51
|
Ma Y, Liu S, Wang Y, Zhao Y, Huang Y, Zhong L, Guan Z, Zhang L, Yang Z. Isonucleotide incorporation into middle and terminal siRNA duplexes exhibits high gene silencing efficacy and nuclease resistance. Org Biomol Chem 2018; 15:5161-5170. [PMID: 28585968 DOI: 10.1039/c7ob01065f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In this study, we introduced a pair of nucleotide enantiomers, d-/l-isonucleotides (d-/l-isoNA), to examine the interactions between siRNAs and their related proteins. The serum stability and gene-silencing activity of the modified siRNAs were systematically evaluated. Gene-silencing activity had a site-specific effect, and the incorporation of a single d-isoNA at the 8th position (counting from the 5'-terminus) in the antisense strand improved the gene-silencing activity by improving RISC loading and affecting the movement of the PIWI domain. d-isoNA incorporated at the terminus of siRNA including the 2nd position in the antisense strand and 3'-overhangs in the sense strand, especially the latter, enhanced nuclease resistance and prolonged the silencing retention time. In addition, l-isoNA incorporation into the middle of the sense strand enhanced activity. These results provide a chemical strategy for the modulation of siRNA gene-silencing activity and nuclease resistance.
Collapse
Affiliation(s)
- Yuan Ma
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China.
| | | | | | | | | | | | | | | | | |
Collapse
|
52
|
Advanced siRNA Designs Further Improve In Vivo Performance of GalNAc-siRNA Conjugates. Mol Ther 2018; 26:708-717. [PMID: 29456020 PMCID: PMC5910670 DOI: 10.1016/j.ymthe.2017.12.021] [Citation(s) in RCA: 193] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 12/18/2017] [Accepted: 12/24/2017] [Indexed: 12/20/2022] Open
Abstract
Significant progress has been made in the advancement of RNAi therapeutics by combining a synthetic triantennary N-acetylgalactosamine ligand targeting the asialoglycoprotein receptor with chemically modified small interfering RNA (siRNA) designs, including the recently described Enhanced Stabilization Chemistry. This strategy has demonstrated robust RNAi-mediated gene silencing in liver after subcutaneous administration across species, including human. Here we demonstrate that substantial efficacy improvements can be achieved through further refinement of siRNA chemistry, optimizing the positioning of 2′-deoxy-2′-fluoro and 2′-O-methyl ribosugar modifications across both strands of the double-stranded siRNA duplex to enhance stability without compromising intrinsic RNAi activity. To achieve this, we employed an iterative screening approach across multiple siRNAs to arrive at advanced designs with low 2′-deoxy-2′-fluoro content that yield significantly improved potency and duration in preclinical species, including non-human primate. Liver exposure data indicate that the improvement in potency is predominantly due to increased metabolic stability of the siRNA conjugates.
Collapse
|
53
|
Lozada-Delgado EL, Grafals-Ruiz N, Vivas-Mejía PE. RNA interference for glioblastoma therapy: Innovation ladder from the bench to clinical trials. Life Sci 2017; 188:26-36. [PMID: 28864225 PMCID: PMC5617340 DOI: 10.1016/j.lfs.2017.08.027] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 08/24/2017] [Accepted: 08/28/2017] [Indexed: 02/07/2023]
Abstract
Glioblastoma multiforme (GBM) is the most common and deadliest type of primary brain tumor with a prognosis of 14months after diagnosis. Current treatment for GBM patients includes "total" tumor resection, temozolomide-based chemotherapy, radiotherapy or a combination of these options. Although, several targeted therapies, gene therapy, and immunotherapy are currently in the clinic and/or in clinical trials, the overall survival of GBM patients has hardly improved over the last two decades. Therefore, novel multitarget modalities are urgently needed. Recently, RNA interference (RNAi) has emerged as a novel strategy for the treatment of most cancers, including GBM. RNAi-based therapies consist of using small RNA oligonucleotides to regulate protein expression at the post-transcriptional level. Despite the therapeutic potential of RNAi molecules, systemic limitations including short circulatory stability and low release into the tumor tissue have halted their progress to the clinic. The effective delivery of RNAi molecules through the blood-brain barrier (BBB) represents an additional challenge. This review focuses on connecting the translational process of RNAi-based therapies from in vitro evidence to pre-clinical studies. We delineate the effect of RNAi in GBM cell lines, describe their effectiveness in glioma mouse models, and compare the proposed drug carriers for the effective transport of RNAi molecules through the BBB to reach the tumor in the brain. Furthermore, we summarize the most important obstacles to overcome before RNAi-based therapy becomes a reality for GBM treatment.
Collapse
Affiliation(s)
- Eunice L Lozada-Delgado
- Department of Biology, University of Puerto Rico, Rio Piedras Campus, San Juan, PR 00927, United States; Comprehensive Cancer Center, University of Puerto Rico, Medical Sciences Campus, San Juan, PR 00935, United States; Department of Biochemistry, University of Puerto Rico, Medical Sciences Campus, San Juan, PR 00935, United States
| | - Nilmary Grafals-Ruiz
- Comprehensive Cancer Center, University of Puerto Rico, Medical Sciences Campus, San Juan, PR 00935, United States; Department of Physiology, University of Puerto Rico, Medical Sciences Campus, San Juan, PR 00935, United States
| | - Pablo E Vivas-Mejía
- Comprehensive Cancer Center, University of Puerto Rico, Medical Sciences Campus, San Juan, PR 00935, United States; Department of Biochemistry, University of Puerto Rico, Medical Sciences Campus, San Juan, PR 00935, United States.
| |
Collapse
|
54
|
Song X, Wang X, Ma Y, Liang Z, Yang Z, Cao H. Site-Specific Modification Using the 2'-Methoxyethyl Group Improves the Specificity and Activity of siRNAs. MOLECULAR THERAPY-NUCLEIC ACIDS 2017; 9:242-250. [PMID: 29246303 PMCID: PMC5675723 DOI: 10.1016/j.omtn.2017.10.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 10/03/2017] [Accepted: 10/03/2017] [Indexed: 11/29/2022]
Abstract
Rapid progress has been made toward small interfering RNA (siRNA)-based therapy for human disorders, but rationally optimizing siRNAs for high specificity and potent silencing remains a challenge. In this study, we explored the effect of chemical modification at the cleavage site of siRNAs. We found that modifications at positions 9 and 10 markedly reduced the silencing potency of the unmodified strand of siRNAs but were well tolerated by the modified strand. Intriguingly, addition of the 2′-methoxyethyl (MOE) group at the cleavage site improved both the specificity and silencing activity of siRNAs by facilitating the oriented RNA-induced silencing complex (RISC) loading of the modified strand. Furthermore, we combined MOE modifications at positions 9 and 10 of one strand together with 2′-O-methylation (OMe) at position 14 of the other strand and found a synergistic effect that improved the specificity of siRNAs. The surprisingly beneficial effect of the combined modification was validated using siRNA-targeting endogenous gene intercellular adhesion molecule 1 (ICAM1). We found that the combined modifications eliminated its off-target effects. In conclusion, we established effective strategies to optimize siRNAs using site-specific MOE modifications. The findings may allow the creation of superior siRNAs for therapy in terms of activity and specificity.
Collapse
Affiliation(s)
- Xinyun Song
- Laboratory of Nucleic Acid Technology, Institute of Molecular Medicine, Peking University, Beijing 100871, China
| | - Xiaoxia Wang
- Laboratory of Nucleic Acid Technology, Institute of Molecular Medicine, Peking University, Beijing 100871, China
| | - Yuan Ma
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Zicai Liang
- Laboratory of Nucleic Acid Technology, Institute of Molecular Medicine, Peking University, Beijing 100871, China
| | - Zhenjun Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China.
| | - Huiqing Cao
- Laboratory of Nucleic Acid Technology, Institute of Molecular Medicine, Peking University, Beijing 100871, China.
| |
Collapse
|
55
|
Kaczmarek JC, Kowalski PS, Anderson DG. Advances in the delivery of RNA therapeutics: from concept to clinical reality. Genome Med 2017; 9:60. [PMID: 28655327 PMCID: PMC5485616 DOI: 10.1186/s13073-017-0450-0] [Citation(s) in RCA: 449] [Impact Index Per Article: 64.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The rapid expansion of the available genomic data continues to greatly impact biomedical science and medicine. Fulfilling the clinical potential of genetic discoveries requires the development of therapeutics that can specifically modulate the expression of disease-relevant genes. RNA-based drugs, including short interfering RNAs and antisense oligonucleotides, are particularly promising examples of this newer class of biologics. For over two decades, researchers have been trying to overcome major challenges for utilizing such RNAs in a therapeutic context, including intracellular delivery, stability, and immune response activation. This research is finally beginning to bear fruit as the first RNA drugs gain FDA approval and more advance to the final phases of clinical trials. Furthermore, the recent advent of CRISPR, an RNA-guided gene-editing technology, as well as new strides in the delivery of messenger RNA transcribed in vitro, have triggered a major expansion of the RNA-therapeutics field. In this review, we discuss the challenges for clinical translation of RNA-based therapeutics, with an emphasis on recent advances in delivery technologies, and present an overview of the applications of RNA-based drugs for modulation of gene/protein expression and genome editing that are currently being investigated both in the laboratory as well as in the clinic.
Collapse
Affiliation(s)
- James C Kaczmarek
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, USA.,David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, USA
| | - Piotr S Kowalski
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, USA
| | - Daniel G Anderson
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, USA. .,David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, USA. .,Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, USA. .,Harvard and MIT Division of Health Science and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, USA.
| |
Collapse
|
56
|
Selvam C, Mutisya D, Prakash S, Ranganna K, Thilagavathi R. Therapeutic potential of chemically modified siRNA: Recent trends. Chem Biol Drug Des 2017; 90:665-678. [PMID: 28378934 DOI: 10.1111/cbdd.12993] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 03/26/2017] [Accepted: 03/27/2017] [Indexed: 12/17/2022]
Abstract
Small interfering RNAs (siRNAs) are one of the valuable tools to investigate the functions of genes and are also used for gene silencing. It has a wide scope in drug discovery through in vivo target validation. siRNA therapeutics are not optimal drug-like molecules due to poor bioavailability and immunogenic and off-target effects. To overcome the challenges associated with siRNA therapeutics, identification of appropriate chemical modifications that improves the stability, specificity and potency of siRNA is essential. This review focuses on the various chemical modifications and their implications in siRNA therapy.
Collapse
Affiliation(s)
- Chelliah Selvam
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, Texas Southern University, Houston, TX, USA
| | - Daniel Mutisya
- Department of Science and Mathematics, Albany State University, Albany, GA, USA
| | - Sandhya Prakash
- Department of Biotechnology, Faculty of Engineering, Karpagam University, Coimbatore, India
| | - Kasturi Ranganna
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, Texas Southern University, Houston, TX, USA
| | - Ramasamy Thilagavathi
- Department of Biotechnology, Faculty of Engineering, Karpagam University, Coimbatore, India
| |
Collapse
|
57
|
Alaaeldin E, Abu Lila AS, Ando H, Fukushima M, Huang CL, Wada H, Sarhan HA, Khaled KA, Ishida T. Co-administration of liposomal l-OHP and PEGylated TS shRNA-lipoplex: A novel approach to enhance anti-tumor efficacy and reduce the immunogenic response to RNAi molecules. J Control Release 2017; 255:210-217. [PMID: 28461099 DOI: 10.1016/j.jconrel.2017.04.040] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 04/20/2017] [Accepted: 04/26/2017] [Indexed: 12/17/2022]
Abstract
Many therapeutic strategies have been applied in efforts to conquer the development and/or progression of cancer. The combination of chemotherapy and an RNAi-based approach has proven to be an efficient anticancer therapy. However, the feasibility of such a therapeutic strategy has been substantially restricted either by the failure to achieve the efficient delivery of RNAi molecules to tumor tissue or by the immunostimulatory response triggered by RNAi molecules. In this study, therefore, we intended to investigate the efficacy of using liposomal oxaliplatin (liposomal l-OHP) to guarantee the efficient delivery of RNAi molecules, namely shRNA against thymidylate synthase (TS shRNA) complexed with cationic liposome (TS shRNA-lipoplex), to solid tumors, and to suppress the immunostimulatory effect of RNAi molecules, TS shRNA, following intravenous administration. Herein, we describe how liposomal l-OHP enhanced the intra-tumor accumulation of TS shRNA-lipoplex and significantly reduced the immunostimulatory response triggered by TS shRNA. Consequently, such enhanced accumulation of TS shRNA-lipoplex along with the cytotoxic effect of liposomal l-OHP led to a remarkable tumor growth suppression (compared to mono-therapy) following systemic administration. Our results, therefore, may have important implications for the provision of a safer and more applicable combination therapy of RNAi molecules and anti-cancer agents that can produce a more reliable anti-tumor effect.
Collapse
Affiliation(s)
- Eman Alaaeldin
- Department of Pharmacokinetics and Biopharmaceutics, Institute of Biomedical Sciences, Tokushima University, 1-78-1, Sho-machi, Tokushima 770-8505, Japan; Department of Pharmaceutics, Faculty of Pharmacy, Minia University, Minia 61519, Egypt
| | - Amr S Abu Lila
- Department of Pharmacokinetics and Biopharmaceutics, Institute of Biomedical Sciences, Tokushima University, 1-78-1, Sho-machi, Tokushima 770-8505, Japan; Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt; Department of Pharmaceutics, College of Pharmacy, Hail University, Hail 81442, Saudi Arabia
| | - Hidenori Ando
- Department of Pharmacokinetics and Biopharmaceutics, Institute of Biomedical Sciences, Tokushima University, 1-78-1, Sho-machi, Tokushima 770-8505, Japan; Department of Cancer Metabolism and Therapy, Institute of Biomedical Sciences,Tokushima University, 1-78-1, Sho-machi, Tokushima 770-8505, Japan
| | - Masakazu Fukushima
- Department of Cancer Metabolism and Therapy, Institute of Biomedical Sciences,Tokushima University, 1-78-1, Sho-machi, Tokushima 770-8505, Japan
| | - Cheng-Long Huang
- Department of Thoracic Surgery, Faculty of Medicine, Kyoto University, Kyoto, Japan
| | - Hiromi Wada
- Department of Thoracic Surgery, Faculty of Medicine, Kyoto University, Kyoto, Japan
| | - Hatem A Sarhan
- Department of Pharmaceutics, Faculty of Pharmacy, Minia University, Minia 61519, Egypt
| | - Khaled A Khaled
- Department of Pharmaceutics, Faculty of Pharmacy, Minia University, Minia 61519, Egypt
| | - Tatsuhiro Ishida
- Department of Pharmacokinetics and Biopharmaceutics, Institute of Biomedical Sciences, Tokushima University, 1-78-1, Sho-machi, Tokushima 770-8505, Japan; Department of Cancer Metabolism and Therapy, Institute of Biomedical Sciences,Tokushima University, 1-78-1, Sho-machi, Tokushima 770-8505, Japan.
| |
Collapse
|
58
|
Elkayam E, Parmar R, Brown CR, Willoughby JL, Theile CS, Manoharan M, Joshua-Tor L. siRNA carrying an (E)-vinylphosphonate moiety at the 5΄ end of the guide strand augments gene silencing by enhanced binding to human Argonaute-2. Nucleic Acids Res 2017; 45:3528-3536. [PMID: 27903888 PMCID: PMC5389677 DOI: 10.1093/nar/gkw1171] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 11/03/2016] [Accepted: 11/09/2016] [Indexed: 01/20/2023] Open
Abstract
Efficient gene silencing by RNA interference (RNAi) in vivo requires the recognition and binding of the 5΄- phosphate of the guide strand of an siRNA by the Argonaute protein. However, for exogenous siRNAs it is limited by the rapid removal of the 5΄- phosphate of the guide strand by metabolic enzymes. Here, we have determined the crystal structure of human Argonaute-2 in complex with the metabolically stable 5΄-(E)-vinylphosphonate (5΄-E-VP) guide RNA at 2.5-Å resolution. The structure demonstrates how the 5΄ binding site in the Mid domain of human Argonaute-2 is able to adjust the key residues in the 5΄-nucleotide binding pocket to compensate for the change introduced by the modified nucleotide. This observation also explains improved binding affinity of the 5΄-E-VP -modified siRNA to human Argonaute-2 in-vitro, as well as the enhanced silencing in the context of the trivalent N-acetylgalactosamine (GalNAc)-conjugated siRNA in mice relative to the un-modified siRNA.
Collapse
Affiliation(s)
- Elad Elkayam
- Keck Structural Biology Lab, Cold Spring Harbor, NY 11724, USA
- Howard Hughes Medical Institute, Cold Spring Harbor, NY 11724, USA
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Rubina Parmar
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA 02142, USA
| | | | | | | | | | - Leemor Joshua-Tor
- Keck Structural Biology Lab, Cold Spring Harbor, NY 11724, USA
- Howard Hughes Medical Institute, Cold Spring Harbor, NY 11724, USA
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| |
Collapse
|
59
|
Harikrishna S, Pradeepkumar PI. Probing the Binding Interactions between Chemically Modified siRNAs and Human Argonaute 2 Using Microsecond Molecular Dynamics Simulations. J Chem Inf Model 2017; 57:883-896. [DOI: 10.1021/acs.jcim.6b00773] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- S. Harikrishna
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai−400076, India
| | - P. I. Pradeepkumar
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai−400076, India
| |
Collapse
|
60
|
Khvorova A, Watts JK. The chemical evolution of oligonucleotide therapies of clinical utility. Nat Biotechnol 2017; 35:238-248. [PMID: 28244990 PMCID: PMC5517098 DOI: 10.1038/nbt.3765] [Citation(s) in RCA: 749] [Impact Index Per Article: 107.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 12/12/2016] [Indexed: 02/07/2023]
Abstract
After nearly 40 years of development, oligonucleotide therapeutics are nearing meaningful clinical productivity. One of the key advantages of oligonucleotide drugs is that their delivery and potency are derived primarily from the chemical structure of the oligonucleotide whereas their target is defined by the base sequence. Thus, as oligonucleotides with a particular chemical design show appropriate distribution and safety profiles for clinical gene silencing in a particular tissue, this will open the door to the rapid development of additional drugs targeting other disease-associated genes in the same tissue. To achieve clinical productivity, the chemical architecture of the oligonucleotide needs to be optimized with a combination of sugar, backbone, nucleobase, and 3'- and 5'-terminal modifications. A portfolio of chemistries can be used to confer drug-like properties onto the oligonucleotide as a whole, with minor chemical changes often translating into major improvements in clinical efficacy. One outstanding challenge in oligonucleotide chemical development is the optimization of chemical architectures to ensure long-term safety. There are multiple designs that enable effective targeting of the liver, but a second challenge is to develop architectures that enable robust clinical efficacy in additional tissues.
Collapse
Affiliation(s)
- Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Jonathan K Watts
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| |
Collapse
|
61
|
Nguyen MK, McMillan A, Huynh CT, Schapira DS, Alsberg E. Photocrosslinkable, biodegradable hydrogels with controlled cell adhesivity for prolonged siRNA delivery to hMSCs to enhance their osteogenic differentiation. J Mater Chem B 2017; 5:485-495. [PMID: 28652917 PMCID: PMC5482539 DOI: 10.1039/c6tb01739h] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Photocrosslinked, biodegradable hydrogels have been extensively investigated for biomedical applications, including drug delivery and tissue engineering. Here, dextran (DEX) was chemically modified with mono(2-acryloyloxyethyl) succinate (MAES) via an esterification reaction, resulting in macromers that could be photocrosslinked to form hydrolytically degradable hydrogels. Hydrogel swelling ratio and degradation rate were controlled by varying the degree of MAES modification. Thiolated cell adhesion peptides (GRGDSPC) were conjugated to acrylated dextran via thiol-acrylate reaction to regulate the interactions of human mesenchymal stem cells (hMSCs) with the photocrosslinkable hydrogels. The hydrogels permitted sustained release of short interfering RNA (siRNA) over 7 weeks and were cytocompatible with hMSCs. Sustained presentation of siRNA from these photocrosslinked DEX hydrogels enhanced the osteogenic differentiation of encapsulated hMSCs. These DEX hydrogels with tunable siRNA delivery and cell adhesive properties may provide an excellent platform for bioactive molecule delivery and tissue regeneration applications.
Collapse
Affiliation(s)
- Minh Khanh Nguyen
- Department of Biomedical Engineering, Case Western Reserve University, 10900 Euclid Ave., Cleveland, Ohio 44106
| | - Alexandra McMillan
- Department of Pathology, Case Western Reserve University, 10900 Euclid Ave., Cleveland, Ohio 44106
| | - Cong Truc Huynh
- Department of Biomedical Engineering, Case Western Reserve University, 10900 Euclid Ave., Cleveland, Ohio 44106
| | - Daniel S Schapira
- Department of Biomedical Engineering, Case Western Reserve University, 10900 Euclid Ave., Cleveland, Ohio 44106
| | - Eben Alsberg
- Department of Biomedical Engineering, Case Western Reserve University, 10900 Euclid Ave., Cleveland, Ohio 44106
- Department of Orthopaedic Surgery, Case Western Reserve University, 10900 Euclid Ave., Cleveland, Ohio 44106
- National Center for Regenerative Medicine, Division of General Medical Sciences, Case Western Reserve University, 10900 Euclid Ave., Cleveland, Ohio 44106
| |
Collapse
|
62
|
Zhu X, Han MY, Li P, Wang L. Photoinduced difunctionalization of 2,3-dihydrofuran for the efficient synthesis of 2,3-disubstituted tetrahydrofurans. Org Chem Front 2017. [DOI: 10.1039/c7qo00242d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
An efficient photoinduced multicomponent difunctionalization of 2,3-dihydrofuran has been developed for the synthesis of 2,3-disubstituted tetrahydrofurans under mild reaction conditions.
Collapse
Affiliation(s)
- Xingxing Zhu
- Department of Chemistry
- Huaibei Normal University
- Huaibei
- P. R. China
| | - Man-Yi Han
- Department of Chemistry
- Huaibei Normal University
- Huaibei
- P. R. China
| | - Pinhua Li
- Department of Chemistry
- Huaibei Normal University
- Huaibei
- P. R. China
| | - Lei Wang
- Department of Chemistry
- Huaibei Normal University
- Huaibei
- P. R. China
- State Key Laboratory of Organometallic Chemistry
| |
Collapse
|
63
|
Simion V, Nadim WD, Benedetti H, Pichon C, Morisset-Lopez S, Baril P. Pharmacomodulation of microRNA Expression in Neurocognitive Diseases: Obstacles and Future Opportunities. Curr Neuropharmacol 2017; 15:276-290. [PMID: 27397479 PMCID: PMC5412696 DOI: 10.2174/1570159x14666160630210422] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 05/31/2016] [Accepted: 06/28/2016] [Indexed: 12/21/2022] Open
Abstract
Given the importance of microRNAs (miRNAs) in modulating brain functions and their implications in neurocognitive disorders there are currently significant efforts devoted in the field of miRNA-based therapeutics to correct and/or to treat these brain diseases. The observation that miRNA 29a/b-1 cluster, miRNA 10b and miRNA 7, for instance, are frequently deregulated in the brains of patients with neurocognitive diseases and in animal models of Alzheimer, Huntington's and Parkinson's diseases, suggest that correction of miRNA expression using agonist or antagonist miRNA oligonucleotides might be a promising approach to correct or even to cure such diseases. The encouraging results from recent clinical trials allow envisioning that pharmacological approaches based on miRNAs might, in a near future, reach the requirements for successful therapeutic outcomes and will improve the healthcare of patients with brain injuries or disorders. This review will focus on the current strategies used to modulate pharmacological function of miRNA using chemically modified oligonucleotides. We will then review the recent literature on strategies to improve nucleic acid delivery across the blood-brain barrier which remains a severe obstacle to the widespread application of miRNA therapeutics to treat brain diseases. Finally, we provide a state-of-art of current preclinical research performed in animal models for the treatment of neurocognitive disorders using miRNA as therapeutic agents and discuss future developments of miRNA therapeutics.
Collapse
Affiliation(s)
- Viorel Simion
- Centre de Biophysique Moléculaire, CNRS UPR4301, Université d’Orléans France, 45071 Orléans Cedex, France
| | - Wissem Deraredj Nadim
- Centre de Biophysique Moléculaire, CNRS UPR4301, Université d’Orléans France, 45071 Orléans Cedex, France
| | - Hélène Benedetti
- Centre de Biophysique Moléculaire, CNRS UPR4301, Université d’Orléans France, 45071 Orléans Cedex, France
| | - Chantal Pichon
- Centre de Biophysique Moléculaire, CNRS UPR4301, Université d’Orléans France, 45071 Orléans Cedex, France
| | - Severine Morisset-Lopez
- Centre de Biophysique Moléculaire, CNRS UPR4301, Université d’Orléans France, 45071 Orléans Cedex, France
| | - Patrick Baril
- Centre de Biophysique Moléculaire, CNRS UPR4301, Université d’Orléans France, 45071 Orléans Cedex, France
| |
Collapse
|
64
|
Achieving HIV-1 Control through RNA-Directed Gene Regulation. Genes (Basel) 2016; 7:genes7120119. [PMID: 27941595 PMCID: PMC5192495 DOI: 10.3390/genes7120119] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 11/28/2016] [Accepted: 11/29/2016] [Indexed: 12/13/2022] Open
Abstract
HIV-1 infection has been transformed by combined anti-retroviral therapy (ART), changing a universally fatal infection into a controllable infection. However, major obstacles for an HIV-1 cure exist. The HIV latent reservoir, which exists in resting CD4+ T cells, is not impacted by ART, and can reactivate when ART is interrupted or ceased. Additionally, multi-drug resistance can arise. One alternate approach to conventional HIV-1 drug treatment that is being explored involves gene therapies utilizing RNA-directed gene regulation. Commonly known as RNA interference (RNAi), short interfering RNA (siRNA) induce gene silencing in conserved biological pathways, which require a high degree of sequence specificity. This review will provide an overview of the silencing pathways, the current RNAi technologies being developed for HIV-1 gene therapy, current clinical trials, and the challenges faced in progressing these treatments into clinical trials.
Collapse
|
65
|
Schirle NT, Kinberger GA, Murray HF, Lima WF, Prakash TP, MacRae IJ. Structural Analysis of Human Argonaute-2 Bound to a Modified siRNA Guide. J Am Chem Soc 2016; 138:8694-7. [PMID: 27380263 PMCID: PMC4993527 DOI: 10.1021/jacs.6b04454] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Incorporation of chemical modifications into small interfering RNAs (siRNAs) increases their metabolic stability and improves their tissue distribution. However, how these modifications impact interactions with Argonaute-2 (Ago2), the molecular target of siRNAs, is not known. Herein we present the crystal structure of human Ago2 bound to a metabolically stable siRNA containing extensive backbone modifications. Comparison to the structure of an equivalent unmodified-siRNA complex indicates that the structure of Ago2 is relatively unaffected by chemical modifications in the bound siRNA. In contrast, the modified siRNA appears to be much more plastic and shifts, relative to the unmodified siRNA, to optimize contacts with Ago2. Structure-activity analysis reveals that even major conformational perturbations in the 3' half of the siRNA seed region have a relatively modest effect on knockdown potency. These findings provide an explanation for a variety of modification patterns tolerated in siRNAs and a structural basis for advancing therapeutic siRNA design.
Collapse
Affiliation(s)
- Nicole T. Schirle
- Department of Integrative Computational and Structural Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Garth A. Kinberger
- Ionis Pharmaceuticals Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, United States
| | - Heather F. Murray
- Ionis Pharmaceuticals Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, United States
| | - Walt F. Lima
- Ionis Pharmaceuticals Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, United States
| | - Thazha P. Prakash
- Ionis Pharmaceuticals Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, United States
| | - Ian J. MacRae
- Department of Integrative Computational and Structural Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| |
Collapse
|
66
|
Nothisen M, Bagilet J, Behr JP, Remy JS, Kotera M. Structure Tuning of Cationic Oligospermine-siRNA Conjugates for Carrier-Free Gene Silencing. Mol Pharm 2016; 13:2718-28. [PMID: 27398779 DOI: 10.1021/acs.molpharmaceut.6b00309] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Oligospermine-siRNA conjugates are able to induce efficient luciferase gene silencing upon carrier-free transfection. These conjugates are readily accessible by a versatile automated chemistry that we developed using a DMT-spermine phosphoramidite reagent. In this article, we used this chemistry to study a wide range of structural modifications of the oligospermine-siRNA conjugates, i.e., variation of conjugate positions and introduction of chemical modifications to increase nuclease resistance. At first we examined gene silencing activity of a series of siRNA-tris(spermine) conjugates with and without chemical modifications in standard carrier assisted conditions. The three spermine units attached at one of the two ends of the sense strand or at the 3'-end of the antisense strand are compatible with gene silencing activity whereas attachment of spermine units at the 5'-end of the antisense strand abolished the activity. 2'-O-Methylated nucleotides introduced in the sense strand are compatible while not in the antisense strand. Thiophosphate links could be used without activity loss at the 3'-end of both strands and at the 5'-end of the sense strand to conjugate oligospermine. Consequently a series of oligospermine-siRNA conjugates containing 15 to 45 spermines units in various configurations were chosen, prepared, and examined in carrier-free conditions. Attachment of 30 spermine units singly at the 5'-end of the sense strand provides the most potent carrier-free siRNA. Longevity of luciferase gene silencing was studied using oligospermine-siRNA conjugates. Five day long efficiency with more than 80% gene expression knockdown was observed upon transfection without vector. Oligospermine-siRNA conjugates targeting cell-constitutive natural lamin A/C gene were prepared. Efficient gene silencing was observed upon carrier-free transfection of siRNA conjugates containing 20 or 30 spermine residues grafted at the 5'-end of the sense strand.
Collapse
Affiliation(s)
- Marc Nothisen
- Laboratoire V-SAT, CAMB, UMR 7199, Université de Strasbourg and CNRS, Faculté de Pharmacie , F-67401 Illkirch, France
| | - Jérémy Bagilet
- Laboratoire V-SAT, CAMB, UMR 7199, Université de Strasbourg and CNRS, Faculté de Pharmacie , F-67401 Illkirch, France
| | - Jean-Paul Behr
- Laboratoire V-SAT, CAMB, UMR 7199, Université de Strasbourg and CNRS, Faculté de Pharmacie , F-67401 Illkirch, France
| | - Jean-Serge Remy
- Laboratoire V-SAT, CAMB, UMR 7199, Université de Strasbourg and CNRS, Faculté de Pharmacie , F-67401 Illkirch, France
| | - Mitsuharu Kotera
- Laboratoire V-SAT, CAMB, UMR 7199, Université de Strasbourg and CNRS, Faculté de Pharmacie , F-67401 Illkirch, France
| |
Collapse
|
67
|
Alagia A, Eritja R. siRNA and RNAi optimization. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 7:316-29. [PMID: 26840434 DOI: 10.1002/wrna.1337] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 12/17/2015] [Accepted: 12/18/2015] [Indexed: 12/12/2022]
Abstract
The discovery and examination of the posttranscriptional gene regulatory mechanism known as RNA interference (RNAi) contributed to the identification of small interfering RNA (siRNA) and the comprehension of its enormous potential for clinical purposes. Theoretically, the ability of specific target gene downregulation makes the RNAi pathway an appealing solution for several diseases. Despite numerous hurdles resulting from the inherent properties of siRNA molecule and proper delivery to the target tissue, more than 50 RNA-based drugs are currently under clinical testing. In this work, we analyze the recent literature in the optimization of siRNA molecules. In detail, we focused on describing the most recent advances of siRNA field aimed at optimize siRNA pharmacokinetic properties. Special attention has been given in describing the impact of RNA modifications in the potential off-target effects (OTEs) such as saturation of the RNAi machinery, passenger strand-mediated silencing, immunostimulation, and miRNA-like OTEs as well as to recent developments on the delivery issue. The novel delivery systems and modified siRNA provide significant steps toward the development of reliable siRNA molecules for therapeutic use. WIREs RNA 2016, 7:316-329. doi: 10.1002/wrna.1337 For further resources related to this article, please visit the WIREs website.
Collapse
Affiliation(s)
- Adele Alagia
- Chemical and Biomolecular Nanotechnology, CIBER-BBN, Institute for Advanced Chemistry of Catalonia, IQAC-CSIC, Barcelona, Spain
| | - Ramon Eritja
- Chemical and Biomolecular Nanotechnology, CIBER-BBN, Institute for Advanced Chemistry of Catalonia, IQAC-CSIC, Barcelona, Spain
| |
Collapse
|
68
|
Gene silencing by 2′- O -methyldithiomethyl-modified siRNA, a prodrug-type siRNA responsive to reducing environment. Bioorg Med Chem Lett 2016; 26:845-848. [DOI: 10.1016/j.bmcl.2015.12.074] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 12/12/2015] [Accepted: 12/22/2015] [Indexed: 11/19/2022]
|
69
|
siRNAmod: A database of experimentally validated chemically modified siRNAs. Sci Rep 2016; 6:20031. [PMID: 26818131 PMCID: PMC4730238 DOI: 10.1038/srep20031] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 12/21/2015] [Indexed: 11/21/2022] Open
Abstract
Small interfering RNA (siRNA) technology has vast potential for functional genomics and development of therapeutics. However, it faces many obstacles predominantly instability of siRNAs due to nuclease digestion and subsequently biologically short half-life. Chemical modifications in siRNAs provide means to overcome these shortcomings and improve their stability and potency. Despite enormous utility bioinformatics resource of these chemically modified siRNAs (cm-siRNAs) is lacking. Therefore, we have developed siRNAmod, a specialized databank for chemically modified siRNAs. Currently, our repository contains a total of 4894 chemically modified-siRNA sequences, comprising 128 unique chemical modifications on different positions with various permutations and combinations. It incorporates important information on siRNA sequence, chemical modification, their number and respective position, structure, simplified molecular input line entry system canonical (SMILES), efficacy of modified siRNA, target gene, cell line, experimental methods, reference etc. It is developed and hosted using Linux Apache MySQL PHP (LAMP) software bundle. Standard user-friendly browse, search facility and analysis tools are also integrated. It would assist in understanding the effect of chemical modifications and further development of stable and efficacious siRNAs for research as well as therapeutics. siRNAmod is freely available at: http://crdd.osdd.net/servers/sirnamod.
Collapse
|
70
|
Wang C, Guo Z, Zhang L, Zhang N, Zhang K, Xu J, Wang H, Shi H, Qin M, Ren L. DNA based signal amplified molecularly imprinted polymer electrochemical sensor for multiplex detection. RSC Adv 2016. [DOI: 10.1039/c6ra05797g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Fabrication process of the electrochemical sensor based on MIPs/GE for the determination of FA, FR, Hg2+, and target DNA.
Collapse
|
71
|
Rahdar M, McMahon MA, Prakash TP, Swayze EE, Bennett CF, Cleveland DW. Synthetic CRISPR RNA-Cas9-guided genome editing in human cells. Proc Natl Acad Sci U S A 2015; 112:E7110-7. [PMID: 26589814 PMCID: PMC4697396 DOI: 10.1073/pnas.1520883112] [Citation(s) in RCA: 130] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Genome editing with the clustered, regularly interspaced, short palindromic repeats (CRISPR)-Cas9 nuclease system is a powerful technology for manipulating genomes, including introduction of gene disruptions or corrections. Here we develop a chemically modified, 29-nucleotide synthetic CRISPR RNA (scrRNA), which in combination with unmodified transactivating crRNA (tracrRNA) is shown to functionally replace the natural guide RNA in the CRISPR-Cas9 nuclease system and to mediate efficient genome editing in human cells. Incorporation of rational chemical modifications known to protect against nuclease digestion and stabilize RNA-RNA interactions in the tracrRNA hybridization region of CRISPR RNA (crRNA) yields a scrRNA with enhanced activity compared with the unmodified crRNA and comparable gene disruption activity to the previously published single guide RNA. Taken together, these findings provide a platform for therapeutic applications, especially for nervous system disease, using successive application of cell-permeable, synthetic CRISPR RNAs to activate and then silence Cas9 nuclease activity.
Collapse
Affiliation(s)
| | - Moira A McMahon
- Ludwig Institute for Cancer Research and Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093
| | | | | | | | - Don W Cleveland
- Ludwig Institute for Cancer Research and Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093
| |
Collapse
|
72
|
Shemesh Y, Yavin E. Postsynthetic conjugation of RNA to carboxylate and dicarboxylate molecules. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2015; 34:753-62. [PMID: 26422297 DOI: 10.1080/15257770.2015.1073299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Carboxylates and dicarboxylates are important phosphate mimics. Herein, we present a simple synthetic route for the preparation of RNA carboxylate/dicarboxylate conjugates, starting from suitably protected NH2- and COOH-containing molecules that are coupled to the RNA on the solid support. The key point in our method was the use of trimethylsilylethanol (TMSE-OH) protecting group, which is removed simultaneously with the silyl protecting group on the 2'-OH of the RNA ribose (e.g. t-Butyldimethylsilyl) during the final RNA cleavage/deprotection steps. The usefulness of this method was demonstrated by preparing different RNA-phosphate mimics oligos.
Collapse
Affiliation(s)
- Yossi Shemesh
- a School of Pharmacy, The Hebrew University of Jerusalem , Hadassah Ein-Kerem , Jerusalem , Israel
| | - Eylon Yavin
- a School of Pharmacy, The Hebrew University of Jerusalem , Hadassah Ein-Kerem , Jerusalem , Israel
| |
Collapse
|
73
|
Li Y, Liu D, Zhou Y, Li Y, Xie J, Lee RJ, Cai Y, Teng L. Silencing of Survivin Expression Leads to Reduced Proliferation and Cell Cycle Arrest in Cancer Cells. J Cancer 2015; 6:1187-94. [PMID: 26516368 PMCID: PMC4615356 DOI: 10.7150/jca.12437] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 07/27/2015] [Indexed: 01/20/2023] Open
Abstract
Survivin is an anti-apoptotic gene that is overexpressed in most human tumors. RNA interference using short interfering RNA (siRNA) can be used to specifically inhibit survivin expression. Tumor cells were treated with a newly designed survivin siRNA, which was modified with 2′-OMe. Cellular survivin mRNA and protein levels were determined by real-time qRT-PCR and Western blot, respectively. Cell cycle and apoptosis were determined by flow cytometry. Cell proliferation was measured by MTT assay. Our data showed that the novel survivin-targeted siRNA could efficiently knockdown the expression of survivin and inhibit cell proliferation. Survivin mRNA was reduced by 95% after 48h treatment with 20nM siRNA. In addition, the siRNA could markedly arrest the cell cycle at the G2/M checkpoint and induce cellular apoptosis in a dose-dependent manner. The percentage of apoptotic cells reached 50% when treated with 40nM siRNA. In conclusion, we have identified a novel chemically modified siRNA against survivin that is highly efficient and delineated its mechanism of action, thus demonstrating a potential therapeutic role for this molecule in cancer. Further evaluation of this siRNA for therapeutic activity is warranted.
Collapse
Affiliation(s)
- Yuhuan Li
- 1. Institute of Life Sciences, Jilin University, Changchun, Jilin, P. R. China
| | - Da Liu
- 1. Institute of Life Sciences, Jilin University, Changchun, Jilin, P. R. China
| | - Yulin Zhou
- 1. Institute of Life Sciences, Jilin University, Changchun, Jilin, P. R. China
| | - Yujing Li
- 1. Institute of Life Sciences, Jilin University, Changchun, Jilin, P. R. China
| | - Jing Xie
- 1. Institute of Life Sciences, Jilin University, Changchun, Jilin, P. R. China
| | - Robert J Lee
- 1. Institute of Life Sciences, Jilin University, Changchun, Jilin, P. R. China ; 2. Division of Pharmaceutics, College of Pharmacy, The Ohio State University, Columbus, OH, U.S.A
| | - Yong Cai
- 1. Institute of Life Sciences, Jilin University, Changchun, Jilin, P. R. China
| | - Lesheng Teng
- 1. Institute of Life Sciences, Jilin University, Changchun, Jilin, P. R. China
| |
Collapse
|
74
|
siRNA Versus miRNA as Therapeutics for Gene Silencing. MOLECULAR THERAPY. NUCLEIC ACIDS 2015; 4:e252. [PMID: 26372022 PMCID: PMC4877448 DOI: 10.1038/mtna.2015.23] [Citation(s) in RCA: 646] [Impact Index Per Article: 71.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 07/18/2015] [Indexed: 02/06/2023]
Abstract
Discovered a little over two decades ago, small interfering RNAs (siRNAs) and microRNAs (miRNAs) are noncoding RNAs with important roles in gene regulation. They have recently been investigated as novel classes of therapeutic agents for the treatment of a wide range of disorders including cancers and infections. Clinical trials of siRNA- and miRNA-based drugs have already been initiated. siRNAs and miRNAs share many similarities, both are short duplex RNA molecules that exert gene silencing effects at the post-transcriptional level by targeting messenger RNA (mRNA), yet their mechanisms of action and clinical applications are distinct. The major difference between siRNAs and miRNAs is that the former are highly specific with only one mRNA target, whereas the latter have multiple targets. The therapeutic approaches of siRNAs and miRNAs are therefore very different. Hence, this review provides a comparison between therapeutic siRNAs and miRNAs in terms of their mechanisms of action, physicochemical properties, delivery, and clinical applications. Moreover, the challenges in developing both classes of RNA as therapeutics are also discussed.
Collapse
|
75
|
Martínez T, Jiménez AI, Pañeda C. Short-interference RNAs: becoming medicines. EXCLI JOURNAL 2015; 14:714-46. [PMID: 26648823 PMCID: PMC4669907 DOI: 10.17179/excli2015-297] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 05/12/2015] [Indexed: 12/30/2022]
Abstract
RNA interference is a cellular mechanism by which small molecules of double stranded RNA modulate gene expression acting on the concentration and/or availability of a given messenger RNA. Almost 10 years after Fire and Mello received the Nobel Prize for the discovery of this mechanism in flat worms, RNA interference is on the edge of becoming a new class of therapeutics. With various phase III studies underway, the following years will determine whether RNAi-therapeutics can rise up to the challenge and become mainstream medicines. The present review gives a thorough overview of the current status of this technology focusing on the path to the clinic of this new class of compounds.
Collapse
Affiliation(s)
- Tamara Martínez
- Sylentis, R&D department c/Santiago Grisolía, Tres Cantos, Madrid, Spain
| | - Ana Isabel Jiménez
- Sylentis, R&D department c/Santiago Grisolía, Tres Cantos, Madrid, Spain
| | - Covadonga Pañeda
- Sylentis, R&D department c/Santiago Grisolía, Tres Cantos, Madrid, Spain
| |
Collapse
|
76
|
Wilton SD, Veedu RN, Fletcher S. The emperor's new dystrophin: finding sense in the noise. Trends Mol Med 2015; 21:417-26. [PMID: 26051381 DOI: 10.1016/j.molmed.2015.04.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 04/29/2015] [Accepted: 04/30/2015] [Indexed: 01/16/2023]
Abstract
Targeted dystrophin exon removal is a promising therapy for Duchenne muscular dystrophy (DMD); however, dystrophin expression in some reports is not supported by the associated data. As in the account of 'The Emperor's New Clothes', the validity of such claims must be questioned, with critical re-evaluation of available data. Is it appropriate to report clinical benefit and induction of dystrophin as dose dependent when the baseline is unclear? The inability to induce meaningful levels of dystrophin does not mean that dystrophin expression as an end point is irrelevant, nor that induced exon skipping as a strategy is flawed, but demands that drug safety and efficacy, and study parameters be addressed, rather than questioning the strategy or the validity of dystrophin as a biomarker.
Collapse
Affiliation(s)
- S D Wilton
- Centre for Comparative Genomics, Murdoch University, 90 South Street, Murdoch, WA 6009, Australia; West Australian Neuroscience Research Institute, Murdoch University, 90 South Street, Murdoch, WA 6009, Australia.
| | - R N Veedu
- Centre for Comparative Genomics, Murdoch University, 90 South Street, Murdoch, WA 6009, Australia; West Australian Neuroscience Research Institute, Murdoch University, 90 South Street, Murdoch, WA 6009, Australia
| | - S Fletcher
- Centre for Comparative Genomics, Murdoch University, 90 South Street, Murdoch, WA 6009, Australia; West Australian Neuroscience Research Institute, Murdoch University, 90 South Street, Murdoch, WA 6009, Australia
| |
Collapse
|
77
|
Dávalos A, Chroni A. Antisense oligonucleotides, microRNAs, and antibodies. Handb Exp Pharmacol 2015; 224:649-89. [PMID: 25523006 DOI: 10.1007/978-3-319-09665-0_22] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The specificity of Watson-Crick base pairing and the development of several chemical modifications to oligonucleotides have enabled the development of novel drug classes for the treatment of different human diseases. This review focuses on promising results of recent preclinical or clinical studies on targeting HDL metabolism and function by antisense oligonucleotides and miRNA-based therapies. Although many hurdles regarding basic mechanism of action, delivery, specificity, and toxicity need to be overcome, promising results from recent clinical trials and recent approval of these types of therapy to treat dyslipidemia suggest that the treatment of HDL dysfunction will benefit from these unique clinical opportunities. Moreover, an overview of monoclonal antibodies (mAbs) developed for the treatment of dyslipidemia and cardiovascular disease and currently being tested in clinical studies is provided. Initial studies have shown that these compounds are generally safe and well tolerated, but ongoing large clinical studies will assess their long-term safety and efficacy.
Collapse
Affiliation(s)
- Alberto Dávalos
- Laboratory of Disorders of Lipid Metabolism and Molecular Nutrition, Madrid Institute for Advanced Studies (IMDEA)-Food, Ctra. de Cantoblanco 8, 28049, Madrid, Spain,
| | | |
Collapse
|
78
|
Prakash TP, Lima WF, Murray HM, Li W, Kinberger GA, Chappell AE, Gaus H, Seth PP, Bhat B, Crooke ST, Swayze EE. Identification of metabolically stable 5'-phosphate analogs that support single-stranded siRNA activity. Nucleic Acids Res 2015; 43:2993-3011. [PMID: 25753666 PMCID: PMC4381071 DOI: 10.1093/nar/gkv162] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 02/16/2015] [Accepted: 02/19/2015] [Indexed: 12/23/2022] Open
Abstract
The ss-siRNA activity in vivo requires a metabolically stable 5'-phosphate analog. In this report we used crystal structure of the 5'-phosphate binding pocket of Ago-2 bound with guide strand to design and synthesize ss-siRNAs containing various 5'-phosphate analogs. Our results indicate that the electronic and spatial orientation of the 5'-phosphate analog was critical for ss-siRNA activity. Chemically modified ss-siRNA targeting human apoC III mRNA demonstrated good potency for inhibiting ApoC III mRNA and protein in transgenic mice. Moreover, ApoC III ss-siRNAs were able to reduce the triglyceride and LDL cholesterol in transgenic mice demonstrating pharmacological effect of ss-siRNA. Our study provides guidance to develop surrogate phosphate analog for ss-siRNA and demonstrates that ss-siRNA provides an alternative strategy for therapeutic gene silencing.
Collapse
Affiliation(s)
- Thazha P Prakash
- Isis Pharmaceuticals Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, USA
| | - Walt F Lima
- Isis Pharmaceuticals Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, USA
| | - Heather M Murray
- Isis Pharmaceuticals Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, USA
| | - Wenyu Li
- Isis Pharmaceuticals Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, USA
| | | | | | - Hans Gaus
- Isis Pharmaceuticals Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, USA
| | - Punit P Seth
- Isis Pharmaceuticals Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, USA
| | - Balkrishen Bhat
- Isis Pharmaceuticals Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, USA
| | - Stanley T Crooke
- Isis Pharmaceuticals Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, USA
| | - Eric E Swayze
- Isis Pharmaceuticals Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, USA
| |
Collapse
|
79
|
Jahns H, Roos M, Imig J, Baumann F, Wang Y, Gilmour R, Hall J. Stereochemical bias introduced during RNA synthesis modulates the activity of phosphorothioate siRNAs. Nat Commun 2015; 6:6317. [PMID: 25744034 PMCID: PMC4366519 DOI: 10.1038/ncomms7317] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Accepted: 01/19/2015] [Indexed: 12/18/2022] Open
Abstract
An established means of improving the pharmacokinetics properties of oligoribonucleotides (ORNs) is to exchange their phosphodiester linkages for phosphorothioates (PSs). However, this strategy has not been pursued for small interfering RNAs (siRNAs), possibly because of sporadic reports that PS siRNAs show reduced inhibitory activity. The PS group is chiral at phosphorous (Rp/Sp centres), and conventional solid-phase synthesis of PS ORNs produces a population of diastereoisomers. Here we show that the choice of the activating agent for the synthesis of a PS ORN influences the Rp/Sp ratio of PS linkages throughout the strand. Furthermore, PS siRNAs composed of ORNs with a higher fraction of Rp centres show greater resistance to nucleases in serum and are more effective inhibitors in cells than their Sp counterparts. The finding that a stereochemically biased population of ORN diastereoisomers can be synthesized and exploited pharmacologically is important because uniform PS modification of siRNAs may provide a useful compromise of their pharmacokinetics and pharmacodynamics properties in RNAi therapeutics. Therapeutic oligonucleotides can be made more stable by substituting their achiral phosphodiester groups for chiral phosphorothioate linkages. Here, the authors present a synthesis of phosphorothioated RNAs, where the activator controls strand stereochemistry, and also the activity of assembled siRNAs.
Collapse
Affiliation(s)
- Hartmut Jahns
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg-4, CH-8093 Zürich, Switzerland
| | - Martina Roos
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg-4, CH-8093 Zürich, Switzerland
| | - Jochen Imig
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg-4, CH-8093 Zürich, Switzerland
| | - Fabienne Baumann
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg-4, CH-8093 Zürich, Switzerland
| | - Yuluan Wang
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg-4, CH-8093 Zürich, Switzerland
| | - Ryan Gilmour
- Institute for Organic Chemistry, Westfälische Wilhelms-Universität Münster, D-48149 Münster, Germany
| | - Jonathan Hall
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg-4, CH-8093 Zürich, Switzerland
| |
Collapse
|
80
|
Yamamoto S, Park S, Sugiyama H. Development of a visible nanothermometer with a highly emissive 2′-O-methylated guanosine analogue. RSC Adv 2015. [DOI: 10.1039/c5ra24756j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We have synthesized a fluorescent base analogue, 2-aminothieno[3,4-d]pyrimidine based G-mimic deoxyribonucleoside, 2′-OMe-thG, and investigated its photophysical properties and DNA incorporation.
Collapse
Affiliation(s)
- Seigi Yamamoto
- Department of Chemistry
- Graduate School of Science
- Kyoto University
- Kyoto 606-8502
- Japan
| | - Soyoung Park
- Department of Chemistry
- Graduate School of Science
- Kyoto University
- Kyoto 606-8502
- Japan
| | - Hiroshi Sugiyama
- Department of Chemistry
- Graduate School of Science
- Kyoto University
- Kyoto 606-8502
- Japan
| |
Collapse
|
81
|
Ittig D, Luisier S, Weiler J, Schümperli D, Leumann CJ. Improving gene silencing of siRNAs via tricyclo-DNA modification. ARTIFICIAL DNA, PNA & XNA 2014; 1:9-16. [PMID: 21687522 DOI: 10.4161/adna.1.1.11385] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2010] [Revised: 01/22/2010] [Accepted: 02/03/2010] [Indexed: 12/16/2022]
Abstract
Small interfering RNAs (siRNAs) can be exploited for the selective silencing of disease-related genes via the RNA interference (RNAi) machinery and therefore raise hope for future therapeutic applications. Especially chemically modified siRNAs are of interest as they are expected to convert lead siRNA sequences into effective drugs. To study the potential of tricyclo-DNA (tc-DNA) in this context we systematically incorporated tc-DNA units at various positions in a siRNA duplex targeted to the EGFP gene that was expressed in HeLa cells. Silencing activity was measured by FACS, mRNA levels were determined by RT-PCR and the biostability of the modifed siRNAs was determined in human serum. We found that modifications in the 3'-overhangs in both the sense and antisense strands were compatible with the RNAi machinery leading to similar activities compared to wild-type (wt) siRNA. Additional modifications at the 3'-end, the 5'-end and in the center of the sense (passenger) strand were also well tolerated and did not compromise activity. Extensive modifications of the 3'- and the 5'-end in the antisense (guide) strand, however, abolished RNAi activity. Interestingly, modifications in the center of the duplex on both strands, corresponding to the position of the cleavage site by AGO2, increased efficacy relative to wt by a factor of 4 at the lowest concentrations (2 nM) investigated. In all cases, reduction of EGFP fluorescence was accompanied with a reduction of the EGFP mRNA level. Serum stability analysis further showed that 3'-overhang modifications only moderately increased stability while more extensive substitution by tc-DNA residues significantly enhanced biostability.
Collapse
Affiliation(s)
- Damian Ittig
- Department of Chemistry and Biochemistry; University of Bern; Bern, Switzerland
| | | | | | | | | |
Collapse
|
82
|
Fan M, Zhang Y, Huang Z, Liu J, Guo X, Zhang H, Luo H. Optimizations of siRNA design for the activation of gene transcription by targeting the TATA-box motif. PLoS One 2014; 9:e108253. [PMID: 25250958 PMCID: PMC4176967 DOI: 10.1371/journal.pone.0108253] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 08/20/2014] [Indexed: 12/24/2022] Open
Abstract
Small interfering RNAs (siRNAs) are widely used to repress gene expression by targeting mRNAs. Some reports reveal that siRNAs can also activate or inhibit gene expression through targeting the gene promoters. Our group has found that microRNAs (miRNAs) could activate gene transcription via interaction with the TATA-box motif in gene promoters. To investigate whether siRNA targeting the same region could upregulate the promoter activity, we test the activating efficiency of siRNAs targeting the TATA-box motif of 16 genes and perform a systematic analysis to identify the common features of the functional siRNAs for effective activation of gene promoters. Further, we try various modifications to improve the activating efficiency of siRNAs and find that it is quite useful to design the promoter-targeting activating siRNA by following several rules such as (a) complementary to the TATA-box-centered region; (b) UA usage at the first two bases of the antisense strand; (c) twenty-three nucleotides (nts) in length; (d) 2'-O-Methyl (2'-OMe) modification at the 3' terminus of the antisense strand; (e) avoiding mismatches at the 3' end of the antisense strand. The optimized activating siRNAs potently enhance the expression of interleukin-2 (IL-2) gene in human and mouse primary CD4+ T cells with a long-time effect. Taken together, our study provides a guideline for rational design the promoter-targeting siRNA to sequence-specifically enhance gene expression.
Collapse
Affiliation(s)
- Miaomiao Fan
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yijun Zhang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Zhuoqiong Huang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jun Liu
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xuemin Guo
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Hui Zhang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- * E-mail: (HZ); (HL)
| | - Haihua Luo
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- * E-mail: (HZ); (HL)
| |
Collapse
|
83
|
Therapeutic potential of siRNA and DNAzymes in cancer. Tumour Biol 2014; 35:9505-21. [PMID: 25149153 DOI: 10.1007/s13277-014-2477-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 08/07/2014] [Indexed: 02/07/2023] Open
Abstract
Cancer is characterized by uncontrolled cell growth, invasion, and metastasis and possess threat to humans worldwide. The scientific community is facing numerous challenges despite several efforts to cure cancer. Though a number of studies were done earlier, the molecular mechanism of cancer progression is not completely understood. Currently available treatments like surgery resection, adjuvant chemotherapy, and radiotherapy are not completely effective in curing all the cancers. Recent advances in the antisense technology provide a powerful tool to investigate various cancer pathways and target them. Small interfering RNAs (siRNAs) could be effective in downregulating the cancer-associated genes, but their in vivo delivery is the main obstacle. DNA enzymes (DNAzymes) have great potential in the treatment of cancer due to high selectivity and significant catalytic efficiency. In this review, we are focusing on antisense molecules such as siRNA and DNAzymes in cancer therapeutics development. This review also describes the challenges and approaches to overcome obstacles involved in using siRNA and DNAzymes in the treatment of cancers.
Collapse
|
84
|
Li T, Wu M, Zhu YY, Chen J, Chen L. Development of RNA Interference–Based Therapeutics and Application of Multi-Target Small Interfering RNAs. Nucleic Acid Ther 2014; 24:302-12. [DOI: 10.1089/nat.2014.0480] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Tiejun Li
- Department of Pathological Anatomy, Nantong University, Nantong, China
- Small RNA Technology and Application Institute, Nantong University, Nantong, China
- Department of Life Science Center, Biomics Biotechnologies Co., Ltd., Nantong, China
| | - Meihua Wu
- Department of Pathological Anatomy, Nantong University, Nantong, China
- Small RNA Technology and Application Institute, Nantong University, Nantong, China
- Department of Life Science Center, Biomics Biotechnologies Co., Ltd., Nantong, China
| | - York Yuanyuan Zhu
- Small RNA Technology and Application Institute, Nantong University, Nantong, China
- Department of Life Science Center, Biomics Biotechnologies Co., Ltd., Nantong, China
| | - Jianxin Chen
- Small RNA Technology and Application Institute, Nantong University, Nantong, China
- Department of Life Science Center, Biomics Biotechnologies Co., Ltd., Nantong, China
| | - Li Chen
- Department of Pathological Anatomy, Nantong University, Nantong, China
| |
Collapse
|
85
|
Vogel P, Schneider MF, Wettengel J, Stafforst T. Chemisch modifizierte guideRNAs verbessern die ortsgerichtete RNA-Editierung in vitro und in Zellkultur. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201402634] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
|
86
|
Vogel P, Schneider MF, Wettengel J, Stafforst T. Improving Site-Directed RNA Editing In Vitro and in Cell Culture by Chemical Modification of the GuideRNA. Angew Chem Int Ed Engl 2014; 53:6267-71. [DOI: 10.1002/anie.201402634] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Indexed: 12/20/2022]
|
87
|
Seth PP, Swayze EE. Unnatural Nucleoside Analogs for Antisense Therapy. METHODS AND PRINCIPLES IN MEDICINAL CHEMISTRY 2014. [DOI: 10.1002/9783527676545.ch12] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|
88
|
Synthesis and gene silencing properties of siRNAs containing terminal amide linkages. BIOMED RESEARCH INTERNATIONAL 2014; 2014:901617. [PMID: 24791003 PMCID: PMC3984766 DOI: 10.1155/2014/901617] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 01/23/2014] [Indexed: 01/04/2023]
Abstract
The active components of the RNAi are 21 nucleotides long dsRNAs containing a 2 nucleotide overhang at the 3′ end, carrying 5′-phosphate and 3′-hydroxyl groups (siRNAs). Structural analysis revealed that the siRNA is functionally bound at both ends to RISC. Terminal modifications are considered with interest as the introduction of chemical moieties interferes with the 3′ overhang recognition by the PAZ domain and the 5′-phosphate recognition by the MID and PIWI domains of RISC. Herein, we report the synthesis of modified siRNAs containing terminal amide linkages by introducing hydroxyethylglycine PNA (hegPNA) moieties at 5′, and at 3′ positions and on both terminals. Results of gene silencing studies highlight that some of these modifications are compatible with the RNAi machinery and markedly increase the resistance to serum-derived nucleases even after 24 h of incubation. Molecular docking simulations were attained to give at atomistic level a clearer picture of the effect of the most performing modifications on the interactions with the human Argonaute 2 PAZ, MID, and PIWI domains. This study adds another piece to the puzzle of the heterogeneous chemical modifications that can be attained to enhance the silencing efficiency of siRNAs.
Collapse
|
89
|
Wu SY, Yang X, Gharpure KM, Hatakeyama H, Egli M, McGuire MH, Nagaraja AS, Miyake TM, Rupaimoole R, Pecot CV, Taylor M, Pradeep S, Sierant M, Rodriguez-Aguayo C, Choi HJ, Previs RA, Armaiz-Pena GN, Huang L, Martinez C, Hassell T, Ivan C, Sehgal V, Singhania R, Han HD, Su C, Kim JH, Dalton HJ, Kovvali C, Keyomarsi K, McMillan NAJ, Overwijk WW, Liu J, Lee JS, Baggerly KA, Lopez-Berestein G, Ram PT, Nawrot B, Sood AK. 2'-OMe-phosphorodithioate-modified siRNAs show increased loading into the RISC complex and enhanced anti-tumour activity. Nat Commun 2014; 5:3459. [PMID: 24619206 DOI: 10.1038/ncomms4459] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 02/17/2014] [Indexed: 12/19/2022] Open
Abstract
Improving small interfering RNA (siRNA) efficacy in target cell populations remains a challenge to its clinical implementation. Here, we report a chemical modification, consisting of phosphorodithioate (PS2) and 2'-O-Methyl (2'-OMe) MePS2 on one nucleotide that significantly enhances potency and resistance to degradation for various siRNAs. We find enhanced potency stems from an unforeseen increase in siRNA loading to the RNA-induced silencing complex, likely due to the unique interaction mediated by 2'-OMe and PS2. We demonstrate the therapeutic utility of MePS2 siRNAs in chemoresistant ovarian cancer mouse models via targeting GRAM domain containing 1B (GRAMD1B), a protein involved in chemoresistance. GRAMD1B silencing is achieved in tumours following MePS2-modified siRNA treatment, leading to a synergistic anti-tumour effect in combination with paclitaxel. Given the previously limited success in enhancing siRNA potency with chemically modified siRNAs, our findings represent an important advance in siRNA design with the potential for application in numerous cancer types.
Collapse
Affiliation(s)
- Sherry Y Wu
- 1] Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas 77054, USA [2]
| | - Xianbin Yang
- 1] AM Biotechnologies LLC, 12521 Gulf Freeway, Houston, Texas 77034, USA [2]
| | - Kshipra M Gharpure
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas 77054, USA
| | - Hiroto Hatakeyama
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas 77054, USA
| | - Martin Egli
- Department of Biochemistry, Vanderbilt University, School of Medicine, Nashville, Tennessee 37232, USA
| | - Michael H McGuire
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas 77054, USA
| | - Archana S Nagaraja
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas 77054, USA
| | - Takahito M Miyake
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas 77054, USA
| | - Rajesha Rupaimoole
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas 77054, USA
| | - Chad V Pecot
- Division of Cancer Medicine, MDACC, Houston, Texas 77054, USA
| | - Morgan Taylor
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas 77054, USA
| | - Sunila Pradeep
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas 77054, USA
| | - Malgorzata Sierant
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, Lodz, Poland
| | - Cristian Rodriguez-Aguayo
- 1] Department of Experimental Therapeutics, MDACC, Houston, Texas 77054, USA [2] Center for RNA Interference and Non-Coding RNA, MDACC, Houston, Texas 77054, USA
| | - Hyun J Choi
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas 77054, USA
| | - Rebecca A Previs
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas 77054, USA
| | - Guillermo N Armaiz-Pena
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas 77054, USA
| | - Li Huang
- Department of Cancer Biology, MDACC, Houston, Texas 77054, USA
| | - Carlos Martinez
- Sigma Life Science, 9186 Six Pines, The Woodlands, Texas 77380, USA
| | - Tom Hassell
- Sigma Life Science, 9186 Six Pines, The Woodlands, Texas 77380, USA
| | - Cristina Ivan
- 1] Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas 77054, USA [2] Center for RNA Interference and Non-Coding RNA, MDACC, Houston, Texas 77054, USA
| | - Vasudha Sehgal
- Department of Systems Biology, MDACC, Houston, Texas 77054, USA
| | - Richa Singhania
- 1] University of Queensland Diamantina Institute, Woolloongabba, Queensland 4102, Australia [2] Centre for Biomolecular Sciences, School of Pharmacy, The University of Nottingham, Nottingham NG7 2RD, UK
| | - Hee-Dong Han
- 1] Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas 77054, USA [2] Center for RNA Interference and Non-Coding RNA, MDACC, Houston, Texas 77054, USA [3] Department of Immunology Laboratory, School of Medicine, Konkuk University, Chungju 380-701, South Korea
| | - Chang Su
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas 77054, USA
| | - Ji Hoon Kim
- 1] Department of Systems Biology, MDACC, Houston, Texas 77054, USA [2] Division of Gastroenterology and Hepatology, Department of Internal Medicine, Korea University College of Medicine, Seoul 136-701, Korea
| | - Heather J Dalton
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas 77054, USA
| | - Chandra Kovvali
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas 77054, USA
| | - Khandan Keyomarsi
- Department of Experimental Radiation Oncology, MDACC, Houston, Texas 77054, USA
| | - Nigel A J McMillan
- 1] University of Queensland Diamantina Institute, Woolloongabba, Queensland 4102, Australia [2] Griffith Health Institute and School of Medical Sciences, Griffith University, Southport, Queensland 4222, Australia
| | - Willem W Overwijk
- Department of Melanoma Medical Oncology, MDACC, Houston, Texas 77054, USA
| | - Jinsong Liu
- Department of Pathology, MDACC, Houston, Texas 77054, USA
| | - Ju-Seog Lee
- Department of Systems Biology, MDACC, Houston, Texas 77054, USA
| | | | - Gabriel Lopez-Berestein
- 1] Department of Experimental Therapeutics, MDACC, Houston, Texas 77054, USA [2] Center for RNA Interference and Non-Coding RNA, MDACC, Houston, Texas 77054, USA
| | - Prahlad T Ram
- Department of Systems Biology, MDACC, Houston, Texas 77054, USA
| | - Barbara Nawrot
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, Lodz, Poland
| | - Anil K Sood
- 1] Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas 77054, USA [2] Center for RNA Interference and Non-Coding RNA, MDACC, Houston, Texas 77054, USA [3] Department of Cancer Biology, MDACC, Houston, Texas 77054, USA
| |
Collapse
|
90
|
Ward AJ, Norrbom M, Chun S, Bennett CF, Rigo F. Nonsense-mediated decay as a terminating mechanism for antisense oligonucleotides. Nucleic Acids Res 2014; 42:5871-9. [PMID: 24589581 PMCID: PMC4027159 DOI: 10.1093/nar/gku184] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Antisense oligonucleotides (ASOs) are synthetic oligonucleotides that alter expression of disease-associated transcripts via Watson-Crick hybridization. ASOs that function through RNase H or the RNA-induced silencing complex (RISC) result in enzymatic degradation of target RNA. ASOs designed to sterically block access of proteins to the RNA modulate mRNA metabolism but do not typically cause degradation. Here, we rationally design steric blocking ASOs to promote mRNA reduction and characterize the terminating mechanism. Transfection of ASOs complementary to constitutive exons in STAT3 and Sod1 results in greater than 70% reduction of mRNA and protein. The ASOs promote aberrant exon skipping and generation of premature termination codon (PTC)-containing mRNAs. We inhibit the nonsense-mediated mRNA decay (NMD) pathway and show that the PTC-containing mRNAs are recognized by the UPF1 ATPase, cleaved by the SMG6 endonuclease and degraded by the XRN1 cytoplasmic exonuclease. NMD surveillance, however, does not entirely explain the mechanism of decreased STAT3 expression. In addition to exon skipping, ASO treatment causes intron retention and reduction of chromatin-associated STAT3 mRNA. The application of steric blocking ASOs to promote RNA degradation allows one to explore more nucleotide modifications than tolerated by RNase H or RISC-dependent ASOs, with the goal of improving ASO drug properties.
Collapse
Affiliation(s)
- Amanda J Ward
- Department of Core Antisense Research, ISIS Pharmaceuticals, Inc., Carlsbad, CA 92010, USA
| | - Michaela Norrbom
- Department of Core Antisense Research, ISIS Pharmaceuticals, Inc., Carlsbad, CA 92010, USA
| | - Seung Chun
- Department of Core Antisense Research, ISIS Pharmaceuticals, Inc., Carlsbad, CA 92010, USA
| | - C Frank Bennett
- Department of Core Antisense Research, ISIS Pharmaceuticals, Inc., Carlsbad, CA 92010, USA
| | - Frank Rigo
- Department of Core Antisense Research, ISIS Pharmaceuticals, Inc., Carlsbad, CA 92010, USA
| |
Collapse
|
91
|
Sekar TV, Mohanram RK, Foygel K, Paulmurugan R. Therapeutic evaluation of microRNAs by molecular imaging. Am J Cancer Res 2013; 3:964-85. [PMID: 24396507 PMCID: PMC3881098 DOI: 10.7150/thno.4928] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 09/22/2013] [Indexed: 02/07/2023] Open
Abstract
MicroRNAs (miRNAs) function as regulatory molecules of gene expression with multifaceted activities that exhibit direct or indirect oncogenic properties, which promote cell proliferation, differentiation, and the development of different types of cancers. Because of their extensive functional involvement in many cellular processes, under both normal and pathological conditions such as various cancers, this class of molecules holds particular interest for cancer research. MiRNAs possess the ability to act as tumor suppressors or oncogenes by regulating the expression of different apoptotic proteins, kinases, oncogenes, and other molecular mechanisms that can cause the onset of tumor development. In contrast to current cancer medicines, miRNA-based therapies function by subtle repression of gene expression on a large number of oncogenic factors, and therefore are anticipated to be highly efficacious. Given their unique mechanism of action, miRNAs are likely to yield a new class of targeted therapeutics for a variety of cancers. More than thousand miRNAs have been identified to date, and their molecular mechanisms and functions are well studied. Furthermore, they are established as compelling therapeutic targets in a variety of cellular complications. However, the notion of using them as therapeutic tool was proposed only recently, given that modern imaging methods are just beginning to be deployed for miRNA research. In this review, we present a summary of various molecular imaging methods, which are instrumental in revealing the therapeutic potential of miRNAs, especially in various cancers. Imaging methods have recently been developed for monitoring the expression levels of miRNAs and their target genes by fluorescence-, bioluminescence- and chemiluminescence-based imaging techniques. Mature miRNAs bind to the untranslated regions (UTRs) of the target mRNAs and regulate target genes expressions. This concept has been used for the development of fluorescent reporter-based imaging strategies to monitor the functional status of endogenous miRNAs, or the respective miRNAs transiently co-expressed in cells. Bioluminescence-based imaging strategies have been used to investigate various stages of miRNA processing and its involvement in different cellular processes. Similarly, chemiluminsecence methods were developed for in vitro miRNA imaging such as monitoring their therapeutic roles in various cancer cell lines.
Collapse
|
92
|
MicroRNAs as Molecular Targets for Cancer Therapy: On the Modulation of MicroRNA Expression. Pharmaceuticals (Basel) 2013; 6:1195-220. [PMID: 24275848 PMCID: PMC3817605 DOI: 10.3390/ph6101195] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Revised: 09/17/2013] [Accepted: 09/17/2013] [Indexed: 02/07/2023] Open
Abstract
The discovery of small RNA molecules with the capacity to regulate messenger RNA (mRNA) stability and translation (and consequently protein synthesis) has revealed an additional level of post-transcriptional gene control. MicroRNAs (miRNAs), an evolutionarily conserved class of small noncoding RNAs that regulate gene expression post-transcriptionally by base pairing to complementary sequences in the 3' untranslated regions of target mRNAs, are part of this modulatory RNA network playing a pivotal role in cell fate. Functional studies indicate that miRNAs are involved in the regulation of almost every biological pathway, while changes in miRNA expression are associated with several human pathologies, including cancer. By targeting oncogenes and tumor suppressors, miRNAs have the ability to modulate key cellular processes that define the cell phenotype, making them highly promising therapeutic targets. Over the last few years, miRNA-based anti-cancer therapeutic approaches have been exploited, either alone or in combination with standard targeted therapies, aiming at enhancing tumor cell killing and, ideally, promoting tumor regression and disease remission. Here we provide an overview on the involvement of miRNAs in cancer pathology, emphasizing the mechanisms of miRNA regulation. Strategies for modulating miRNA expression are presented and illustrated with representative examples of their application in a therapeutic context.
Collapse
|
93
|
Gore KR, Harikrishna S, Pradeepkumar PI. Influence of 2'-fluoro versus 2'-O-methyl substituent on the sugar puckering of 4'-C-aminomethyluridine. J Org Chem 2013; 78:9956-62. [PMID: 24016294 DOI: 10.1021/jo4012333] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Herein, we report the synthesis of 4'-C-aminomethyl-2'-deoxy-2'-fluorouridine, a therapeutically appealing RNA modification. Conformational analysis by DFT calculations and molecular dynamics simulations using trinucleotide model systems revealed that modified sugar adopts C3'-endo conformation. In this conformer, a weak intramolecular C-H···F H-bond between the hydrogen atom of the 4'-C-CH2 group and the F atom at the 2' position is observed. Comparative studies with unmodified, 2'-fluoro-, 2'-O-methyl-, and 4'-C-aminomethyl-2'-O-methyluridine showed the chemical nature of 2'-substituent dictates the sugar puckering of 2',4'-modified nucleotides.
Collapse
Affiliation(s)
- Kiran R Gore
- Department of Chemistry, Indian Institute of Technology Bombay , Mumbai 400076, India
| | | | | |
Collapse
|
94
|
Plevnik M, Cevec M, Plavec J. NMR structure of 2'-O-(2-methoxyethyl) modified and C5-methylated RNA dodecamer duplex. Biochimie 2013; 95:2385-91. [PMID: 24012551 DOI: 10.1016/j.biochi.2013.08.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 08/26/2013] [Indexed: 10/26/2022]
Abstract
The solution-state structure of 2'-O-(2-methoxyethly) substituted dodecamer r(*CG*CGAA*U*U*CG*C)d(G), 2'-MOE RNA, with all cytosines and uracils methylated at the C5-position has been determined by NMR spectroscopy. The chemical modifications were used to improve the oligonucleotide's drug-like properties. The 2'-MOE group drives pseudorotational equilibrium of the ribofuranose moiety to the N-type conformation and supposedly results in structural preorganization leading to high affinity of a modified oligonucleotide towards its complementary biological target, improved pharmacokinetic and toxicological properties. The high melting temperature of the antiparallel duplex structure adopted by 2'-MOE RNA was explained through the formation of a stable A-form RNA consistent with effective base-pairing and stacking interactions. The comparison of the solution-state structure with the crystal structure of a non-methylated analogue shows an increase in the stacking at the base pair steps for the C5-methylated 2'-MOE RNA duplex. The MOE substituents adopt a well-defined structure in the minor groove with the predominant gauche conformations around the ethylene bond.
Collapse
Affiliation(s)
- Miha Plevnik
- Krka, d.d., Šmarješka cesta 6, 8501 Novo mesto, Slovenia
| | | | | |
Collapse
|
95
|
Prakash TP, Lima WF, Murray HM, Elbashir S, Cantley W, Foster D, Jayaraman M, Chappell AE, Manoharan M, Swayze EE, Crooke ST. Lipid nanoparticles improve activity of single-stranded siRNA and gapmer antisense oligonucleotides in animals. ACS Chem Biol 2013; 8:1402-6. [PMID: 23614580 DOI: 10.1021/cb4001316] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We evaluated the abilities of an antisense oligonucleotide (ASO), a small interfering RNA (siRNA), and a single-stranded siRNA (ss-siRNA) to inhibit expression from the PTEN gene in mice when formulated identically with lipid nanoparticles (LNPs). Significantly greater reductions in levels of PTEN mRNA were observed for LNP-formulated agents compared to unformulated drugs when gene silencing was evaluated after a single dose in the livers of mice. An unformulated ss-siRNA modified with a metabolically stable phosphate mimic 5'-(E)-vinylphosphonate showed dose-dependent reduction of PTEN mRNA in mice, albeit at doses significantly higher than those observed for formulated ss-siRNA. These results demonstrate that LNPs can be used to deliver functional antisense and ss-siRNA therapeutics to the liver, indicating that progress in the field of siRNA delivery is transferable to other classes of nucleic acid-based drugs.
Collapse
Affiliation(s)
- Thazha P. Prakash
- Department of Medicinal Chemistry, Isis Pharmaceuticals, Inc., 1896 Rutherford Road, Carlsbad,
California 92008, United States
| | - Walt F. Lima
- Department of Medicinal Chemistry, Isis Pharmaceuticals, Inc., 1896 Rutherford Road, Carlsbad,
California 92008, United States
| | - Heather M. Murray
- Department of Medicinal Chemistry, Isis Pharmaceuticals, Inc., 1896 Rutherford Road, Carlsbad,
California 92008, United States
| | - Sayda Elbashir
- Alnylam Pharmaceuticals, 300 Third Street,
Cambridge, Massachusetts 02142, United States
| | - William Cantley
- Alnylam Pharmaceuticals, 300 Third Street,
Cambridge, Massachusetts 02142, United States
| | - Don Foster
- Alnylam Pharmaceuticals, 300 Third Street,
Cambridge, Massachusetts 02142, United States
| | - Muthusamy Jayaraman
- Alnylam Pharmaceuticals, 300 Third Street,
Cambridge, Massachusetts 02142, United States
| | - Alfred E. Chappell
- Department of Medicinal Chemistry, Isis Pharmaceuticals, Inc., 1896 Rutherford Road, Carlsbad,
California 92008, United States
| | - Muthiah Manoharan
- Alnylam Pharmaceuticals, 300 Third Street,
Cambridge, Massachusetts 02142, United States
| | - Eric E. Swayze
- Department of Medicinal Chemistry, Isis Pharmaceuticals, Inc., 1896 Rutherford Road, Carlsbad,
California 92008, United States
| | - Stanley T. Crooke
- Department of Medicinal Chemistry, Isis Pharmaceuticals, Inc., 1896 Rutherford Road, Carlsbad,
California 92008, United States
| |
Collapse
|
96
|
|
97
|
Zheng J, Zhang L, Zhang J, Wang X, Ye K, Xi Z, Du Q, Liang Z. Single modification at position 14 of siRNA strand abolishes its gene-silencing activity by decreasing both RISC loading and target degradation. FASEB J 2013; 27:4017-26. [PMID: 23771927 DOI: 10.1096/fj.13-228668] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Normally siRNA has to be chemically stabilized in therapeutic applications. It is a challenge to obtain optimal stabilizing effects while maintaining full silencing activity due to a lack of understanding of how different chemical modifications would influence the efficacy of siRNA. In the current study, the effect of single 2'-sugar modifications was profiled across the length of the siRNA guide strand. This led to the surprising finding that a single 2'-OMe modification at position 14 of the siRNA guide strand substantially compromised its gene-silencing activity in a manner that was independent of the nucleotide identity at this site or the sequence context around it. We found that modification at position 14 of the siRNA guide strand reduced its RNA-induced silencing complex (RISC) loading tremendously, whereas the loading of the siRNA sense strand was only marginally affected. When comparing the silencing potency of 14th position-modified siRNA (transfected at 16.7 nM) and native control (transfected at 1 nM) at equivalent Ago2 loading levels, the silencing potency of modified siRNA was much lower, even lower than the level of native siRNA transfected at 0.1 nM. These data indicated that modification at position 14 of the siRNA guide strand abolishes its gene-silencing activity by decreasing both RISC loading and target degradation. Using a computational modeling approach, we demonstrated an intimate interaction between the 14th nucleotide of guide strand and the amino acid Q675 in the AGO protein, which is located in a highly conserved loop of PIWI domain. In addition to gaining insights into siRNA-AGO interactions, this study of structure-activity relationship further established a general principle for siRNA modification in siRNA drug development.
Collapse
Affiliation(s)
- Jie Zheng
- 1Z.L., Institute of Molecular Medicine, Peking University, Beijing, 100871, China.
| | | | | | | | | | | | | | | |
Collapse
|
98
|
Guzaev AP. Solid-phase supports for oligonucleotide synthesis. CURRENT PROTOCOLS IN NUCLEIC ACID CHEMISTRY 2013; Chapter 3:3.1.1-3.1.60. [PMID: 23775808 DOI: 10.1002/0471142700.nc0301s53] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
This unit attempts to provide a reasonably complete inventory of over 280 solid supports available to oligonucleotide chemists for preparation of natural and 3'-modified oligonucleotides. Emphasis is placed on non-nucleosidic solid supports. The relationship between the structural features of linkers and their behavior in oligonucleotide synthesis and deprotection is discussed wherever the relevant observations are available.
Collapse
|
99
|
Abstract
Though the pharmaceutical industry's infatuation with the therapeutic potential of RNA interference (RNAi) technology has finally come down from its initial lofty levels,[1] hope is by no means lost for the once-burgeoning enterprise, as recent clinical trials are beginning to show efficacy in areas ranging from amyloidosis to hypercholesterolemia to muscular dystrophy. With such resurgence comes a more informed perspective on the needs of such therapeutics: a renewed focus on true RNA drug development, and a desire for enhanced site-specific delivery.[2] In this review, we will discuss the latter with regard to hepatic targeting by synthetic vectors, covering the implications of organ and cellular physiology on conjugate structure, particle morphology, and active targeting. In presenting efficacy in a variety of disease models, we emphasize as well the extraordinary degree to which synthetic formulation improves upon and coordinates efforts with oligonucleotide development. Such advances in the understanding of and the technology behind RNAi have the potential to finally stabilize the long-term prospects RNA therapeutic development.
Collapse
|
100
|
Maeda Y, Iwata R, Wada T. Synthesis and properties of cationic oligopeptides with different side chain lengths that bind to RNA duplexes. Bioorg Med Chem 2013; 21:1717-23. [DOI: 10.1016/j.bmc.2013.01.053] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Revised: 01/22/2013] [Accepted: 01/23/2013] [Indexed: 10/27/2022]
|