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Agrawal S. Considerations for Creating the Next Generation of RNA Therapeutics: Oligonucleotide Chemistry and Innate Immune Responses to Nucleic Acids. Nucleic Acid Ther 2024; 34:37-51. [PMID: 38578231 DOI: 10.1089/nat.2024.29009.sud] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024] Open
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2
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Li XQ, Elebring M, Dahlén A, Weidolf L. In Vivo Metabolite Profiles of an N-Acetylgalactosamine-Conjugated Antisense Oligonucleotide AZD8233 Using Liquid Chromatography High-Resolution Mass Spectrometry: A Cross-Species Comparison in Animals and Humans. Drug Metab Dispos 2023; 51:1350-1361. [PMID: 37429729 DOI: 10.1124/dmd.123.001370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/28/2023] [Accepted: 06/29/2023] [Indexed: 07/12/2023] Open
Abstract
AZD8233, a liver-targeting antisense oligonucleotide (ASO), inhibits subtilisin/kexin type 9 protein synthesis. It is a phosphorothioated 3-10-3 gapmer with a central DNA sequence flanked by constrained 2'-O-ethyl 2',4'-bridged nucleic acid (cEt-BNA) wings and conjugated to a triantennary N-acetylgalactosamine (GalNAc) ligand at the 5'-end. Herein we report the biotransformation of AZD8233, as given by liver, kidney, plasma and urine samples, after repeated subcutaneous administration to humans, mice, rats, rabbits, and monkeys. Metabolite profiles were characterized using liquid chromatography high-resolution mass spectrometry. Metabolite formation was consistent across species, mainly comprising hydrolysis of GalNAc sugars, phosphodiester-linker hydrolysis releasing the full-length ASO, and endonuclease-mediated hydrolysis within the central DNA gap followed by exonuclease-mediated 5'- or 3'-degradation. All metabolites contained the 5'- or 3'-cEt-BNA terminus. Most shortmer metabolites had the free terminal alcohol at 5'- and 3'-positions of ribose, although six were found retaining the terminal 5'-phosphorothioate group. GalNAc conjugated shortmer metabolites were also observed in urine. Synthesized metabolite standards were applied for (semi)quantitative metabolite assessment. Intact AZD8233 was the major component in plasma, whereas the unconjugated full-length ASO was predominant in tissues. In plasma, most metabolites were shortmers retaining the 3'-cEt-BNA terminus, whereas metabolites containing the 5'- or 3'-cEt-BNA terminus were detected in both tissues and urine. All metabolites in human plasma were also detected in all nonclinical species, and all human urine metabolites were detected in monkey urine. In general, metabolite profiles in animal species were qualitatively similar and quantitatively exceeded the exposures of the circulating metabolites in humans at the doses studied. SIGNIFICANCE STATEMENT: This study presents metabolite identification and profiling of AZD8233, an N-acetylgalactosamine-conjugated antisense oligonucleotide (ASO), across species. A biotransformation strategy for ASOs was established by utilizing biologic samples collected from toxicology and/or clinical studies and liquid chromatography high-resolution mass spectrometry analysis without conducting bespoke radiolabeled absorption, distribution, metabolism, and excretion studies. The generated biotransformation package was considered adequate by health authorities to progress AZD8233 into a phase 3 program, proving its applicability to future metabolism studies of ASOs in drug development.
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Affiliation(s)
- Xue-Qing Li
- DMPK, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden (X.-Q.L., M.E., L.W.); and Oligonucleotide Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden (A.D.)
| | - Marie Elebring
- DMPK, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden (X.-Q.L., M.E., L.W.); and Oligonucleotide Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden (A.D.)
| | - Anders Dahlén
- DMPK, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden (X.-Q.L., M.E., L.W.); and Oligonucleotide Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden (A.D.)
| | - Lars Weidolf
- DMPK, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden (X.-Q.L., M.E., L.W.); and Oligonucleotide Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden (A.D.)
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3
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Sarli SL, Watts JK. Harnessing nucleic acid technologies for human health on earth and in space. LIFE SCIENCES IN SPACE RESEARCH 2022; 35:113-126. [PMID: 36336357 DOI: 10.1016/j.lssr.2022.08.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 08/01/2022] [Accepted: 08/18/2022] [Indexed: 06/16/2023]
Abstract
Nucleic acid therapeutics are a versatile class of sequence-programmable drugs that offer a robust and clinically viable strategy to modulate expression or correct genetic defects contributing to disease. The majority of drugs currently on the market target proteins; however, proteins only represent a subset of possible disease targets. Nucleic acid therapeutics allow intuitive engagement with genome sequences providing a more direct way to target many diseases at their genetic root cause. Their clinical success depends on platform technologies which can support durable and well tolerated pharmacological activity in a given tissue. Nucleic acid drugs possess a potent combination of target specificity and adaptability required to advance drug development for many diseases. As these therapeutic technologies mature, their clinical applications can also expand access to personalized therapies for patients with rare or solo genetic diseases. Spaceflight crew members exposed to the unique hazards of spaceflight, especially those related to galactic cosmic radiation (GCR) exposure, represent another patient subset who may also benefit from nucleic acid drugs as countermeasures. In this review, we will discuss the various classes of RNA- and DNA-targeted nucleic acid drugs, provide an overview of their present-day clinical applications, and describe major strategies to improve their delivery, safety, and overall efficacy.
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Affiliation(s)
- Samantha L Sarli
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jonathan K Watts
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA.
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4
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Agrawal S. The Evolution of Antisense Oligonucleotide Chemistry-A Personal Journey. Biomedicines 2021; 9:503. [PMID: 34063675 PMCID: PMC8147625 DOI: 10.3390/biomedicines9050503] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 04/30/2021] [Accepted: 05/02/2021] [Indexed: 01/03/2023] Open
Abstract
Over the last four decades, tremendous progress has been made in use of synthetic oligonucleotides as therapeutics. This has been possible largely by introducing chemical modifications to provide drug like properties to oligonucleotides. In this article I have summarized twists and turns on use of chemical modifications and their road to success and highlight areas of future directions.
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Affiliation(s)
- Sudhir Agrawal
- ARNAY Sciences LLC, Shrewsbury, MA 01545, USA; or
- Department of Medicine, University of Massachusetts Medical School, 55 N Lake Ave, Worcester, MA 01655, USA
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5
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Piao X, Wang H, Binzel DW, Guo P. Assessment and comparison of thermal stability of phosphorothioate-DNA, DNA, RNA, 2'-F RNA, and LNA in the context of Phi29 pRNA 3WJ. RNA (NEW YORK, N.Y.) 2018; 24:67-76. [PMID: 29051199 PMCID: PMC5733572 DOI: 10.1261/rna.063057.117] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 10/03/2017] [Indexed: 05/27/2023]
Abstract
The question of whether RNA is more stable or unstable compared to DNA or other nucleic acids has long been a subject of extensive scrutiny and public attention. Recently, thermodynamically stable and degradation-resistant RNA motifs have been utilized in RNA nanotechnology to build desired architectures and integrate multiple functional groups. Here we report the effects of phosphorothioate deoxyribonucleotides (PS-DNA), deoxyribonucleotides (DNA), ribonucleotides (RNA), 2'-F nucleotides (2'-F), and locked nucleic acids (LNA) on the thermal and in vivo stability of the three-way junction (3WJ) of bacteriophage phi29 motor packaging RNA. It was found that the thermal stability gradually increased following the order of PS-DNA/PS-DNA < DNA/DNA < DNA/RNA < RNA/RNA < RNA/2'-F RNA < 2'-F RNA/2'-F RNA < 2'-F RNA/LNA < LNA/LNA. This proposition is supported by studies on strand displacement and the melting of homogeneous and heterogeneous 3WJs. By simply mixing different chemically modified oligonucleotides, the thermal stability of phi29 pRNA 3WJ can be tuned to cover a wide range of melting temperatures from 21.2°C to over 95°C. The 3WJLNA was resistant to boiling temperature denaturation, urea denaturation, and 50% serum degradation. Intravenous injection of fluorescent LNA/2'-F hybrid 3WJs into mice revealed its exceptional in vivo stability and presence in urine. It is thus concluded that incorporation of LNA nucleotides, alone or in combination with 2'-F, into RNA nanoparticles derived from phi29 pRNA 3WJ can extend the half-life of the RNA nanoparticles in vivo and improve their pharmacokinetics profile.
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Affiliation(s)
- Xijun Piao
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, Ohio 43210, USA
- College of Pharmacy, Division of Pharmaceutics and Pharmaceutical Chemistry, The Ohio State University, Columbus, Ohio 43210, USA
- College of Medicine; Dorothy M. Davis Heart and Lung Research Institute; The Ohio State University, Columbus, Ohio 43210, USA
- James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
| | - Hongzhi Wang
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, Ohio 43210, USA
- College of Pharmacy, Division of Pharmaceutics and Pharmaceutical Chemistry, The Ohio State University, Columbus, Ohio 43210, USA
- College of Medicine; Dorothy M. Davis Heart and Lung Research Institute; The Ohio State University, Columbus, Ohio 43210, USA
- James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
| | - Daniel W Binzel
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, Ohio 43210, USA
- College of Pharmacy, Division of Pharmaceutics and Pharmaceutical Chemistry, The Ohio State University, Columbus, Ohio 43210, USA
- College of Medicine; Dorothy M. Davis Heart and Lung Research Institute; The Ohio State University, Columbus, Ohio 43210, USA
- James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, Ohio 43210, USA
- College of Pharmacy, Division of Pharmaceutics and Pharmaceutical Chemistry, The Ohio State University, Columbus, Ohio 43210, USA
- College of Medicine; Dorothy M. Davis Heart and Lung Research Institute; The Ohio State University, Columbus, Ohio 43210, USA
- James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
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Perschbacher K, Smestad JA, Peters JP, Standiford MM, Denic A, Wootla B, Warrington AE, Rodriguez M, Maher LJ. Quantitative PCR analysis of DNA aptamer pharmacokinetics in mice. Nucleic Acid Ther 2014; 25:11-9. [PMID: 25536292 PMCID: PMC4296750 DOI: 10.1089/nat.2014.0515] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
DNA aptamer oligonucleotides and their protein conjugates show promise as therapeutics in animal models of diseases such as multiple sclerosis. These molecules are large and highly charged, raising questions about their biodistribution and pharmacokinetics in mammals. Here we exploit the power of quantitative polymerase chain reaction to accurately quantitate the tissue distribution of 40-nucleotide DNA aptamers and their streptavidin conjugates after intraperitoneal injection in mice. We show remarkably rapid distribution to peripheral tissues including the central nervous system. Modeling of tissue distribution data reveals the importance of DNA aptamer sequence, 3′ modification, and protein conjugation in enhancing tissue exposure. These data help to interpret the previously observed effectiveness of aptamer conjugates, as opposed to free aptamers, in stimulating central nervous system remyelination in a mouse model of multiple sclerosis.
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Affiliation(s)
- Katherine Perschbacher
- 1 Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine , Rochester, Minnesota
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7
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Bhagat L, Putta MR, Wang D, Yu D, Lan T, Jiang W, Sun Z, Wang H, Tang JX, La Monica N, Kandimalla ER, Agrawal S. Novel oligonucleotides containing two 3'-ends complementary to target mRNA show optimal gene-silencing activity. J Med Chem 2011; 54:3027-36. [PMID: 21466154 DOI: 10.1021/jm200113t] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Oligonucleotides are being employed for gene-silencing activity by a variety of mechanisms, including antisense, ribozyme, and siRNA. In the present studies, we designed novel oligonucleotides complementary to targeted mRNAs and studied the effect of 3'-end exposure and oligonucleotide length on gene-silencing activity. We synthesized both oligoribonucleotides (RNAs) and oligodeoxynucleotides (DNAs) with phosphorothioate backbones, consisting of two identical segments complementary to the targeted mRNA attached through their 5'-ends, thereby containing two accessible 3'-ends; these compounds are referred to as gene-silencing oligonucleotides (GSOs). RNA and/or DNA GSOs targeted to MyD88, VEGF, and TLR9 mRNAs had more potent gene-silencing activity than did antisense phosphorothioate oligonucleotides (PS-oligos) in cell-based assays and in vivo. Of the different lengths of GSOs evaluated, 19-mer long RNA and DNA GSOs had the best gene-silencing activity both in vitro and in vivo. These results suggest that GSOs are novel agents for gene silencing that can be delivered systemically with broader applicability.
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Affiliation(s)
- Lakshmi Bhagat
- Idera Pharmaceuticals, Inc., Cambridge, Massachusetts 02139, United States
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8
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Abstract
BACKGROUND The use of oligonucleotides as therapeutic agents has elicited a great deal of interest. Basic understanding and evaluation of the pharmacokinetic properties of oligonucleotides is foundational to their appropriate design and application. OBJECTIVE To review the primary pharmacokinetic properties that drive successful use and delivery of oligonucleotides. METHODS The primary data set available in the published literature for summarizing the pharmacokinetic properties of oligonucleotides exists for single strand phosphorothioate antisense oligonucleotides and their chimeric chemical modifications (second generation). Where possible, data from other classes of compounds are contrasted with this base class. RESULTS/CONCLUSION Although there are several different classes of oligonucleotides being developed as therapeutic agents, their pharmacokinetic properties by class are primarily a function of their backbone chemistry and the resulting chemical relationship to biological stability and plasma protein binding properties.
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Affiliation(s)
- Richard S Geary
- Isis Pharmaceuticals, Inc., 1896 Rutherford Rd, Carlsbad, CA 92008, USA.
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9
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Saavedra-Rodríguez L, Vázquez A, Ortiz-Zuazaga HG, Chorna NE, González FA, Andrés L, Rodríguez K, Ramírez F, Rodríguez A, de Ortiz SP. Identification of flap structure-specific endonuclease 1 as a factor involved in long-term memory formation of aversive learning. J Neurosci 2009; 29:5726-37. [PMID: 19420241 PMCID: PMC2699464 DOI: 10.1523/jneurosci.4033-08.2009] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2008] [Revised: 03/11/2009] [Accepted: 03/24/2009] [Indexed: 01/19/2023] Open
Abstract
We previously proposed that DNA recombination/repair processes play a role in memory formation. Here, we examined the possible role of the fen-1 gene, encoding a flap structure-specific endonuclease, in memory consolidation of conditioned taste aversion (CTA). Quantitative real-time PCR showed that amygdalar fen-1 mRNA induction was associated to the central processing of the illness experience related to CTA and to CTA itself, but not to the central processing resulting from the presentation of a novel flavor. CTA also increased expression of the Fen-1 protein in the amygdala, but not the insular cortex. In addition, double immunofluorescence analyses showed that amygdalar Fen-1 expression is mostly localized within neurons. Importantly, functional studies demonstrated that amygdalar antisense knockdown of fen-1 expression impaired consolidation, but not short-term memory, of CTA. Overall, these studies define the fen-1 endonuclease as a new DNA recombination/repair factor involved in the formation of long-term memories.
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Affiliation(s)
- Lorena Saavedra-Rodríguez
- Molecular and Cellular Cognition Laboratory and
- Functional Genomics Research Center, Department of Biology, and
| | - Adrinel Vázquez
- Molecular and Cellular Cognition Laboratory and
- Functional Genomics Research Center, Department of Biology, and
| | - Humberto G. Ortiz-Zuazaga
- High Performance Computing Facility, University of Puerto Rico, Central Administration, San Juan, Puerto Rico 00931
| | - Nataliya E. Chorna
- Department of Chemistry, University of Puerto Rico, Río Piedras Campus, San Juan, Puerto Rico 00931-3360, and
| | - Fernando A. González
- Department of Chemistry, University of Puerto Rico, Río Piedras Campus, San Juan, Puerto Rico 00931-3360, and
| | | | | | | | | | - Sandra Peña de Ortiz
- Molecular and Cellular Cognition Laboratory and
- Functional Genomics Research Center, Department of Biology, and
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10
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Ivashuta SI, Petrick JS, Heisel SE, Zhang Y, Guo L, Reynolds TL, Rice JF, Allen E, Roberts JK. Endogenous small RNAs in grain: semi-quantification and sequence homology to human and animal genes. Food Chem Toxicol 2009; 47:353-60. [PMID: 19068223 DOI: 10.1016/j.fct.2008.11.025] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2008] [Revised: 11/05/2008] [Accepted: 11/14/2008] [Indexed: 12/29/2022]
Abstract
Small interfering RNAs (siRNAs) and microRNAs (miRNAs) are effector molecules of RNA interference (RNAi), a highly conserved RNA-based gene suppression mechanism in plants, mammals and other eukaryotes. Endogenous RNAi-based gene suppression has been harnessed naturally and through conventional breeding to achieve desired plant phenotypes. The present study demonstrates that endogenous small RNAs, such as siRNAs and miRNAs, are abundant in soybean seeds, corn kernels, and rice grain, plant tissues that are traditionally used for food and feed. Numerous endogenous plant small RNAs were found to have perfect complementarity to human genes as well as those of other mammals. The abundance of endogenous small RNA molecules in grain from safely consumed food and feed crops such as soybean, corn, and rice and the homology of a number of these dietary small RNAs to human and animal genomes and transcriptomes establishes a history of safe consumption for dietary small RNAs.
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Affiliation(s)
- Sergey I Ivashuta
- Monsanto Company, 800N. Lindbergh Blvd., Mail Code O3F, St. Louis, MO 63167, USA
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11
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Crooke ST. Monthly Updates: Monthly Update Biologicals & Immunologicals: Progress in the development of antisense drugs. Expert Opin Investig Drugs 2008. [DOI: 10.1517/13543784.5.8.1047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Stanley T Crooke
- Isis Pharmaceuticals, Inc., 2292 Faraday Avenue, Carlsbad, California, 92008, USA
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12
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Stoyanova R, Hachem P, Hensley H, Khor LY, Mu Z, Hammond MEH, Agrawal S, Pollack A. Antisense-MDM2 sensitizes LNCaP prostate cancer cells to androgen deprivation, radiation, and the combination in vivo. Int J Radiat Oncol Biol Phys 2007; 68:1151-60. [PMID: 17637390 PMCID: PMC2763094 DOI: 10.1016/j.ijrobp.2007.03.047] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2007] [Revised: 03/06/2007] [Accepted: 03/23/2007] [Indexed: 11/24/2022]
Abstract
PURPOSE To test the effects of antisense (AS)-MDM2 alone and with androgen deprivation (AD), radiotherapy (RT), and AD + RT on wild-type LNCaP cells in an orthotopic in vivo model. METHODS Androgen-sensitive LNCaP cells were grown in the prostates of nude mice. Magnetic resonance imaging-based tumor volume and serum prostate-specific antigen (PSA) measurements were used to assess effects on tumor response. Tumor response was measured by biochemical and tumor volume failure definitions and doubling time estimates from fitted PSA and tumor volume growth curves. Expression of MDM2, p53, p21, and Ki-67 was quantified using immunohistochemical staining and image analysis of formalin-fixed tissue, analogous to methods used clinically. RESULTS Antisense-MDM2 significantly inhibited the growth of LNCaP tumors over the mismatch controls. The most significant increase in tumor growth delay and tumor doubling time was from AS-MDM2 + AD + RT, although the effect of AS-MDM2 + AD was substantial. Expression of MDM2 was significantly reduced by AS-MDM2 in the setting of RT. CONCLUSIONS This is the first in vivo investigation of the effects of AS-MDM2 in an orthotopic model and the first to demonstrate incremental sensitization when added to AD and AD + RT. The results with AD underscore the potential to affect micrometastatic disease, which is probably responsible for treatment failure in 30-40% of men with high-risk disease.
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Affiliation(s)
- Radka Stoyanova
- Department of Radiation Oncology, Fox Chase Cancer Center, Philadelphia, PA
| | - Paul Hachem
- Department of Radiation Oncology, Fox Chase Cancer Center, Philadelphia, PA
| | - Harvey Hensley
- Department of Basic Science, Fox Chase Cancer Center, Philadelphia, PA
| | - Li-Yan Khor
- Department of Radiation Oncology, Fox Chase Cancer Center, Philadelphia, PA
| | - Zhaomei Mu
- Department of Radiation Oncology, Fox Chase Cancer Center, Philadelphia, PA
| | | | | | - Alan Pollack
- Department of Radiation Oncology, Fox Chase Cancer Center, Philadelphia, PA
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13
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Yu RZ, Kim TW, Hong A, Watanabe TA, Gaus HJ, Geary RS. Cross-species pharmacokinetic comparison from mouse to man of a second-generation antisense oligonucleotide, ISIS 301012, targeting human apolipoprotein B-100. Drug Metab Dispos 2006; 35:460-8. [PMID: 17172312 DOI: 10.1124/dmd.106.012401] [Citation(s) in RCA: 184] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The pharmacokinetics of a 2'-O-(2-methoxyethyl)-modified oligonucleotide, ISIS 301012 [targeting human apolipoprotein B-100 (apoB-100)], was characterized in mouse, rat, monkey, and human. Plasma pharmacokinetics following parental administration was similar across species, exhibiting a rapid distribution phase with t(1/2alpha) of several hours and a prolonged elimination phase with t(1/2beta) of days. The prolonged elimination phase represents equilibrium between tissues and circulating drug due to slow elimination from tissues. Absorption was nearly complete following s.c. injection, with bioavailability ranging from 80 to 100% in monkeys. Plasma clearance scaled well across species as a function of body weight alone, and this correlation was improved when corrected for plasma protein binding. In all of the animal models studied, the highest tissue concentrations of ISIS 301012 were observed in kidney and liver. Urinary excretion was less than 3% in monkeys and human in the first 24 h. ISIS 301012 is highly bound to plasma proteins, probably preventing rapid removal by renal filtration. However, following 25 mg/kg s.c. administration in mouse and 5-mg/kg i.v. bolus administration in rat, plasma concentrations of ISIS 301012 exceeded their respective protein binding capacity. Thus, urinary excretion increased to 16% or greater within the first 24 h. Albeit slow, urinary excretion of ISIS 301012 and its shortened metabolites is the ultimate elimination pathway of this compound, as demonstrated by 32% of dose recovered in total excreta by 14 days in a rat mass balance study. The pharmacokinetics of ISIS 301012 in human is predictable from the pharmacokinetics measured in animals. The pharmacokinetic properties of ISIS 301012 provide guidance for clinical development and support infrequent dose administration.
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Affiliation(s)
- Rosie Z Yu
- Isis Pharmaceuticals, 1896 Rutherford Rd., Carlsbad, CA 92008, USA.
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14
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Drygin D, Koo S, Perera R, Barone S, Bennett CF. Induction of toll-like receptors and NALP/PAN/PYPAF family members by modified oligonucleotides in lung epithelial carcinoma cells. Oligonucleotides 2006; 15:105-18. [PMID: 15989425 DOI: 10.1089/oli.2005.15.105] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
ISIS 199044 is a chimeric 2'-O-methyl-containing oligonucleotide that produces toxicity in several cultured cell lines. Upon investigation into the mechanism of cytotoxicity, we discovered that treatment of lung epithelial carcinoma cells, A549, with ISIS 199044 and several other cytotoxic oligonucleotides induces a group of genes that are not normally expressed in these cells. These genes are involved in host response to foreign materials. Among them were toll-like receptor 7 (TLR7) and TLR9, members of the toll-like receptor family, responsible for immune response to nucleic acids and cryopyrin, a member of NALP/PAN/PYPAF family, which is known to assemble with ASC and regulate NF-kappaB activation and to modulate apoptosis. Maximal induction occurred 12-24 hours posttreatment with 500 nM oligonucleotide in the presence of Lipofectin reagent. Furthermore, we have shown that this induction is chemistry dependent; it can be negated by certain modifications, such as replacement of 2'-O-methyl with 2'-O-methoxyethyl groups or substitution of phosphorothioates with phosphodiester linkages. DNA microarray analysis identified additional genes modulated by ISIS 199044, particularly genes involved in DNA damage/repair.
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15
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Schmidtke M, Knorre C, Blei L, Stelzner A, Birch-Hirschfeld E. Penetration and Antiviral Activity of Coxsackievirus B3 (Cvb3)-Specific Phosphorothioate Oligodeoxynucleotides (Ps-Odn). ACTA ACUST UNITED AC 2006. [DOI: 10.1080/07328319808004686] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- M. Schmidtke
- a Institute of Virology, Friedrich Schiller University , 07745 , Jena , Germany
| | - C. Knorre
- a Institute of Virology, Friedrich Schiller University , 07745 , Jena , Germany
| | - L. Blei
- b Hans-Knöll-Institute for Natural Product Research , 07745 , Jena , Germany
| | - A. Stelzner
- a Institute of Virology, Friedrich Schiller University , 07745 , Jena , Germany
| | - E. Birch-Hirschfeld
- a Institute of Virology, Friedrich Schiller University , 07745 , Jena , Germany
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16
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Yanze MF, Ho EA, Macgregor RB, Piquette-Miller M. In vivo disposition and stability of DNA frayed wires in mice. Int J Biol Macromol 2006; 39:310-6. [PMID: 16777215 DOI: 10.1016/j.ijbiomac.2006.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2006] [Revised: 05/04/2006] [Accepted: 05/08/2006] [Indexed: 11/21/2022]
Abstract
DNA frayed wires (DNA(FW)) are an alternate form of DNA organization formed by the self-association of several strands of guanine-rich oligonucleotides. The purpose of this study was to define for the first time the blood clearance kinetics, tissue distribution, and stability of DNA(FW) in vivo in mice. Single bolus doses (1200 pmol/mouse) of (32)P-DNA(FW) and (32)P-random DNA were administered intravenously (IV) and intraperitoneally (IP) followed by scheduled blood, urine, fecal and tissue samplings. Blood clearance kinetics was described well by a first order two-compartment open model. The overall half-lives of elimination from the central compartment (T(1/2))(K10) were 3.57+/-0.1h for IV and 2.38+/-0.11 h for IP. In contrast, random DNA was completely degraded after 15 min regardless of the route of administration. Tissue distribution results demonstrated that DNA(FW) were primarily distributed and retained in the liver, intestines, kidneys, and heart. Low levels could also be detected in brain. Autoradiographs of blood, tissues, feces and urine extracts established that DNA(FW) remained intact after administration as no measurable levels of metabolites or degradation products were found after 24h. (32)P-DNA(FW) was primarily eliminated via hepato-biliary excretion into feces after either IV or IP administration (51.8+/-4.53% and 36.2+/-3.4%, respectively). The improved stability and longer half-life of DNA(FW), previously shown in vitro, is also seen in vivo, indicating that DNA(FW) may provide a stable delivery system for DNA gene therapies. In conclusion, this is the first study demonstrating the in vivo stability, pharmacokinetics, and disposition of DNA superstructures.
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Affiliation(s)
- Maximum F Yanze
- Department of Pharmaceutical Sciences, University of Toronto, 19 Russell Street, Toronto, Ont, Canada
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17
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Wang H, Li M, Rhie JK, Hockenbery DM, Covey JM, Zhang R, Hill DL. Preclinical pharmacology of 2-methoxyantimycin A compounds as novel antitumor agents. Cancer Chemother Pharmacol 2005; 56:291-8. [PMID: 15883820 DOI: 10.1007/s00280-004-0978-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2004] [Accepted: 07/06/2004] [Indexed: 11/25/2022]
Abstract
PURPOSE The present study was designed to determine pharmacological and biochemical properties of 2-methoxyantimycin A analogs (OMe-A1, OMe-A2, OMe-A3, and OMe-A5), which are novel antitumor compounds, and provide a basis for future pharmaceutical development, preclinical evaluation, and clinical trials. METHODS A high-performance liquid chromatography (HPLC) method was established and employed to assess the biostability of these analogs and to determine their pharmacokinetic properties in mice and rats. RESULTS In vitro biostability of the 2-methoxyantimycin analogs was esterase-dependent, compound-dependent, and species-dependent. In the absence of esterase inhibitors, all of the analogs were relatively unstable. Stability was greater, however, in human and dog plasma than in rat and mouse plasma. In the presence of esterase inhibitors, OMe-A1 was stable at 37 degrees C for 60 min in mouse and rat plasma, moderately stable in human plasma, and unstable in dog plasma. OMe-A2 was generally stable in all types of plasma. OMe-A3 was stable in dog and rat plasma, but not in human or mouse plasma. OMe-A5 was stable in human and dog plasma, but not in mouse or rat plasma. Each of these analogs was highly bound to plasma proteins. Of S9 fractions from four species, human S9 was least efficient in metabolizing OMe-A3. Following an intravenous dose of OMe-A1 in mice, plasma levels decreased rapidly, with an initial half-life of 2.7 min and a terminal half life of 34 min. Following an intraperitoneal dose in mice, plasma levels decreased less rapidly with a terminal half-life of 215 min. Following an intravenous dose of OMe-A1 or OMe-A3 in rats, plasma levels decreased more rapidly with initial half-lives of about 1.0 min. At an equivalent dose, OMe-A3 had a faster clearance than OMe-A1. CONCLUSIONS For 2-methoxyantimycin A analogs, species differences in biostability, metabolism, and pharmacokinetics may be pertinent in assessing their pharmacological and toxicological profiles and antitumor activity in humans.
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Affiliation(s)
- Hui Wang
- Department of Pharmacology and Toxicology, Division of Clinical Pharmacology, Cancer Pharmacology Laboratory, Comprehensive Cancer Center, University of Alabama, Birmingham, AL, 35294, USA.
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18
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Biodistribution and metabolism of immunostimulatory oligodeoxynucleotide CPG 7909 in mouse and rat tissues following subcutaneous administration. Biochem Pharmacol 2005; 69:981-91. [PMID: 15748709 DOI: 10.1016/j.bcp.2004.12.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2004] [Accepted: 12/28/2004] [Indexed: 11/18/2022]
Abstract
To evaluate pharmacokinetics (PK) and biodistribution, CPG 7909, a 24-mer immunostimulatory fully phosphorothioated oligodeoxynucleotide (PS-ODN), was administered by subcutaneous injection at 2, 5 and 12.5mg/kg to mice and at 9mg/kg to rats. Parent compound and metabolites were isolated from plasma and tissues and quantified by capillary gel electrophoresis with UV detection (CGE-UV) and molecular masses were determined by matrix-assisted-laser-desorption-ionization time of flight detection (MALDI-TOF). An established method for PS-ODN isolation from plasma and tissue was modified to prevent oxidation of the phosphorothioate bonds during the extraction process, significantly increasing sensitivity in the subsequent MALDI-TOF analysis. Concentrations of CPG 7909 and metabolites were highest at the injection site (>600mg/kg at 4h). Maximal concentrations in local (draining) lymph nodes (LLN), kidney and liver were 10-15% of that at the injection site. The highest total amount of PS-ODN (percentage of administered dose) was found in the liver (32% at 4h), followed closely by the injection site (23% at 4h). Only very low levels of CPG 7909 and metabolites were found in plasma and only during the first hours. Metabolites identified by MALDI-TOF were similar for both species and all analyzed tissues, although the relative amounts of the different metabolites varied with tissue and over time. Degradation of CPG 7909 in vivo occurred predominantly by 3'exonucleases with additional cleavage by endonucleases.
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19
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Galderisi U, Cipollaro M, Cascino A. Antisense oligonucleotides as drugs for HIV treatment. Expert Opin Ther Pat 2005. [DOI: 10.1517/13543776.11.10.1605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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20
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Galderisi U, Cipollaro M, Cascino A. Clinical trials of a new class of therapeutic agents: antisense oligonucleotides. ACTA ACUST UNITED AC 2005; 6:69-79. [PMID: 15989497 DOI: 10.1517/14728214.6.1.69] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Antisense oligodeoxynucleotides (ODNs) are short stretches of DNA complementary to a target mRNA. The ODNs selectively hybridise to their complementary RNA by Watson-Crick base pairing rules. In theory, the use of antisense ODNs provides a method to specifically inhibit the intracellular expression of any disorder whose genetic aetiology is well known. For this reason, researchers thought that if antisense drugs proved to be so specific there would be no side effects. However, toxicity-related problems arose in initial animal studies of antisense drugs in the early 1990s and since then companies have been using these compounds cautiously. In order to be useful therapeutically, an ODN must (a) exhibit reasonable stability in the physiological environment, (b) be taken up and retained in adequate quantities by the target cells, (c) specifically bind target mRNA with high affinity, (d) have an acceptable therapeutic ratio, free of unwanted toxic and non-specific side effects and (e) be easily synthesised in sufficient quantities to allow clinical use. Most of these criteria have already been met by ODNs recently used in this way. This review describes certain therapeutic applications of antisense techniques currently under investigation in oncology, haematopathology and inflammatory diseases.
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Affiliation(s)
- U Galderisi
- Dipartimento di Medicina Sperimentale, Via Costantinopoli 16, 80138 Napoli, Italy.
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21
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Affiliation(s)
- C F Bennett
- ISIS Pharmaceuticals, 2280 Faraday Ave., Carlsbad, CA 92008, USA.
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22
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Abstract
About 25 years ago, researchers first demonstrated that a short synthetic oligodeoxynucleotide, referred to as antisense, can inhibit replication of Rous sarcoma virus through hybridization to viral RNA. Since then, several hybridization-based oligonucleotide approaches have been developed to elucidate the functions of genes and their potential as therapeutic agents. Short-interfering (si) RNA is the most recent example. To effectively inhibit gene expression, an antisense or siRNA must be resistant to nucleases, be taken up efficiently by cells, hybridize efficiently with the target mRNA and activate selective degradation of the target mRNA or block its translation without causing undesirable side effects. However, both antisense and siRNA agents have been shown to exert non-target-related biological effects including immune stimulation. Do antisense and siRNA agents work as ligands for Toll-like receptors (TLRs), a family of pathogen-associated, molecular pattern recognition receptors?
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Affiliation(s)
- Sudhir Agrawal
- Hybridon, Inc., 345 Vassar Street, Cambridge, Massachusetts 02139, USA.
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23
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Abstract
Antisense technology exploits oligonucleotide analogs to bind to target RNAs via Watson-Crick hybridization. Once bound, the antisense agent either disables or induces the degradation of the target RNA. Antisense agents can also alter splicing. During the past decade, much has been learned about the basic mechanisms of antisense, the medicinal chemistry, and the pharmacologic, pharmacokinetic, and toxicologic properties of antisense molecules. Antisense technology has proven valuable in gene functionalization and target validation. With one drug marketed, Vitravenetm, and approximately 20 antisense drugs in clinical development, it appears that antisense drugs may prove important in the treatment of a wide range of diseases.
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Affiliation(s)
- Stanley T Crooke
- Isis Pharmaceuticals, 2292 Faraday Avenue, Carlsbad, California 92008, USA.
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24
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Siwkowski AM, Malik L, Esau CC, Maier MA, Wancewicz EV, Albertshofer K, Monia BP, Bennett CF, Eldrup AB. Identification and functional validation of PNAs that inhibit murine CD40 expression by redirection of splicing. Nucleic Acids Res 2004; 32:2695-706. [PMID: 15148357 PMCID: PMC419592 DOI: 10.1093/nar/gkh584] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Cognate recognition between the CD40 receptor and its ligand, CD154, is thought to play a central role in the initiation and propagation of immune responses. We describe the specific down regulation of cell surface associated CD40 protein expression by use of a peptide nucleic acid (PNA) antisense inhibitor, ISIS 208529, that is designed to bind to the 3' end of the exon 6 splice junction within the primary CD40 transcript. Binding of ISIS 208529 was found to alter constitutive splicing, leading to the accumulation of a transcript lacking exon 6. The resulting protein product lacks the transmembrane domain. ISIS 208529-mediated CD40 protein depletion was found to be sequence specific and dose dependent, and was dependent on the length of the PNA oligomer. CD40-dependent induction of IL-12 in primary murine macrophages was attenuated in cells treated with ISIS 208529. Oligolysine conjugation to the PNA inhibitor produced an inhibitor, ISIS 278647, which maintained its specificity and displayed efficacy in BCL1 cells and in primary murine macrophages in the absence of delivery agents. These results demonstrate that PNA oligomers can be effective inhibitors of CD40 expression and hence may be useful as novel immuno-modulatory agents.
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Affiliation(s)
- Andrew M Siwkowski
- Department of Medicinal Chemistry, ISIS Pharmaceuticals, 2292 Faraday Avenue, Carlsbad, CA 92008, USA
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25
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Geary RS, Yu RZ, Watanabe T, Henry SP, Hardee GE, Chappell A, Matson J, Sasmor H, Cummins L, Levin AA. Pharmacokinetics of a tumor necrosis factor-alpha phosphorothioate 2'-O-(2-methoxyethyl) modified antisense oligonucleotide: comparison across species. Drug Metab Dispos 2004; 31:1419-28. [PMID: 14570775 DOI: 10.1124/dmd.31.11.1419] [Citation(s) in RCA: 127] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The pharmacokinetics of a 2'-O-(2-methoxyethyl)-ribose modified phosphorothioate oligonucleotide, ISIS 104838 (human tumor necrosis factor-alpha antisense), have been characterized in mouse, rat, dog, monkey, and human. Plasma pharmacokinetics after i.v. administration exhibited relatively rapid distribution from plasma to tissues with a distribution half-life estimated from approximately 15 to 45 min in all species. Absorption after s.c. injection was high (80-100%), and absorption after intrajejunal administration in proprietary formulations was as high as 10% bioavailability compared with i.v. administration. Urinary excretion of the parent drug was low, with less than 1% of the administered dose excreted in urine after i.v. infusion in monkeys at clinically relevant doses (< or = 5 mg/kg). ISIS 104838 is highly bound to plasma proteins, likely preventing renal filtration. However, shortened oligonucleotide metabolites of ISIS 104838 lose their affinity to bind plasma proteins. Thus, excretion of radiolabel (mostly as metabolites) in urine (75%) and feces (5-10%) was nearly complete by 90 days. Elimination of ISIS 104838 from tissue was slow (multiple days) for all species, depending on the tissue or organ. The highest concentrations of ISIS 104838 in tissues were seen in kidney, liver, lymph nodes, bone marrow, and spleen. In general, concentrations of ISIS 104838 were higher in monkey tissues than in rodents at body weight-equivalent doses. Plasma pharmacokinetics scale well across species as a function of body weight alone. This favorable pharmacokinetic profile for ISIS 104838 provides guidance for clinical development and appears to support infrequent and convenient dose administration.
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Affiliation(s)
- Richard S Geary
- Isis Pharmaceuticals, Inc., 2292 Faraday Avenue, Carlsbad, CA 92008, USA.
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26
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Abstract
There has been steady progress in antisense technology over the past 14 years. We now have a far better appreciation of the attributes and limitations of the technology. Antisense oligonucleotides have been used to selectively inhibit thousands of genes in mammalian cells, hundreds, if not thousands, of genes in rodents and other species and multiple genes in humans. There are over 20 antisense drugs currently in clinical trials, several of which are showing promising results. Like any other class of drugs in development, there will continue to be successes and failures in the clinic. Despite some disappointments with the technology, it appears to be a valid platform for both drug discovery and as an experimental tool for functionalizing genes. Advances in the medicinal chemistry and formulation of antisense oligonucleotides will further enhance their therapeutic and commercial potential.
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Affiliation(s)
- Nicholas M Dean
- ISIS Pharmaceuticals, 2282 Faraday Ave, Carlsbad, CA 92008, USA
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27
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Affiliation(s)
- G F Joyce
- Skaggs Institute for Chemical Biology, Scripps Research Institute, La Jolla, California 92037, USA
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28
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Abstract
Antisense oligonucleotides have been the subject of intense interest as research tools to elucidate the functions of gene products and as therapeutic agents. Initially, their mode of action was poorly understood and the biological effects of oligonucleotides were often misinterpreted. However, research into these gene-based inhibitors of cellular action recently has succeeded in realising their exciting potential, particularly as novel therapeutic agents. An emerging application of this technology is in cutaneous therapy. The demand for more effective dermatological drugs will ensure further development of antisense strategies in skin, with key issues being drug delivery, therapeutic target selection, and clinical applicability.
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Affiliation(s)
- C J Wraight
- Centre for Hormone Research, Murdoch Childrens Research Institute, Flemington Road, Parkville, Victoria 3052, Australia.
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29
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Ma DD, Rede T, Naqvi NA, Cook PD. Synthetic oligonucleotides as therapeutics: the coming of age. BIOTECHNOLOGY ANNUAL REVIEW 2000; 5:155-96. [PMID: 10875000 DOI: 10.1016/s1387-2656(00)05035-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Synthetic oligonucleotides (ODNs) are short nucleic acid chains that can act in a sequence specific manner to control gene expression. Significant progress has been made in the development of synthetic ODN therapeutics since the first demonstration of gene inhibition by antisense ODNs in a cell culture system two decades ago. This new class of therapeutic agents can potentially target any abnormally expressed genes in a broad range of diseases from viral infections to psychoneurological disorders. A number of "first" generation synthetic ODNs have entered into human clinical trials in the last few years. The eminent approval of the first ODN for the treatment of cytomaglovirus retinitis by the FDA in USA will provide much excitement that this new class of compounds holds great promise as a therapeutic "magic bullet". However, many obstacles still exist in the development of this technology. In this review, the current status of synthetic ODN chemistry, drug delivery methods, mechanisms of ODN action, potential clinical applications and its limitations in a wide range of human disorders will be described.
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Affiliation(s)
- D D Ma
- Department of Haematology, St Vincents Hospital, Sydney, New South Wales, Australia
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30
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Rusckowski M, Qu T, Roskey A, Agrawal S. Biodistribution and metabolism of a mixed backbone oligonucleotide (GEM 231) following single and multiple dose administration in mice. ANTISENSE & NUCLEIC ACID DRUG DEVELOPMENT 2000; 10:333-45. [PMID: 11079573 DOI: 10.1089/oli.1.2000.10.333] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Biodistribution and metabolism of a mixed backbone oligonucleotide (MBO), GEM 231, targeted to the RIalpha subunit of protein kinase A has been studied in normal and tumor xenografted mice. The study has been carried out using [35S]-labeled MBO following single and multiple administrations of doses varying from 2 to 50 mg/kg. MBO showed wide tissue distribution following intravenous and subcutaneous administration. The highest concentration of MBO was in the kidney and liver. The general disposition of MBO was followed by digitized autoradiographic pictures of tumored mice and further confirmed wide tissue disposition and also showed defined intratumor uptake of MBO. Multiple dose administration showed increased disposition in the majority of the tissues/organs, with the exception of the kidneys. Analysis of the extracted MBO by polyacrylamide gel electrophoresis (PAGE) showed the presence of primarily intact MBO along with its degraded forms. Based on our radioactivity levels, the primary route of excretion was in urine, analysis of which showed mainly degraded forms of MBO.
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Affiliation(s)
- M Rusckowski
- Department of Radiology, University of Massachusetts Medical School, Worcester 01655, USA
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31
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Agrawal S, Kandimalla ER. Antisense therapeutics: is it as simple as complementary base recognition? MOLECULAR MEDICINE TODAY 2000; 6:72-81. [PMID: 10652480 DOI: 10.1016/s1357-4310(99)01638-x] [Citation(s) in RCA: 103] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Antisense oligonucleotides provide a simple and efficient approach for developing target-selective drugs because they can modulate gene expression sequence-specifically. Antisense oligonucleotides have also become efficient molecular biological tools to investigate the function of any protein in the cell. As the application of antisense oligonucleotides has expanded, multiple mechanisms of oligonucleotides have been characterized that impede their routine use. Here, we discuss different mechanisms of action of oligonucleotides and the possible ways of minimizing non-antisense-related [corrected] effects to improve their specificity.
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Affiliation(s)
- S Agrawal
- Hybridon, 155 Fortune Boulevard, Milford, MA 01757, USA.
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32
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Sierakowska H, Gorman L, Kang SH, Kole R. Antisense oligonucleotides and RNAs as modulators of pre-mRNA splicing. Methods Enzymol 2000; 313:506-21. [PMID: 10595376 DOI: 10.1016/s0076-6879(00)13032-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Affiliation(s)
- H Sierakowska
- Lineberger Cancer Center, University of North Carolina, Chapel Hill 27599, USA
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33
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Agrawal S. Importance of nucleotide sequence and chemical modifications of antisense oligonucleotides. BIOCHIMICA ET BIOPHYSICA ACTA 1999; 1489:53-68. [PMID: 10806997 DOI: 10.1016/s0167-4781(99)00141-4] [Citation(s) in RCA: 122] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The antisense approach is conceptually simple and elegant; to design an inhibitor of a specific mRNA, one needs only to know the sequence of the targeted mRNA and an appropriately modified complementary oligonucleotide. Of the many analogs of oligodeoxynucleotides explored as antisense agents, phosphorothioate analogs have been studied the most extensively. The use of phosphorothioate oligodeoxynucleotides as antisense agents in various studies have shown promising results. However, they have also indicated that quite often, biological effects observed could be solely or partly non-specific in nature. It is becoming clear that not all phosphorothioate oligodeoxynucleotides of varying length and base composition are the same, and important consideration should be given to maintain antisense mechanisms while identifying effective antisense oligonucleotides. In this review, I have summarized the progress made in my laboratory in understanding the specificity and mechanism of actions of phosphorothioate oligonucleotides and the rationale for designing second-generation mixed-backbone oligonucleotides.
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Affiliation(s)
- S Agrawal
- Hybridon, Inc., Milford, MA 01757, USA.
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34
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Wang H, Cai Q, Zeng X, Yu D, Agrawal S, Zhang R. Antitumor activity and pharmacokinetics of a mixed-backbone antisense oligonucleotide targeted to the RIalpha subunit of protein kinase A after oral administration. Proc Natl Acad Sci U S A 1999; 96:13989-94. [PMID: 10570186 PMCID: PMC24178 DOI: 10.1073/pnas.96.24.13989] [Citation(s) in RCA: 101] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Overexpression of the RIalpha subunit of cAMP-dependent protein kinase (PKA) has been demonstrated in various human cancers. PKA has been suggested as a potential target for cancer therapy. The goal of the present study was to evaluate an anti-PKA antisense oligonucleotide (mixed-backbone oligonucleotide) as a therapeutic approach to human cancer treatment. The identified oligonucleotide inhibited the growth of cell lines of human colon cancer (LS174T, DLD-1), leukemia (HL-60), breast cancer (MCF-7, MDA-MB-468), and lung cancer (A549) in a time-, concentration-, and sequence-dependent manner. In a dose-dependent manner, the oligonucleotide displayed in vivo antitumor activity in severe combined immunodeficient and nude mice bearing xenografts of human cancers of the colon (LS174T), breast (MDA-MB-468), and lung (A549). The routes of drug administration were intraperitoneal and oral. Synergistic effects were found when the antisense oligonucleotide was used in combination with the cancer chemotherapeutic agent cisplatin. The pharmacokinetics of the oligonucleotide after oral administration of (35)S-labeled oligonucleotide into tumor-bearing mice indicated an accumulation and retention of the oligonucleotide in tumor tissue. This study further provides a basis for clinical studies of the antisense oligonucleotide targeted to the RIalpha subunit of PKA (GEM 231) as a cancer therapeutic agent used alone or in combination with conventional chemotherapy.
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Affiliation(s)
- H Wang
- Division of Clinical Pharmacology, Department of Pharmacology, Comprehensive Cancer Center, University of Alabama, Birmingham, AL 35294-0019, USA
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35
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The 3rd Annual NIH Symposium on Therapeutic Oligonucleotides. Bethesda, Maryland, USA. December 4, 1998. Abstracts. ANTISENSE & NUCLEIC ACID DRUG DEVELOPMENT 1999; 9:359-431. [PMID: 10498436 DOI: 10.1089/oli.1.1999.9.359] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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36
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Schmajuk G, Sierakowska H, Kole R. Antisense oligonucleotides with different backbones. Modification of splicing pathways and efficacy of uptake. J Biol Chem 1999; 274:21783-9. [PMID: 10419493 DOI: 10.1074/jbc.274.31.21783] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A novel, positive read-out assay that quantifies only sequence-specific nuclear activity of antisense oligonucleotides was used to evaluate morpholino and 2'-O-methyl sugar-phosphate oligonucleotides. The assay is based on modification of the splicing pathway of human beta-globin pre-mRNA. In addition, scrape-loading of cells with oligonucleotides allows the separate assessment of intracellular antisense activity of the oligonucleotides and their ability to penetrate the cell membrane barrier. The results show that, with scrape-loading, the morpholino oligonucleotides were approximately 3-fold more effective in their intrinsic antisense activity than alternating phosphodiester/phosphorothioate 2'-O-methyl-oligoribonucleotides and 6-9- and almost 200-fold more effective than the exclusively phosphorothioate and phosphodiester derivatives, respectively. The morpholino oligonucleotides were over 20-fold more effective than the phosphorothioate 2'-O-methyl-oligoribonucleotides in free uptake from the culture media. The antisense activity of the morpholino oligonucleotides was detectable not only in monolayer HeLa cells but also in suspension K562 cells. Time course experiments suggest that both the free uptake and efflux of morpholino oligonucleotides are slow.
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Affiliation(s)
- G Schmajuk
- Lineberger Comprehensive Cancer Center and Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
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37
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Srivastava RK, Srivastava AR, Seth P, Agrawal S, Cho-Chung YS. Growth arrest and induction of apoptosis in breast cancer cells by antisense depletion of protein kinase A-RI alpha subunit: p53-independent mechanism of action. Mol Cell Biochem 1999; 195:25-36. [PMID: 10395066 DOI: 10.1023/a:1006990231186] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The enhanced expression of the RI alpha subunit of cyclic AMP-dependent protein kinase type 1 (PKA-1) has been correlated with cancer cell growth. We have investigated the effects of sequence-specific inhibition of RI alpha gene expression on the growth of MCF-7 human breast cancer cells. We report that RI alpha antisense treatment results in a reduction in RI alpha expression at both mRNA and protein levels and inhibition of cell growth. The growth inhibition was accompanied by changes in cell morphology, cleavage of poly(ADP-ribose) polymerase (PARP) and appearance of apoptotic nuclei. In addition, bcl-2 protein level was reduced and p53 expression increased in growth arrested cells. Interestingly, RI alpha antisense inhibited cell viability and induced apoptosis in the absence of p53, suggesting that these actions of RI alpha antisense are exerted independent of p53. In contrast, two- and four-base mismatched control oligonucleotides had no effect on either cell growth or morphology. These results demonstrate that the RI alpha antisense, which efficiently depletes the growth stimulatory molecule RI alpha, induces cell differentiation and apoptosis, providing a new approach to combat breast cancer cell growth.
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Affiliation(s)
- R K Srivastava
- Cellular Biochemistry Section, Laboratory of Tumor Immunology and Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-1750, USA
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38
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Zhou W, Agrawal S. Mixed-backbone oligonucleotides as second-generation antisense agents with reduced phosphorothioate-related side effects. Bioorg Med Chem Lett 1998; 8:3269-74. [PMID: 9873716 DOI: 10.1016/s0960-894x(98)00591-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Mixed-backbone oligonucleotides containing alternative phosphorothioate and phosphodiester linkages in the 2'-O-methylribonucleosides segment show increased affinity with complementary targets, increased stability towards nucleases in vitro and in vivo, and reduced phosphorothioate-related prolongation of partial thromboplastin time compared to phosphorothioate oligodeoxynucleotides, thereby providing antisense agents with reduced side effects.
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Affiliation(s)
- W Zhou
- Hybridon Inc., Milford, MA 01757, USA
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Soni PN, Brown D, Saffie R, Savage K, Moore D, Gregoriadis G, Dusheiko GM. Biodistribution, stability, and antiviral efficacy of liposome-entrapped phosphorothioate antisense oligodeoxynucleotides in ducks for the treatment of chronic duck hepatitis B virus infection. Hepatology 1998; 28:1402-10. [PMID: 9794928 DOI: 10.1002/hep.510280532] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
This study investigated the feasibility of using liposomes to increase the hepatic delivery and antiviral efficacy of phosphorothioate antisense oligodeoxynucleotides (PS-ODN) for the in vivo treatment of hepatitis B virus (HBV) infection. Ducks infected with duck hepatitis B virus (DHBV) were used as the model. We studied the stability of an antisense PS-ODN in duck plasma, its integrity during the process of liposome entrapment, its in vivo biodistribution, plasma clearance, and excretion. In addition, the intrahepatic distribution of a labeled free and liposome-entrapped ODN was also investigated. The results of our studies show that: 1) phosphorothioate ODN remain stable during the process of liposome entrapment; 2) are stable in duck plasma for many hours; 3) are rapidly cleared from the plasma when injected intravenously; 4) intravenous injection of antisense ODNs entrapped within liposomes enhances delivery of the ODN to the liver; and 5) inhibit DHBV replication. Serum DHBV DNA levels fell rapidly, with a corresponding decrease in intrahepatic viral replicative intermediates at the end of the 5-day study period. Although inhibition of viral replication and a fall in the target protein was observed, a marked inhibition of viral replication was also observed with high doses of a random-sequence ODN. Thus, it is not certain that inhibition of viral replication was entirely through an antisense mechanism. Therefore, liposomes may be effective vehicles to improve the delivery of antisense oligonucleotides to the liver for the therapy of hepatotropic viruses.
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Affiliation(s)
- P N Soni
- Department of Medicine, University of Natal, Durban, South Africa
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Shen LX, Kandimalla ER, Agrawal S. Impact of mixed-backbone oligonucleotides on target binding affinity and target cleaving specificity and selectivity by Escherichia coli RNase H. Bioorg Med Chem 1998; 6:1695-705. [PMID: 9839001 DOI: 10.1016/s0968-0896(98)00131-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
All phosphorothioate mixed-backbone oligonucleotides (MBOs) composed of deoxyribonucleotide and 2'-O-methylribonucleotide segments were studied for their target binding affinity, specificity, and RNase H activation properties. The 2'-O-methylribonucleotide segment, which does not activate RNase H, serves as a high affinity target-binding domain and the deoxyribonucleotide (DNA) segment, which binds to the target with a lower affinity than the former domain, serves as an RNase H-activation or target-cleaving domain. In order to understand the influence of the size and position of the DNA segment of MBOs on RNase H-mediated cleavage of the RNA target, we designed and synthesized a series of 18-mer MBOs with the DNA segment varying from a stretch of two to eight deoxyribonucleotides in the middle, at the 5'-end, or at the 3'-end, of the MBOs. UV absorbance melting experiments of the duplexes of the MBOs with the complementary and singly mismatched RNA targets suggest that the target binding affinity of the MBOs increases as the number of 2'-O-methylribonucleotides increases, and that the binding specificity is influenced by the size and position of the DNA segment. Analysis of RNase H assay results indicates that the minimum substrate cleavage site and cleavage efficiency of RNase H are influenced by the position of the DNA segment in the MBO sequence. RNA cleavage efficiency decreases as the position of the DNA segment of the MBO.RNA heteroduplex is changed from the 3'-end to the middle and to the 5'-end of the target strand. Studies with singly mismatched targets indicate that the RNase H-dependent point mutation selectivity of the MBOs is affected by both the position and size of the DNA segment in the MBO sequence.
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Affiliation(s)
- L X Shen
- Hybridon, Inc., Cambridge, MA 02139, USA
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Gilar M, Belenky A, Budman Y, Smisek DL, Cohen AS. Study of phosphorothioate-modified oligonucleotide resistance to 3'-exonuclease using capillary electrophoresis. JOURNAL OF CHROMATOGRAPHY. B, BIOMEDICAL SCIENCES AND APPLICATIONS 1998; 714:13-20. [PMID: 9746230 DOI: 10.1016/s0378-4347(98)00160-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The effect of phosphorothioate (PS) internucleotide linkages on the stability of phosphodiester oligodeoxyribonucleotides (ODNs) was investigated using 25-mer ODNs containing single or multiple PS backbone modifications. The in vitro stability of the oligomers was measured both in 3'-exonuclease solution and in plasma. For the separation of ODNs, capillary electrophoresis with a replaceable polymer separation matrix was used. As expected, DNA fragments with PS linkages at the 3'-end were found to be more resistant to 3'-exonuclease hydrolysis. Also increasing exonuclease resistance was the non-specific adsorption of phosphorothioate ODNs to enzyme.
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Affiliation(s)
- M Gilar
- Hybridon, Inc., Cambridge, MA 02139, USA
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Srivastava RK, Srivastava AR, Park YG, Agrawal S, Cho-Chung YS. Antisense depletion of RIalpha subunit of protein kinase A induces apoptosis and growth arrest in human breast cancer cells. Breast Cancer Res Treat 1998; 49:97-107. [PMID: 9696392 DOI: 10.1023/a:1005905723550] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In recent years, several laboratories have explored the possibility of using antisense oligodeoxynucleotides for specific manipulation of gene expression leading to cancer treatment. The enhanced expression of the RIalpha subunit of cyclic AMP-dependent protein kinase type I (PKA-I) has been correlated with cancer cell growth. In the present study, the effects of an antisense oligodeoxynucleotide targeted against RIalpha subunit of PKA-I on growth inhibition and apoptosis in MDA-MB-231 human breast cancer cells were investigated. The growth inhibitory effects of RIalpha antisense oligodeoxynucleotide correlated with a decrease in the RIalpha mRNA and protein levels. The growth inhibition was accompanied by changes in the cell cycle phase distribution, cell morphology, cleavage of poly (ADP-ribose) polymerase (PARP), and appearance of apoptotic nuclei. By comparison, mismatched control oligodeoxynucleotide had no effect. On the basis of these results, it can be suggested that the RIalpha antisense oligodeoxynucleotide, which efficiently depletes the growth stimulatory RIalpha and induces apoptosis/differentiation, could be used as a therapeutic agent for breast cancer treatment.
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Affiliation(s)
- R K Srivastava
- Cellular Biochemistry Section, Laboratory of Tumor and Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Nicklin PL, Bayley D, Giddings J, Craig SJ, Cummins LL, Hastewell JG, Phillips JA. Pulmonary bioavailability of a phosphorothioate oligonucleotide (CGP 64128A): comparison with other delivery routes. Pharm Res 1998; 15:583-91. [PMID: 9587955 DOI: 10.1023/a:1011934011690] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
PURPOSE Phosphorothioate antisense oligodeoxynucleotides are promising therapeutic candidates. When given systemically in clinical trials they are administered via slow intravenous infusion to avoid their putative plasma concentration-dependent haemodynamic side-effects. In this study, we have evaluated alternative parenteral and non-parenteral administration routes which have the potential to enhance the therapeutic and commercial potential of these agents. METHODS The delivery of CGP 64128A by intravenous, subcutaneous, intra-peritoneal, oral and intra-tracheal (pulmonary) routes was investigated in rats using radiolabelled compound and supported by more specific capillary gel electrophoretic analyses. RESULTS Intravenously administered CGP 64128A exhibited the rapid blood clearance and distinctive tissue distribution which are typical for phosphorothioate oligodeoxynucleotides. Subcutaneous and intraperitoneal administration resulted in significant bioavailabilities (30.9% and 28.1% over 360 min, respectively) and reduced peak plasma levels when compared with intravenous dosing. Administration via the gastrointestinal tract gave negligible bioavailability (< 2%). Intra-tracheal administration resulted in significant but dose-dependent bioavailabilities of 3.2, 16.5 and 39.8% at 0.06, 0.6 and 6.0 mg/kg, respectively. CONCLUSIONS Significant bioavailabilities of CGP 64128A were achieved following subcutaneous, intra-peritoneal and intra-tracheal administration. Pulmonary delivery represents a promising mode of non-parenteral dosing for antisense oligonucleotides. The dose-dependent increase in pulmonary bioavailability suggests that low doses may be retained in the lungs for local effects whereas higher doses may be suitable for the treatment of a broader spectrum of systemic diseases.
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Affiliation(s)
- P L Nicklin
- Novartis Horsham Research Centre, Horsham, West Sussex, UK.
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Broaddus WC, Prabhu SS, Gillies GT, Neal J, Conrad WS, Chen ZJ, Fillmore H, Young HF. Distribution and stability of antisense phosphorothioate oligonucleotides in rodent brain following direct intraparenchymal controlled-rate infusion. J Neurosurg 1998; 88:734-42. [PMID: 9525721 DOI: 10.3171/jns.1998.88.4.0734] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
OBJECT High-flow microinfusion is a novel technique for delivery of compounds directly into brain parenchyma, bypassing the blood-brain barrier. The feasibility of this technique has been demonstrated with low-molecular-weight compounds, macromolecular dyes, and proteins. Delivery of antisense oligonucleotides into brain parenchyma represents an additional potential application of this technique not previously described. In this report the authors sought to examine the distribution and disposition of phosphorothioate oligodeoxynucleotide (PS-ODN) for this reason. METHODS An 18-mer 35S-PS-ODN (Mr approximately 6000) was infused over 1 hour into the caudate putamen of Fischer 344 rats. At 1, 6, 12, 24, and 48 hours after beginning the infusion, the brains were extracted and analyzed using quantitative autoradiographic techniques. Cerebrospinal fluid (CSF) was also aspirated from the cisterna magna and was analyzed to determine the radioactivity and stability of the 35S-PS-ODN. At 1 hour, the infused ODN was uniformly distributed in brain tissue, with a maximum average concentration of 4806.5 +/- 210.5 nCi/g. This represents a tissue concentration of 19.2 +/- 0.84 microM. Extensive spread into surrounding parenchyma was observed over the ensuing 47 hours. The 35S-PS-ODN radioactivity peaked in the CSF at the end of the 1-hour infusion, containing 1% (50 +/- 20 nCi) of the infused radioactivity. Activity then decayed exponentially over 11 hours, but stabilized at a lower CSF content of 0.2% (1 +/- 0.1 nCi) thereafter. The volume of distribution was 105 +/- 7.9 mm3 at 1 hour, representing a volume of distribution/volume of infusion ratio of 5.2. The volume of distribution increased to 443 +/- 62.3 mm3 at the end of 48 hours, whereas the average minimum tissue concentration decreased from 15.2 microM to 3.2 microM. Undegraded 18-mer was observed throughout the 48-hour period by means of 20% polyacrylamide/7 M urea gel electrophoresis. The animals tolerated the infusion without evidence of toxicity and minimal structural changes in tissue were observed on histological investigation. CONCLUSIONS The authors found that PS-ODNs can be safely delivered in high concentrations to wide areas of rat brain by using high-flow microinfusion and are stable even after 48 hours in situ.
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Affiliation(s)
- W C Broaddus
- Division of Neurosurgery, Medical College of Virginia, Virginia Commonwealth University, Richmond 23298-0631, USA
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Takakura Y, Oka Y, Hashida M. Cellular uptake properties of oligonucleotides in LLC-PK1 renal epithelial cells. ANTISENSE & NUCLEIC ACID DRUG DEVELOPMENT 1998; 8:67-73. [PMID: 9512098 DOI: 10.1089/oli.1.1998.8.67] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The objective of this study was to clarify the renal uptake characteristics of oligonucleotides at a cellular level using LLC-PK1 renal epithelial cells derived from the proximal tubule. The association of [35S]-labeled 20-mer phosphodiester (PO) and phosphorothioate (PS) oligonucleotides with the monolayers of polarized LLC-PK1 cells cultured on polycarbonate filter was characterized after apical or basolateral application. The cellular association of PO and PS at both apical and basolateral membranes was time dependent and temperature dependent, and the apparent association amount of PS was larger than that of PO. The PO and PS association after apical application was saturable, with the apparent Km and Vmax values determined to be 5.4 microM and 0.14 nmol/mg protein for PO and 0.22 microM and 0.11 nmol/mg protein for PS, respectively. In contrast, almost linear kinetics were observed after basolateral application within a tested concentration range. The association was inhibited significantly by sodium azide and chloroquine, suggesting that an energy-dependent endocytotic process was involved. Internalization and subsequent transport to endosome and lysosome compartments of FITC-labeled oligonucleotides were shown by confocal laser scanning microscopy. The present study has demonstrated that both types of oligonucleotides are taken up by LLC-PK1 cells from both apical and basolateral surfaces probably via an endocytosis mechanism.
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Affiliation(s)
- Y Takakura
- Department of Drug Delivery Research, Graduate School of Pharmaceutical Sciences, Kyoto University, Japan
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Grindel JM, Musick TJ, Jiang Z, Roskey A, Agrawal S. Pharmacokinetics and metabolism of an oligodeoxynucleotide phosphorothioate (GEM91) in cynomolgus monkeys following intravenous infusion. ANTISENSE & NUCLEIC ACID DRUG DEVELOPMENT 1998; 8:43-52. [PMID: 9512095 DOI: 10.1089/oli.1.1998.8.43] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The pharmacokinetics and metabolism of an antisense oligonucleotide phosphorothioate (GEM91) were studied in cynomolgus monkeys following intravenous infusion. [35S]-Labeled GEM91 was administered to 12 monkeys by means of a 2-hour intravenous infusion at a dose of 4 mg/kg. Plasma pharmacokinetic analysis revealed that the maximum plasma concentration was 41.7 microg equivalents/ml, which was achieved in 2.13 hours. The plasma elimination half-life was 55.8 hours based on radioactivity levels. Urinary excretion represented the major pathway of elimination, with 70% of the administered dose excreted in urine over 240 hours. The oligonucleotide was widely distributed to tissues. The highest concentrations were observed in the liver and kidney. Analysis of the extracted oligonucleotide following post-labeling with [32p] on polyacrylamide gel electrophoresis showed the presence of both intact and degraded oligonucleotide in plasma, kidney, liver, spleen, and lymph nodes. Based on the methods used for post-labeling (either 3'-end or 5'-end), different patterns of bands were observed on polyacrylamide gel electrophoresis, suggesting metabolic modification of the administered oligonucleotide.
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Agrawal S, Zhang R. Pharmacokinetics of oligonucleotides. CIBA FOUNDATION SYMPOSIUM 1998; 209:60-75; discussion 75-8. [PMID: 9383569 DOI: 10.1002/9780470515396.ch6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The effectiveness of antisense oligonucleotides as therapeutic agents depends on their pharmacokinetics, tissue disposition, stability, elimination and safety profile. Pharmacokinetic data allow one to determine the frequency of administration and any potential toxicity associated with chronic administration. Phosphorothioate oligonucleotides degrade from the 3' end, the 5' end, and both the 3' and 5' ends in a time- and tissue-dependent manner. After intravenous administration in mice, rats and monkeys, phosphorothioate oligonucleotides are detected in plasma; they distribute rapidly and are retained in the majority of tissues. The major route of elimination is the urine. The pharmacokinetic profile is similar following subcutaneous, intradermal or intraperitoneal administration, but with lower maximum plasma concentrations. Phosphorothioate oligonucleotides have a short plasma half-life in humans. End-modified, mixed-backbone oligonucleotides (MBOs) contain nuclease-resistant 2'-O-alkylribonucleotides or methylphosphonate internucleotide linkages at both the 3' and 5' ends of phosphorothioate oligonucleotides. These end-modified MBOs have pharmacokinetic profiles similar to those of the parent phosphorothioate oligonucleotides, but they are significantly more stable in vivo and they can be administered orally. Centrally modified MBOs contain modified RNA or DNA in the centre of a phosphorothioate oligonucleotide. They show controlled degradation and elimination following administration in rats. The pharmacokinetics of antisense oligonucleotides depends on the sequence, the nature of the oligonucleotide linkages and the secondary structure.
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Affiliation(s)
- S Agrawal
- Hybridon Inc., Cambridge, MA 02139, USA
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Barker RH, Metelev V, Coakley A, Zamecnik P. Plasmodium falciparum: effect of chemical structure on efficacy and specificity of antisense oligonucleotides against malaria in vitro. Exp Parasitol 1998; 88:51-9. [PMID: 9501848 DOI: 10.1006/expr.1998.4192] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Antisense oligodeoxynucleotides (AS ODNs) have shown promise both as potential anti-malarial chemotherapeutic agents and as a means for identifying genes critical for parasite survival. Because conventional ODNs containing phosphodiester (PO) groups are subject to rapid nuclease degradation, ODNs with phosphorothioate (PS) groups are commonly used. However, at high concentration, these lose target specificity, and in some animal models, they become toxic. We compared a variety of chemical modifications (PO, PS, PO-PS hybrids, 2'-O-methyl-2'-deoxy chimeras) and structural modifications (sequence alterations favoring self-stabilizing loop formation) for their ability to inhibit Plasmodium falciparum malaria cultured in vitro. All modifications were done using an AS ODN sequence targeted against dihydrofolate reductase thymidylate synthase (DHFR). Inhibition by PO-PS hybrids containing as few as three PS groups at the 3'- and 5'-ends did not differ significantly from that obtained using compounds containing all-PS groups. Similarly, inhibition by PS chimeric compounds containing 2'-O-methyl modifications did not differ significantly from that of conventional PS compounds. In contrast, while inhibition by PO-PS hybrid chimeras did not differ significantly from that of all-PS compounds at low concentrations, at 1 microM they inhibited parasite growth 25% less (P < 0.001) than all-compounds or PS 2'-O-methyl-2'-deoxy chimeras. Extension of the nucleotide sequence to increase stem-loop formation yielded two compounds which inhibited parasite growth about 20% more than unmodified compounds, though this difference was not significant. Furthermore, most of this increase appears to correlate with the greater number of PS groups associated with the increased ODN length. We conclude that limiting the number of PS groups and inclusion of PO 2'-O-methyl groups may yield compounds with high antisense activity but low non-sequence-dependent effects. Such compounds are currently being tested in vivo.
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Affiliation(s)
- R H Barker
- Hybridon, Inc., Worcester, Massachusetts 01605, USA
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Abstract
Antisense oligonucleotides are widely used as tools to explore the pharmacological effects of inhibiting expression of a selected gene product. In addition, they are being investigated as therapeutic agents for the treatment of viral infections, cancers, and inflammatory disorders. Proof that the pharmacological effects produced by the oligonucleotides are attributable to an antisense mechanism of action requires careful experimentation. Central to this problem is the finding that oligonucleotides are capable of interacting with and modulating function of specific proteins in both a sequence-independent and -dependent manner. Despite these undesired interactions, it has been possible to demonstrate that oligonucleotides are capable of binding to a specific RNA in cultured cells, or within tissues, resulting in selective reduction of the targeted gene product and pharmacological activity. In general, these oligonucleotides were identified after a selection process in which multiple oligonucleotides targeting different regions on the RNA were evaluated for direct inhibition of targeted gene product, resulting in the identification of a potent and selective oligonucleotide. Similar to other drug-receptor interactions, selection of the most potent inhibitor results in an increase in the signal-to-noise ratio, yielding increased confidence that activity observed is the result of a desired effect of the inhibitor. With careful selection, proper controls, and careful dose-response curves it is possible to utilize antisense oligonucleotides as effective research tools and potentially as therapeutic agents.
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Affiliation(s)
- C F Bennett
- ISIS Pharmaceuticals, Carlsbad, CA 92008, USA
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Agrawal S, Zhao Q, Jiang Z, Oliver C, Giles H, Heath J, Serota D. Toxicologic effects of an oligodeoxynucleotide phosphorothioate and its analogs following intravenous administration in rats. ANTISENSE & NUCLEIC ACID DRUG DEVELOPMENT 1997; 7:575-84. [PMID: 9450915 DOI: 10.1089/oli.1.1997.7.575] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The aim of the present study is to evaluate the in vivo toxicologic effects of a phosphorothioate oligodeoxynucleotide (PS oligo) and three of its analogs [PS oligo containing four methylphosphonate linkages at the 3' and 5'-ends (MBO 1), PS oligo containing four 2'-O-methylribonucleosides at both the 3'- and 5'-ends (MBO 2), and PS oligo containing an 8 bp loop region at the 3'-end (self-stabilized oligo)]. Oligodeoxynucleotides were administrated intravenously to male and female rats at doses of 3, 10, and 30 mg/kg/day for 14 days. Rats were killed on day 15, blood samples were collected for hematology and clinical chemistry determinations, and tissues, including lymph nodes, spleens, livers, and kidneys, were subjected to pathologic examinations. The toxicity profiles of the four oligodeoxynucleotides were very similar, but differed in magnitude. In terms of the severity of the abnormalities caused by the oligodeoxynucleotides, the order was MBO 2 > PS oligo > self-stabilized oligo > MBO 1. Alterations in hematology parameters included thrombocytopenia, anemia, and neutropenia. Abnormalities in clinical chemistry parameters observed with PS oligo or MBO 2 were dose-dependent elevation of liver transaminases and reduction of the levels of alkaline phosphatase, albumin, and total protein. In addition, MBO 2 caused elevation of the total bilirubin level in male rats at the 30 mg/kg dose. No major alterations in hematology or clinical chemistry were observed in rats receiving MBO 1 or self-stabilized oligo. Dose-dependent enlargements of spleen, liver, and kidney were observed, especially in rats receiving PS oligo and MBO 2. Pathologic studies showed a generalized hyperplasia of the reticuloendothelial (RE) system in the tissues examined. Alterations in the spleen were mainly RE cell hyperplasia and hematopoietic cell proliferation. In addition to RE cell hyperplasia, lymph nodes showed necrosis, hepatocytes showed cytologic alterations and necrosis, and kidneys showed renal tubule regeneration. The severity of pathologic changes observed was oligodeoxynucleotide dependent, in the order of MBO 2 > PS oligo > self-stabilized oligo > MBO 1.
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Affiliation(s)
- S Agrawal
- Hybridon, Inc., Cambridge, MA 02139, USA
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