:e10895. [PMID: 33665030 PMCID: PMC7908872 DOI: 10.7717/peerj.10895] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 01/13/2021] [Indexed: 12/24/2022] Open
Abstract
Biomphalaria glabrata is one of the snail intermediate hosts of Schistosoma mansoni, the causative agent of intestinal schistosomiasis disease. Numerous molecular studies using comparative approaches between susceptible and resistant snails to S. mansoni infection have helped identify numerous snail key candidates supporting such susceptible/resistant status. The functional approach using RNA interference (RNAi) remains crucial to validate the function of such candidates. CRISPR-Cas systems are still under development in many laboratories, and RNA interference remains the best tool to study B. glabrata snail genetics. Herein, we describe the use of modified small interfering RNA (siRNA) molecules to enhance cell delivery, especially into hemocytes, the snail immune cells. Modification of siRNA with 5′ Cholesteryl TriEthylene Glycol (Chol-TEG) promotes cellular uptake by hemocytes, nearly eightfold over that of unmodified siRNA. FACS analysis reveals that more than 50% of hemocytes have internalized Chol-TEG siRNA conjugated to Cy3 fluorophores, 2 hours only after in vivo injection into snails. Chol-TEG siRNA targeting BgTEP1 (ThioEster-containing Protein), a parasite binding protein, reduced BgTEP1 transcript expression by 70–80% compared to control. The level of BgTEP1 protein secreted in the hemolymph was also decreased. However, despite the BgTEP1 knock-down at both RNA and protein levels, snail compatibility with its sympatric parasite is not affected suggesting functional redundancy among the BgTEP genes family in snail-schistosoma interaction.
Collapse
Affiliation(s)
- Anaïs Portet
- IHPE UMR 5244, CNRS, IFREMER, University of Montpellier, University of Perpignan, Perpignan, France.,Department of Medicine, Molecular Immunity Unit, University of Cambridge, Cambridge, United Kingdom
| | - Richard Galinier
- IHPE UMR 5244, CNRS, IFREMER, University of Montpellier, University of Perpignan, Perpignan, France
| | - Damien Lassalle
- IHPE UMR 5244, CNRS, IFREMER, University of Montpellier, University of Perpignan, Perpignan, France
| | - Alexandre Faille
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom.,Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom.,Cambridge Institute for Medical Research, Cambridge, United Kingdom
| | - Benjamin Gourbal
- IHPE UMR 5244, CNRS, IFREMER, University of Montpellier, University of Perpignan, Perpignan, France
| | - David Duval
- IHPE UMR 5244, CNRS, IFREMER, University of Montpellier, University of Perpignan, Perpignan, France
| |
Collapse
|
19
|
Koizumi M, Hirota Y, Nakayama M, Tamura M, Obuchi W. RNA interference activity of single-stranded oligonucleotides linked between the passenger strand and the guide strand with an aryl phosphate linker. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2021; 40:647-664. [PMID: 34047248 DOI: 10.1080/15257770.2021.1927077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 04/20/2021] [Accepted: 05/03/2021] [Indexed: 10/21/2022]
Abstract
Recently, we demonstrated that asymmetrical 18 base-paired double-strand oligonucleotides comprised of alternately combined 2'-O-methyl RNA and DNA, termed MED-siRNAs, show high RNase resistance, efficient cleavage of target mRNA, and the subsequent reduction of target protein expression. The 5'-terminal phosphate group and the 3'-overhang of the guide strand were required to fully activate the RNAi activity of MED-siRNAs. Here, we evaluated MED-siRNAs modified with aryl phosphate groups at the 5'-end of the guide strand. The 5'-aryl phosphorylated MED-siRNAs showed highly efficient reduction of target protein expression comparable to 5'-phosphorylated MED-siRNAs. Moreover, 5'-aryl phosphorylated MED-siRNAs linked between the aryl phosphate group at the 5'-end of the guide strand and the hydroxyl group at the 3'-end of the passenger strand with alkyl amide linkers or peptides (e.g., DL-Ser-L-Ala-L-Tyr), resulted in single-stranded MED-siRNAs with a highly efficient cleavage activity of target mRNA with binding to Argonaute 2 via an RNA interference mechanism. These linker techniques could also be used to create siRNAs composed of naturally-occurring molecules such as amino acids. These findings suggest the possibility of using these single-stranded MED-siRNAs as siRNA reagents.Supplemental data for this article is available online at https://doi.org/10.1080/15257770.2021.1927077 .
Collapse
Affiliation(s)
- Makoto Koizumi
- R&D and Biologics Divisions, Daiichi Sankyo Co., Ltd, Shinagawa, Tokyo, Japan
| | - Yasuhide Hirota
- R&D and Biologics Divisions, Daiichi Sankyo Co., Ltd, Shinagawa, Tokyo, Japan
| | - Makiko Nakayama
- R&D and Biologics Divisions, Daiichi Sankyo Co., Ltd, Shinagawa, Tokyo, Japan
| | - Masakazu Tamura
- R&D and Biologics Divisions, Daiichi Sankyo Co., Ltd, Shinagawa, Tokyo, Japan
| | - Wataru Obuchi
- R&D and Biologics Divisions, Daiichi Sankyo Co., Ltd, Shinagawa, Tokyo, Japan
| |
Collapse
|