1
|
Wortham M, Ramms B, Zeng C, Benthuysen JR, Sai S, Pollow DP, Liu F, Schlichting M, Harrington AR, Liu B, Prakash TP, Pirie EC, Zhu H, Baghdasarian S, Auwerx J, Shirihai OS, Sander M. Metabolic control of adaptive β-cell proliferation by the protein deacetylase SIRT2. bioRxiv 2024:2024.02.24.581864. [PMID: 38464227 PMCID: PMC10925077 DOI: 10.1101/2024.02.24.581864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Selective and controlled expansion of endogenous β-cells has been pursued as a potential therapy for diabetes. Ideally, such therapies would preserve feedback control of β-cell proliferation to avoid excessive β-cell expansion and an increased risk of hypoglycemia. Here, we identified a regulator of β-cell proliferation whose inactivation results in controlled β-cell expansion: the protein deacetylase Sirtuin 2 (SIRT2). Sirt2 deletion in β-cells of mice increased β-cell proliferation during hyperglycemia with little effect in homeostatic conditions, indicating preservation of feedback control of β-cell mass. SIRT2 restrains proliferation of human islet β-cells cultured in glucose concentrations above the glycemic set point, demonstrating conserved SIRT2 function. Analysis of acetylated proteins in islets treated with a SIRT2 inhibitor revealed that SIRT2 deacetylates enzymes involved in oxidative phosphorylation, dampening the adaptive increase in oxygen consumption during hyperglycemia. At the transcriptomic level, Sirt2 inactivation has context-dependent effects on β-cells, with Sirt2 controlling how β-cells interpret hyperglycemia as a stress. Finally, we provide proof-of-principle that systemic administration of a GLP1-coupled Sirt2-targeting antisense oligonucleotide achieves β-cell selective Sirt2 inactivation and stimulates β-cell proliferation under hyperglycemic conditions. Overall, these studies identify a therapeutic strategy for increasing β-cell mass in diabetes without circumventing feedback control of β-cell proliferation.
Collapse
Affiliation(s)
- Matthew Wortham
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center, University of California San Diego, La Jolla, CA, USA
| | - Bastian Ramms
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center, University of California San Diego, La Jolla, CA, USA
| | - Chun Zeng
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center, University of California San Diego, La Jolla, CA, USA
| | - Jacqueline R. Benthuysen
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center, University of California San Diego, La Jolla, CA, USA
| | - Somesh Sai
- Institute of Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Dennis P. Pollow
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center, University of California San Diego, La Jolla, CA, USA
| | - Fenfen Liu
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center, University of California San Diego, La Jolla, CA, USA
| | - Michael Schlichting
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center, University of California San Diego, La Jolla, CA, USA
| | - Austin R. Harrington
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center, University of California San Diego, La Jolla, CA, USA
| | - Bradley Liu
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center, University of California San Diego, La Jolla, CA, USA
| | - Thazha P. Prakash
- Department of Antisense Drug Discovery, Ionis Pharmaceuticals Inc., Carlsbad, CA, USA
| | - Elaine C Pirie
- Department of Antisense Drug Discovery, Ionis Pharmaceuticals Inc., Carlsbad, CA, USA
| | - Han Zhu
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center, University of California San Diego, La Jolla, CA, USA
| | - Siyouneh Baghdasarian
- Departments of Medicine and Molecular & Medical Pharmacology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Johan Auwerx
- Laboratory of Integrated Systems Physiology, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Orian S. Shirihai
- Departments of Medicine and Molecular & Medical Pharmacology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Maike Sander
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center, University of California San Diego, La Jolla, CA, USA
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| |
Collapse
|
2
|
Neumayer C, Ng D, Requena D, Jiang CS, Qureshi A, Vaughan R, Prakash TP, Revenko A, Simon SM. GalNAc-conjugated siRNA targeting the DNAJB1-PRKACA fusion junction in fibrolamellar hepatocellular carcinoma. Mol Ther 2024; 32:140-151. [PMID: 37980543 PMCID: PMC10787139 DOI: 10.1016/j.ymthe.2023.11.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 10/12/2023] [Accepted: 11/09/2023] [Indexed: 11/20/2023] Open
Abstract
Fibrolamellar hepatocellular carcinoma (FLC) is a rare liver cancer caused by a dominant recurrent fusion of the heat shock protein (DNAJB1) and the catalytic subunit of protein kinase A (PRKACA). Current therapies such as chemotherapy and radiation have limited efficacy, and new treatment options are needed urgently. We have previously shown that FLC tumors are dependent on the fusion kinase DNAJB1::PRKACA, making the oncokinase an ideal drug target. mRNA degrading modalities such as antisense oligonucleotides or small interfering RNAs (siRNAs) provide an opportunity to specifically target the fusion junction. Here, we identify a potent and specific siRNA that inhibits DNAJB1::PRKACA expression. We found expression of the asialoglycoprotein receptor in FLC to be maintained at sufficient levels to effectively deliver siRNA conjugated to the GalNAc ligand. We observe productive uptake and siRNA activity in FLC patient-derived xenografts (PDX) models in vitro and in vivo. Knockdown of DNAJB1::PRKACA results in durable growth inhibition of FLC PDX in vivo with no detectable toxicities. Our results suggest that this approach could be a treatment option for FLC patients.
Collapse
Affiliation(s)
- Christoph Neumayer
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, NY, USA
| | - Denise Ng
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, NY, USA
| | - David Requena
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, NY, USA
| | - Caroline S Jiang
- Hospital Biostatistics, The Rockefeller University, New York, NY, USA
| | - Adam Qureshi
- Hospital Biostatistics, The Rockefeller University, New York, NY, USA
| | - Roger Vaughan
- Hospital Biostatistics, The Rockefeller University, New York, NY, USA
| | | | | | - Sanford M Simon
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, NY, USA.
| |
Collapse
|
3
|
Gurlo T, Prakash TP, Wang Z, Archang M, Pei L, Rosenberger M, Pirie E, Lee RG, Butler PC. Efficacy of IAPP suppression in mouse and human islets by GLP-1 analogue conjugated antisense oligonucleotide. Front Mol Biosci 2023; 10:1096286. [PMID: 36814640 PMCID: PMC9939749 DOI: 10.3389/fmolb.2023.1096286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 01/20/2023] [Indexed: 02/09/2023] Open
Abstract
Insulin resistance is the major risk factor for Type 2 diabetes (T2D). In vulnerable individuals, insulin resistance induces a progressive loss of insulin secretion with islet pathology revealing a partial deficit of beta cells and islet amyloid derived from islet amyloid polypeptide (IAPP). IAPP is co-expressed and secreted with insulin by beta cells, expression of both proteins being upregulated in response to insulin resistance. If IAPP expression exceeds the threshold for clearance of misfolded proteins, beta cell failure occurs exacerbated by the action of IAPP toxicity to compromise the autophagy lysosomal pathway. We postulated that suppression of IAPP expression by an IAPP antisense oligonucleotide delivered to beta cells by the GLP-1 agonist exenatide (eGLP1-IAPP-ASO) is a potential disease modifying therapy for T2D. While eGLP1-IAPP-ASO suppressed mouse IAPP and transgenic human IAPP expression in mouse islets, it had no discernable effects on IAPP expression in human islets under the conditions studied. Suppression of transgenic human IAPP expression in mouse islets attenuated disruption of the autophagy lysosomal pathway in beta cells, supporting the potential of this strategy.
Collapse
Affiliation(s)
- Tatyana Gurlo
- Larry L. Hillblom Islet Research Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States,*Correspondence: Tatyana Gurlo, ; Peter C. Butler,
| | | | - Zhongying Wang
- Larry L. Hillblom Islet Research Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Maani Archang
- Larry L. Hillblom Islet Research Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Lina Pei
- Larry L. Hillblom Islet Research Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Madeline Rosenberger
- Larry L. Hillblom Islet Research Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Elaine Pirie
- IONIS Pharmaceuticals, Carlsbad, CA, United States
| | | | - Peter C. Butler
- Larry L. Hillblom Islet Research Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States,*Correspondence: Tatyana Gurlo, ; Peter C. Butler,
| |
Collapse
|
4
|
Li Y, Li J, Wang J, Zhang S, Giles K, Prakash TP, Rigo F, Napierala JS, Napierala M. Premature transcription termination at the expanded GAA repeats and aberrant alternative polyadenylation contributes to the Frataxin transcriptional deficit in Friedreich's ataxia. Hum Mol Genet 2022; 31:3539-3557. [PMID: 35708503 PMCID: PMC9558844 DOI: 10.1093/hmg/ddac134] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/12/2022] [Accepted: 06/05/2022] [Indexed: 11/18/2022] Open
Abstract
Frataxin deficiency in Friedreich's ataxia results from transcriptional downregulation of the FXN gene caused by expansion of the intronic trinucleotide guanine-adenine-adenine (GAA) repeats. We used multiple transcriptomic approaches to determine the molecular mechanism of transcription inhibition caused by long GAAs. We uncovered that transcription of FXN in patient cells is prematurely terminated upstream of the expanded repeats leading to the formation of a novel, truncated and stable RNA. This FXN early terminated transcript (FXN-ett) undergoes alternative, non-productive splicing and does not contribute to the synthesis of functional frataxin. The level the FXN-ett RNA directly correlates with the length of the longer of the two expanded GAA tracts. Targeting GAAs with antisense oligonucleotides or excision of the repeats eliminates the transcription impediment, diminishes expression of the aberrant FXN-ett, while increasing levels of FXN mRNA and frataxin. Non-productive transcription may represent a common phenomenon and attractive therapeutic target in diseases caused by repeat-mediated transcription aberrations.
Collapse
Affiliation(s)
- Yanjie Li
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, 1825 University Blvd., Birmingham, AL 35294, USA
| | - Jixue Li
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, 1825 University Blvd., Birmingham, AL 35294, USA
| | - Jun Wang
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, 1825 University Blvd., Birmingham, AL 35294, USA
| | - Siyuan Zhang
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, 1825 University Blvd., Birmingham, AL 35294, USA
| | - Keith Giles
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, 1825 University Blvd., Birmingham, AL 35294, USA
| | - Thazha P Prakash
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Frank Rigo
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Jill S Napierala
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, 1825 University Blvd., Birmingham, AL 35294, USA
- Department of Neurology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Marek Napierala
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, 1825 University Blvd., Birmingham, AL 35294, USA
- Department of Neurology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| |
Collapse
|
5
|
Kuo C, Nikan M, Yeh ST, Chappell AE, Tanowitz M, Seth PP, Prakash TP, Mullick AE. Targeted Delivery of Antisense Oligonucleotides Through Angiotensin Type 1 Receptor. Nucleic Acid Ther 2022; 32:300-311. [PMID: 35612431 DOI: 10.1089/nat.2021.0105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We evaluated the potential of AGTR1, the principal receptor for angiotensin II (Ang II) and a member of the G protein-coupled receptor family, for targeted delivery of antisense oligonucleotides (ASOs) in cells and tissues with abundant AGTR1 expression. Ang II peptide ASO conjugates maintained robust AGTR1 signaling and receptor internalization when ASO was placed at the N-terminus of the peptide, but not at C-terminus. Conjugation of Ang II peptide improved ASO potency up to 12- to 17-fold in AGTR1-expressing cells. Additionally, evaluation of Ang II conjugates in cells lacking AGTR1 revealed no enhancement of ASO potency. Ang II peptide conjugation improves potency of ASO in mouse heart, adrenal, and adipose tissues. The data presented in this report add to a growing list of approaches for improving ASO potency in extrahepatic tissues.
Collapse
Affiliation(s)
- Carol Kuo
- Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Mehran Nikan
- Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Steve T Yeh
- Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | | | | | - Punit P Seth
- Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | | | | |
Collapse
|
6
|
Yong J, Parekh VS, Reilly SM, Nayak J, Chen Z, Lebeaupin C, Jang I, Zhang J, Prakash TP, Sun H, Murray S, Guo S, Ayala JE, Satin LS, Saltiel AR, Kaufman RJ. Chop/ Ddit3 depletion in β cells alleviates ER stress and corrects hepatic steatosis in mice. Sci Transl Med 2021; 13:13/604/eaba9796. [PMID: 34321322 DOI: 10.1126/scitranslmed.aba9796] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 04/07/2021] [Accepted: 06/23/2021] [Indexed: 12/21/2022]
Abstract
Type 2 diabetes (T2D) is a metabolic disorder characterized by hyperglycemia, hyperinsulinemia, and insulin resistance (IR). During the early phase of T2D, insulin synthesis and secretion by pancreatic β cells is enhanced, which can lead to proinsulin misfolding that aggravates endoplasmic reticulum (ER) protein homeostasis in β cells. Moreover, increased circulating insulin may contribute to fatty liver disease. Medical interventions aimed at alleviating ER stress in β cells while maintaining optimal insulin secretion are therefore an attractive therapeutic strategy for T2D. Previously, we demonstrated that germline Chop gene deletion preserved β cells in high-fat diet (HFD)-fed mice and in leptin receptor-deficient db/db mice. In the current study, we further investigated whether targeting Chop/Ddit3 specifically in murine β cells conferred therapeutic benefits. First, we showed that Chop deletion in β cells alleviated β cell ER stress and delayed glucose-stimulated insulin secretion (GSIS) in HFD-fed mice. Second, β cell-specific Chop deletion prevented liver steatosis and hepatomegaly in aged HFD-fed mice without affecting basal glucose homeostasis. Third, we provide mechanistic evidence that Chop depletion reduces ER Ca2+ buffering capacity and modulates glucose-induced islet Ca2+ oscillations, leading to transcriptional changes of ER chaperone profile ("ER remodeling"). Last, we demonstrated that a GLP1-conjugated Chop antisense oligonucleotide strategy recapitulated the reduction in liver triglycerides and pancreatic insulin content. In summary, our results demonstrate that Chop depletion in β cells provides a therapeutic strategy to alleviate dysregulated insulin secretion and consequent fatty liver disease in T2D.
Collapse
Affiliation(s)
- Jing Yong
- Division of Metabolism and Endocrinology, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA. .,Degenerative Diseases Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Rd., La Jolla, CA 92037, USA
| | - Vishal S Parekh
- Degenerative Diseases Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Rd., La Jolla, CA 92037, USA.,Department of Pharmacology, University of Michigan Medical School, 1000 Wall St., Ann Arbor, MI 48105, USA
| | - Shannon M Reilly
- Department of Pharmacology, University of Michigan Medical School, 1000 Wall St., Ann Arbor, MI 48105, USA.,Division of Metabolism and Endocrinology, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Jonamani Nayak
- Division of Metabolism and Endocrinology, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA.,Degenerative Diseases Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Rd., La Jolla, CA 92037, USA
| | - Zhouji Chen
- Division of Metabolism and Endocrinology, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA.,Degenerative Diseases Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Rd., La Jolla, CA 92037, USA
| | - Cynthia Lebeaupin
- Division of Metabolism and Endocrinology, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA.,Department of Pharmacology, University of Michigan Medical School, 1000 Wall St., Ann Arbor, MI 48105, USA.,Degenerative Diseases Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Rd., La Jolla, CA 92037, USA.,Division of Metabolism and Endocrinology, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Insook Jang
- Division of Metabolism and Endocrinology, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA.,Degenerative Diseases Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Rd., La Jolla, CA 92037, USA
| | - Jiangwei Zhang
- Cardiometabolic Phenotyping Core, Sanford-Burnham Medical Research Institute, 6400 Sanger Road, Orlando, FL 32827, USA.,Department of Antisense Drug Discovery, Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Thazha P Prakash
- Cardiometabolic Phenotyping Core, Sanford-Burnham Medical Research Institute, 6400 Sanger Road, Orlando, FL 32827, USA.,Department of Antisense Drug Discovery, Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Hong Sun
- Cardiometabolic Phenotyping Core, Sanford-Burnham Medical Research Institute, 6400 Sanger Road, Orlando, FL 32827, USA.,Department of Antisense Drug Discovery, Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Sue Murray
- Cardiometabolic Phenotyping Core, Sanford-Burnham Medical Research Institute, 6400 Sanger Road, Orlando, FL 32827, USA.,Department of Antisense Drug Discovery, Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Shuling Guo
- Cardiometabolic Phenotyping Core, Sanford-Burnham Medical Research Institute, 6400 Sanger Road, Orlando, FL 32827, USA.,Department of Antisense Drug Discovery, Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Julio E Ayala
- Department of Molecular Physiology & Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.,Cardiometabolic Phenotyping Core, Sanford-Burnham Medical Research Institute, 6400 Sanger Road, Orlando, FL 32827, USA.,Department of Molecular Physiology & Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Leslie S Satin
- Degenerative Diseases Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Rd., La Jolla, CA 92037, USA.,Department of Pharmacology, University of Michigan Medical School, 1000 Wall St., Ann Arbor, MI 48105, USA
| | - Alan R Saltiel
- Department of Pharmacology, University of Michigan Medical School, 1000 Wall St., Ann Arbor, MI 48105, USA.,Division of Metabolism and Endocrinology, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA.,Department of Pharmacology, University of California San Diego, La Jolla, CA 92093, USA
| | - Randal J Kaufman
- Degenerative Diseases Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Rd., La Jolla, CA 92037, USA.
| |
Collapse
|
7
|
Prakash TP, Yu J, Shen W, De Hoyos CL, Berdeja A, Gaus H, Liang XH, Crooke ST, Seth PP. Site-specific Incorporation of 2',5'-Linked Nucleic Acids Enhances Therapeutic Profile of Antisense Oligonucleotides. ACS Med Chem Lett 2021; 12:922-927. [PMID: 34141070 DOI: 10.1021/acsmedchemlett.1c00072] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 04/01/2021] [Indexed: 12/30/2022] Open
Abstract
Site-specific incorporation of 2'-modifications and neutral linkages in the deoxynucleotide gap region of toxic phosphorothioate (PS) gapmer ASOs can enhance therapeutic index and safety. In this manuscript, we determined the effect of introducing 2',5'-linked RNA in the deoxynucleotide gap region on toxicity and potency of PS ASOs. Our results demonstrate that incorporation of 2',5'-linked RNA in the gap region dramatically improved hepatotoxicity profile of PS-ASOs without compromising potency and provide a novel alternate chemical approach for improving therapeutic index of ASO drugs.
Collapse
Affiliation(s)
- Thazha P. Prakash
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Jinghua Yu
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Wen Shen
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Cheryl Li De Hoyos
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Andres Berdeja
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Hans Gaus
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Xue-hai Liang
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Stanley T. Crooke
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Punit P. Seth
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, California 92010, United States
| |
Collapse
|
8
|
Knerr L, Prakash TP, Lee R, Drury Iii WJ, Nikan M, Fu W, Pirie E, Maria LD, Valeur E, Hayen A, Ölwegård-Halvarsson M, Broddefalk J, Ämmälä C, Østergaard ME, Meuller J, Sundström L, Andersson P, Janzén D, Jansson-Löfmark R, Seth PP, Andersson S. Glucagon Like Peptide 1 Receptor Agonists for Targeted Delivery of Antisense Oligonucleotides to Pancreatic Beta Cell. J Am Chem Soc 2021; 143:3416-3429. [PMID: 33626278 DOI: 10.1021/jacs.0c12043] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The extra hepatic delivery of antisense oligonucleotides (ASOs) remains a challenge and hampers the widespread application of this powerful class of therapeutic agents. In that regard, pancreatic beta cells are a particularly attractive but challenging cell type because of their pivotal role in diabetes and the fact that they are refractory to uptake of unconjugated ASOs. To circumvent this, we have expanded our understanding of the structure activity relationship of ASOs conjugated to Glucagon Like Peptide 1 Receptor (GLP1R) agonist peptide ligands. We demonstrate the key role of the linker chemistry and its optimization to design maleimide based conjugates with improved in vivo efficacy. In addition, truncation studies and scoping of a diverse set of GLP1R agonists proved fruitful to identify additional targeting ligands efficacious in vivo including native hGLP1(7-36)NH2. Variation of the carrier peptide also shed some light on the dramatic impact of subtle sequence differences on the corresponding ASO conjugate performance in vivo, an area which clearly warrant further investigations. We have confirmed the remarkable potential of GLP1R agonist conjugation for the delivery of ASOs to pancreatic beta cell by effectively knocking down islet amyloid polypeptide (IAPP) mRNA, a potential proapoptotic target, in mice.
Collapse
Affiliation(s)
- Laurent Knerr
- Medicinal Chemistry, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Thazha P Prakash
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Richard Lee
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - William J Drury Iii
- Medicinal Chemistry, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Mehran Nikan
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Wuxia Fu
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Elaine Pirie
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Leonardo De Maria
- Medicinal Chemistry, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Eric Valeur
- Medicinal Chemistry, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Ahlke Hayen
- Medicinal Chemistry, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Maria Ölwegård-Halvarsson
- Medicinal Chemistry, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Johan Broddefalk
- Medicinal Chemistry, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Carina Ämmälä
- Bioscience, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Michael E Østergaard
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Johan Meuller
- Mechanistic Biology & Profiling, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Linda Sundström
- Mechanistic Biology & Profiling, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Patrik Andersson
- Respiratory and Immunology Safety, Clinical Pharmacology & Safety Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - David Janzén
- DMPK, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Rasmus Jansson-Löfmark
- DMPK, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Punit P Seth
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Shalini Andersson
- Research and early Development, Discovery Sciences,, AstraZeneca, Gothenburg, Sweden
| |
Collapse
|
9
|
Vasquez G, Freestone GC, Wan WB, Low A, De Hoyos CL, Yu J, Prakash TP, Ǿstergaard ME, Liang XH, Crooke ST, Swayze EE, Migawa MT, Seth PP. Site-specific incorporation of 5'-methyl DNA enhances the therapeutic profile of gapmer ASOs. Nucleic Acids Res 2021; 49:1828-1839. [PMID: 33544849 PMCID: PMC7913697 DOI: 10.1093/nar/gkab047] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/07/2021] [Accepted: 02/02/2021] [Indexed: 01/01/2023] Open
Abstract
We recently showed that site-specific incorporation of 2′-modifications or neutral linkages in the oligo-deoxynucleotide gap region of toxic phosphorothioate (PS) gapmer ASOs can enhance therapeutic index and safety. In this manuscript, we determined if introducing substitution at the 5′-position of deoxynucleotide monomers in the gap can also enhance therapeutic index. Introducing R- or S-configured 5′-Me DNA at positions 3 and 4 in the oligodeoxynucleotide gap enhanced the therapeutic profile of the modified ASOs suggesting a different positional preference as compared to the 2′-OMe gap modification strategy. The generality of these observations was demonstrated by evaluating R-5′-Me and R-5′-Ethyl DNA modifications in multiple ASOs targeting HDAC2, FXI and Dynamin2 mRNA in the liver. The current work adds to a growing body of evidence that small structural changes can modulate the therapeutic properties of PS ASOs and ushers a new era of chemical optimization with a focus on enhancing the therapeutic profile as opposed to nuclease stability, RNA-affinity and pharmacokinetic properties. The 5′-methyl DNA modified ASOs exhibited excellent safety and antisense activity in mice highlighting the therapeutic potential of this class of nucleic acid analogs for next generation ASO designs.
Collapse
Affiliation(s)
- Guillermo Vasquez
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | | | - W Brad Wan
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Audrey Low
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | | | - Jinghua Yu
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Thazha P Prakash
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | | | - Xue-Hai Liang
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Stanley T Crooke
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Eric E Swayze
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Michael T Migawa
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Punit P Seth
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| |
Collapse
|
10
|
Nikan M, Tanowitz M, Dwyer CA, Jackson M, Gaus HJ, Swayze EE, Rigo F, Seth PP, Prakash TP. Targeted Delivery of Antisense Oligonucleotides Using Neurotensin Peptides. J Med Chem 2020; 63:8471-8484. [PMID: 32677436 DOI: 10.1021/acs.jmedchem.0c00840] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Despite recent advances, targeted delivery of therapeutic oligonucleotide to extra-hepatic tissues continues to be a challenging endeavor and efficient ligand-receptor systems need to be identified. To determine the feasibility of using neurotensin to improve the productive uptake of antisense oligonucleotides (ASO), we synthesized neurotensin-ASO conjugates and evaluated their cellular uptake and activity in cells and in mice. We performed a comprehensive structure-activity relationship study of the conjugates and determined the influence of ASO charge, ASO length, peptide charge, linker chemistry and ligand identity on receptor binding and internalization. We identified a modified neurotensin peptide capable of improving the cellular uptake and activity of gapmer ASOs in sortilin expressing cells (sixfold) and in spinal cord in mice (twofold). Neurotensin conjugation also improved the potency of morpholino ASO designed to correct splicing of survival motor neuron pre-mRNA in the cortex and striatum after intracerebroventricular injection. Neurotensin-mediated targeted delivery represents a possible approach for enhancing the potency of ASOs with diverse nucleic acid modifications.
Collapse
Affiliation(s)
- Mehran Nikan
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Michael Tanowitz
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Chrissa A Dwyer
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Michaela Jackson
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Hans J Gaus
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Eric E Swayze
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Frank Rigo
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Punit P Seth
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Thazha P Prakash
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| |
Collapse
|
11
|
Chappell AE, Gaus HJ, Berdeja A, Gupta R, Jo M, Prakash TP, Oestergaard M, Swayze EE, Seth PP. Mechanisms of palmitic acid-conjugated antisense oligonucleotide distribution in mice. Nucleic Acids Res 2020; 48:4382-4395. [PMID: 32182359 PMCID: PMC7192618 DOI: 10.1093/nar/gkaa164] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 02/28/2020] [Accepted: 03/04/2020] [Indexed: 12/20/2022] Open
Abstract
Conjugation of antisense oligonucleotide (ASO) with a variety of distinct lipophilic moieties like fatty acids and cholesterol increases ASO accumulation and activity in multiple tissues. While lipid conjugation increases tissue exposure in mice and reduces excretion of ASO in urine, histological review of skeletal and cardiac muscle indicates that the increased tissue accumulation of lipid conjugated ASO is isolated to the interstitium. Administration of palmitic acid-conjugated ASO (Palm-ASO) in mice results in a rapid and substantial accumulation in the interstitium of muscle tissue followed by relatively rapid clearance and only slight increases in intracellular accumulation in myocytes. We propose a model whereby increased affinity for lipid particles, albumin, and other plasma proteins by lipid-conjugation facilitates ASO transport across endothelial barriers into tissue interstitium. However, this increased affinity for lipid particles and plasma proteins also facilitates the transport of ASO from the interstitium to the lymph and back into circulation. The cumulative effect is only a slight (∼2-fold) increase in tissue accumulation and similar increase in ASO activity. To support this proposal, we demonstrate that the activity of lipid conjugated ASO was reduced in two mouse models with defects in endothelial transport of macromolecules: caveolin-1 knockout (Cav1-/-) and FcRn knockout (FcRn-/-).
Collapse
Affiliation(s)
- Alfred E Chappell
- Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Hans J Gaus
- Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Andres Berdeja
- Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Ruchi Gupta
- Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Minji Jo
- Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Thazha P Prakash
- Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | | | - Eric E Swayze
- Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Punit P Seth
- Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| |
Collapse
|
12
|
Vickers TA, Rahdar M, Prakash TP, Crooke ST. Kinetic and subcellular analysis of PS-ASO/protein interactions with P54nrb and RNase H1. Nucleic Acids Res 2020; 47:10865-10880. [PMID: 31495875 PMCID: PMC6846478 DOI: 10.1093/nar/gkz771] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 08/21/2019] [Accepted: 08/28/2019] [Indexed: 01/16/2023] Open
Abstract
The rapid RNase H1-dependent mislocalization of heterodimer proteins P54nrb and PSF to nucleoli is an early event in the pathway that explains the effects of most toxic phosphorothioate ASOs (PS-ASOs). Using a recently developed NanoLuciferace (NLuc)-based structural complementation reporter system which allows us to observe ASO/protein interactions in real time in live cells, we have determined that safe and toxic PS-ASOs associate with these proteins with kinetics and impact on subcellular localization that differ. Toxic PS-ASOs interact in a complex that includes RNase H1, P54nrb and PSF; but RNase H1/P54nrb complexes were observed in only the cells treated with toxic, but not safe PS-ASOs. In addition, experiments performed in vitro suggest that RNA is also a required component of the complex. The protein–protein interaction between P54nrb and RNase H1 requires the spacer region of RNAse H1, while the P54nrb core domains are required for association with RNase H1. In addition, we have determined that PS-ASOs bind P54nrb via RRM1 and RRM2, while they bind RNase H1 primarily via the hybrid binding domain, however catalytic domain interactions also contribute to overall affinity. These ASO–protein interactions are highly influenced by the chemistry of the PS-ASO binding environment, however little correlation between affinity for specific proteins and PS-ASO toxicity was observed.
Collapse
Affiliation(s)
- Timothy A Vickers
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, CA, USA
| | - Meghdad Rahdar
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, CA, USA
| | - Thazha P Prakash
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, CA, USA
| | - Stanley T Crooke
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, CA, USA
| |
Collapse
|
13
|
Østergaard ME, Jackson M, Low A, E Chappell A, G Lee R, Peralta RQ, Yu J, Kinberger GA, Dan A, Carty R, Tanowitz M, Anderson P, Kim TW, Fradkin L, Mullick AE, Murray S, Rigo F, Prakash TP, Bennett CF, Swayze EE, Gaus HJ, Seth PP. Conjugation of hydrophobic moieties enhances potency of antisense oligonucleotides in the muscle of rodents and non-human primates. Nucleic Acids Res 2020; 47:6045-6058. [PMID: 31076766 PMCID: PMC6614849 DOI: 10.1093/nar/gkz360] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 04/18/2019] [Accepted: 04/26/2019] [Indexed: 12/15/2022] Open
Abstract
We determined the effect of attaching palmitate, tocopherol or cholesterol to PS ASOs and their effects on plasma protein binding and on enhancing ASO potency in the muscle of rodents and monkeys. We found that cholesterol ASO conjugates showed 5-fold potency enhancement in the muscle of rodents relative to unconjugated ASOs. However, they were toxic in mice and as a result were not evaluated in the monkey. In contrast, palmitate and tocopherol-conjugated ASOs showed enhanced potency in the skeletal muscle of rodents and modest enhancements in potency in the monkey. Analysis of the plasma-protein binding profiles of the ASO-conjugates by size-exclusion chromatography revealed distinct and species-specific differences in their association with plasma proteins which likely rationalizes their behavior in animals. Overall, our data suggest that modulating binding to plasma proteins can influence ASO activity and distribution to extra-hepatic tissues in a species-dependent manner and sets the stage to identify other strategies to enhance ASO potency in muscle tissues.
Collapse
Affiliation(s)
| | - Michaela Jackson
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Audrey Low
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | | | - Richard G Lee
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Rachel Q Peralta
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Jinghua Yu
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | | | - Amy Dan
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Rick Carty
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Michael Tanowitz
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Patrick Anderson
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Tae-Won Kim
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Linda Fradkin
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Adam E Mullick
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Sue Murray
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Frank Rigo
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Thazha P Prakash
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - C Frank Bennett
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Eric E Swayze
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Hans J Gaus
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Punit P Seth
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| |
Collapse
|
14
|
Prakash TP, Mullick AE, Lee RG, Yu J, Yeh ST, Low A, Chappell AE, Østergaard ME, Murray S, Gaus HJ, Swayze EE, Seth PP. Fatty acid conjugation enhances potency of antisense oligonucleotides in muscle. Nucleic Acids Res 2020; 47:6029-6044. [PMID: 31127296 PMCID: PMC6614804 DOI: 10.1093/nar/gkz354] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 04/19/2019] [Accepted: 04/26/2019] [Indexed: 12/21/2022] Open
Abstract
Enhancing the functional uptake of antisense oligonucleotide (ASO) in the muscle will be beneficial for developing ASO therapeutics targeting genes expressed in the muscle. We hypothesized that improving albumin binding will facilitate traversal of ASO from the blood compartment to the interstitium of the muscle tissues to enhance ASO functional uptake. We synthesized structurally diverse saturated and unsaturated fatty acid conjugated ASOs with a range of hydrophobicity. The binding affinity of ASO fatty acid conjugates to plasma proteins improved with fatty acid chain length and highest binding affinity was observed with ASO conjugates containing fatty acid chain length from 16 to 22 carbons. The degree of unsaturation or conformation of double bond appears to have no influence on protein binding or activity of ASO fatty acid conjugates. Activity of fatty acid ASO conjugates correlated with the affinity to albumin and the tightest albumin binder exhibited the highest activity improvement in muscle. Palmitic acid conjugation increases ASO plasma Cmax and improved delivery of ASO to interstitial space of mouse muscle. Conjugation of palmitic acid improved potency of DMPK, Cav3, CD36 and Malat-1 ASOs (3- to 7-fold) in mouse muscle. Our approach provides a foundation for developing more effective therapeutic ASOs for muscle disorders.
Collapse
Affiliation(s)
| | - Adam E Mullick
- Antisense Drug Discovery, 2855 Gazelle Ct., Carlsbad, CA 92010, USA
| | - Richard G Lee
- Antisense Drug Discovery, 2855 Gazelle Ct., Carlsbad, CA 92010, USA
| | - Jinghua Yu
- Ionis Pharmaceuticals, Medicinal Chemistry, USA
| | - Steve T Yeh
- Antisense Drug Discovery, 2855 Gazelle Ct., Carlsbad, CA 92010, USA
| | - Audrey Low
- Antisense Drug Discovery, 2855 Gazelle Ct., Carlsbad, CA 92010, USA
| | | | | | - Sue Murray
- Antisense Drug Discovery, 2855 Gazelle Ct., Carlsbad, CA 92010, USA
| | - Hans J Gaus
- Ionis Pharmaceuticals, Medicinal Chemistry, USA
| | | | | |
Collapse
|
15
|
Kim Y, Jo M, Schmidt J, Luo X, Prakash TP, Zhou T, Klein S, Xiao X, Post N, Yin Z, MacLeod AR. Enhanced Potency of GalNAc-Conjugated Antisense Oligonucleotides in Hepatocellular Cancer Models. Mol Ther 2019; 27:1547-1557. [PMID: 31303442 PMCID: PMC6731179 DOI: 10.1016/j.ymthe.2019.06.009] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 06/08/2019] [Accepted: 06/19/2019] [Indexed: 02/07/2023] Open
Abstract
Antisense oligonucleotides (ASOs) are a novel therapeutic approach to target difficult-to-drug protein classes by targeting their corresponding mRNAs. Significantly enhanced ASO activity has been achieved by the targeted delivery of ASOs to selected tissues. One example is the targeted delivery of ASOs to hepatocytes, achieved with N-acetylgalactosamine (GalNAc) conjugation to ASO, which results in selective uptake by asialoglycoprotein receptor (ASGR). Here we have evaluated the potential of GalNAc-conjugated ASOs as a therapeutic approach to targeting difficult-to-drug pathways in hepatocellular carcinoma (HCC). The activity of GalNAc-conjugated ASOs was superior to that of the unconjugated parental ASO in ASGR (+) human HCC cells in vitro, but not in ASGR (-) cells. Both human- and mouse-derived HCC displayed reduced levels of ASGR, however, despite this, GalNAc-conjugated ASOs showed a 5- to 10-fold increase in potency in tumors. Systemically administered GalNAc-conjugated ASOs demonstrated both enhanced antisense activity and antitumor activity in the diethylnitrosamine-induced HCC tumor model. Finally, GalNAc conjugation enhanced ASO activity in human circulating tumor cells from HCC patients, demonstrating the potential of this approach in primary human HCC tumor cells. Taken together, these results provide a strong rationale for a potential therapeutic use of GalNAc-conjugated ASOs for the treatment of HCC.
Collapse
Affiliation(s)
- Youngsoo Kim
- Department of Antisense Drug Discovery, Ionis Pharmaceuticals Inc., Carlsbad, CA 92010, USA.
| | - Minji Jo
- Department of Antisense Drug Discovery, Ionis Pharmaceuticals Inc., Carlsbad, CA 92010, USA
| | - Joanna Schmidt
- Department of Antisense Drug Discovery, Ionis Pharmaceuticals Inc., Carlsbad, CA 92010, USA
| | - Xiaolin Luo
- Department of Antisense Drug Discovery, Ionis Pharmaceuticals Inc., Carlsbad, CA 92010, USA
| | - Thazha P Prakash
- Department of Medicinal Chemistry, Ionis Pharmaceuticals Inc., Carlsbad, CA 92010, USA
| | - Tianyuan Zhou
- Department of Antisense Drug Discovery, Ionis Pharmaceuticals Inc., Carlsbad, CA 92010, USA
| | - Stephanie Klein
- Department of Antisense Drug Discovery, Ionis Pharmaceuticals Inc., Carlsbad, CA 92010, USA
| | - Xiaokun Xiao
- Department of Antisense Drug Discovery, Ionis Pharmaceuticals Inc., Carlsbad, CA 92010, USA
| | - Noah Post
- Department of Pharmacokinetics, Ionis Pharmaceuticals Inc., Carlsbad, CA 92010, USA
| | - Zhengfeng Yin
- Molecular Oncology Laboratory, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - A Robert MacLeod
- Department of Antisense Drug Discovery, Ionis Pharmaceuticals Inc., Carlsbad, CA 92010, USA.
| |
Collapse
|
16
|
Wang S, Allen N, Prakash TP, Liang XH, Crooke ST. Lipid Conjugates Enhance Endosomal Release of Antisense Oligonucleotides Into Cells. Nucleic Acid Ther 2019; 29:245-255. [PMID: 31158063 DOI: 10.1089/nat.2019.0794] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Antisense oligonucleotides modified with phosphorothioate linkages (PS-ASOs) can enter cells via endocytic pathways and must escape from membraned organelles to reach target RNAs. We recently found that membrane destabilization induced by different lipid species contributes to PS-ASO release from late endosomes (LEs). In this study, we characterized intracellular uptake, trafficking, and activities of PS-ASOs conjugated with different lipid species. We found that palmitic acid-, tocopherol-, and cholesterol-conjugated PS-ASOs have increased protein binding and enhanced intracellular uptake compared to unconjugated PS-ASOs. Similar to the parental PS-ASO, the lipid-conjugated PS-ASOs traffic from early to LEs without incorporation into lipid droplets. Unlike parental PS-ASOs, the lipid-conjugated PS-ASOs tend to remain associated with plasma or endosomal membranes, and this appears to influence their release from endosomes. The lipid-conjugated PS-ASOs were released more rapidly than parental PS-ASO. These results suggest that lipid conjugation enhances the interactions of PS-ASOs with proteins or membranes, in turn facilitating intracellular trafficking and endosomal release.
Collapse
Affiliation(s)
- Shiyu Wang
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California
| | - Nickolas Allen
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California
| | - Thazha P Prakash
- Department of Medicinal Chemistry, Ionis Pharmaceuticals, Inc., Carlsbad, California
| | - Xue-Hai Liang
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California
| | - Stanley T Crooke
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California
| |
Collapse
|
17
|
Prakash TP, Yu J, Kinberger GA, Low A, Jackson M, Rigo F, Swayze EE, Seth PP. Evaluation of the effect of 2'-O-methyl, fluoro hexitol, bicyclo and Morpholino nucleic acid modifications on potency of GalNAc conjugated antisense oligonucleotides in mice. Bioorg Med Chem Lett 2018; 28:3774-3779. [PMID: 30342955 DOI: 10.1016/j.bmcl.2018.10.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 09/07/2018] [Accepted: 10/09/2018] [Indexed: 01/22/2023]
Abstract
The potency of antisense oligonucleotide (ASO) drugs has significantly improved in the clinic after exploiting asialoglycoprotein receptor (ASGR) mediated delivery to hepatocytes. To further this technology, we evaluated the structure-activity relationships of oligonucleotide chemistry on in vivo potency of GalNAc-conjugated Gapmer ASOs. GalNAc conjugation improved potency of ASOs containing 2'-O-methyl (2'-O-Me), 3'-fluoro hexitol nucleic acid (FHNA), locked nucleic acid (LNA), and constrained ethyl bicyclo nucleic acid (cEt BNA) 10-20-fold compared to unconjugated ASOs. We further demonstrate that GalNAc conjugation improves activity of 2'-O-(2-methoxyethyl) (2'-O-MOE) and Morpholino ASOs designed to correct splicing of survival motor neuron (SMN2) pre-mRNA in liver after subcutaneous administration. GalNAc modification thus represents a viable strategy for enhancing potency of ASO with diverse nucleic acid modifications and mechanisms of action for targets expressed in hepatocytes.
Collapse
Affiliation(s)
- Thazha P Prakash
- Ionis Pharmaceuticals, Inc., 2855 Gazelle Ct., Carlsbad, CA 92010, United States.
| | - Jinghua Yu
- Ionis Pharmaceuticals, Inc., 2855 Gazelle Ct., Carlsbad, CA 92010, United States
| | - Garth A Kinberger
- Ionis Pharmaceuticals, Inc., 2855 Gazelle Ct., Carlsbad, CA 92010, United States
| | - Audrey Low
- Ionis Pharmaceuticals, Inc., 2855 Gazelle Ct., Carlsbad, CA 92010, United States
| | - Michaela Jackson
- Ionis Pharmaceuticals, Inc., 2855 Gazelle Ct., Carlsbad, CA 92010, United States
| | - Frank Rigo
- Ionis Pharmaceuticals, Inc., 2855 Gazelle Ct., Carlsbad, CA 92010, United States
| | - Eric E Swayze
- Ionis Pharmaceuticals, Inc., 2855 Gazelle Ct., Carlsbad, CA 92010, United States
| | - Punit P Seth
- Ionis Pharmaceuticals, Inc., 2855 Gazelle Ct., Carlsbad, CA 92010, United States
| |
Collapse
|
18
|
Shen X, Kilikevicius A, O'Reilly D, Prakash TP, Damha MJ, Rigo F, Corey DR. Activating frataxin expression by single-stranded siRNAs targeting the GAA repeat expansion. Bioorg Med Chem Lett 2018; 28:2850-2855. [PMID: 30076049 PMCID: PMC6129981 DOI: 10.1016/j.bmcl.2018.07.033] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 07/17/2018] [Accepted: 07/18/2018] [Indexed: 11/18/2022]
Abstract
Friedreich's ataxia (FRDA) is an incurable neurodegenerative disorder caused by reduced expression of the mitochondrial protein frataxin (FXN). The genetic cause of the disease is an expanded GAA repeat within the FXN gene. Agents that increase expression of FXN protein are a potential approach to therapy. We previously described anti-trinucleotide GAA duplex RNAs (dsRNAs) and antisense oligonucleotides (ASOs) that activate FXN protein expression in multiple patient derived cell lines. Here we test two distinct series of compounds for their ability to increase FXN expression. ASOs with butane linkers showed low potency, which is consistent with the low Tm values and suggesting that flexible conformation impairs activity. By contrast, single-stranded siRNAs (ss-siRNAs) that combine the strengths of dsRNA and ASO approaches had nanomolar potencies. ss-siRNAs provide an additional option for developing nucleic acid therapeutics to treat FRDA.
Collapse
Affiliation(s)
- Xiulong Shen
- Department of Pharmacology, UT Southwestern Medical Center at Dallas, Dallas, TX 75390, United States; Department of Biochemistry, UT Southwestern Medical Center at Dallas, Dallas, TX 75390, United States
| | - Audrius Kilikevicius
- Department of Pharmacology, UT Southwestern Medical Center at Dallas, Dallas, TX 75390, United States; Department of Biochemistry, UT Southwestern Medical Center at Dallas, Dallas, TX 75390, United States
| | - Daniel O'Reilly
- Department of Chemistry, McGill University, Montreal, QC H3A 0B8, Canada
| | | | - Masad J Damha
- Department of Chemistry, McGill University, Montreal, QC H3A 0B8, Canada
| | - Frank Rigo
- Ionis Pharmaceuticals, Carlsbad, CA 92010, United States
| | - David R Corey
- Department of Pharmacology, UT Southwestern Medical Center at Dallas, Dallas, TX 75390, United States; Department of Biochemistry, UT Southwestern Medical Center at Dallas, Dallas, TX 75390, United States.
| |
Collapse
|
19
|
McMahon MA, Prakash TP, Cleveland DW, Bennett CF, Rahdar M. Chemically Modified Cpf1-CRISPR RNAs Mediate Efficient Genome Editing in Mammalian Cells. Mol Ther 2018; 26:1228-1240. [PMID: 29650467 PMCID: PMC5993945 DOI: 10.1016/j.ymthe.2018.02.031] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 02/27/2018] [Accepted: 02/27/2018] [Indexed: 11/17/2022] Open
Abstract
CRISPR-based gene editing is a powerful technology for engineering mammalian genomes. It holds the potential as a therapeutic, although much-needed in vivo delivery systems have yet to be established. Here, using the Cpf1-crRNA (CRISPR RNA) crystal structure as a guide, we synthesized a series of systematically truncated and chemically modified crRNAs, and identify positions that are amenable to modification while retaining gene-editing activity. Modified crRNAs were designed with the same modifications that provide protection against nucleases and enable wide distribution in vivo. We show crRNAs with chemically modified terminal nucleotides are exonuclease resistant while retaining gene-editing activity. Chemically modified or DNA-substituted nucleotides at select positions and up to 70% of the crRNA DNA specificity region are also well tolerated. In addition, gene-editing activity is maintained with phosphorothioate backbone substitutions in the crRNA DNA specificity region. Finally, we demonstrate that 42-mer synthetic crRNAs from the similar CRISPR-Cas9 system are taken up by cells, an attractive property for in vivo delivery. Our study is the first to show that chemically modified crRNAs of the CRISPR-Cpf1 system can functionally replace and mediate comparable gene editing to the natural crRNA, which holds the potential for enhancing both viral- and non-viral-mediated in vivo gene editing.
Collapse
Affiliation(s)
- Moira A McMahon
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA 92093, USA; Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA; Ionis Pharmaceuticals, Carlsbad, CA 92010, USA
| | | | - Don W Cleveland
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA 92093, USA; Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | | | | |
Collapse
|
20
|
Miller CM, Tanowitz M, Donner AJ, Prakash TP, Swayze EE, Harris EN, Seth PP. Receptor-Mediated Uptake of Phosphorothioate Antisense Oligonucleotides in Different Cell Types of the Liver. Nucleic Acid Ther 2018; 28:119-127. [PMID: 29425080 DOI: 10.1089/nat.2017.0709] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Oligonucleotide therapeutics have emerged as a third distinct platform for drug discovery within the pharmaceutical industry. Five oligonucleotide-based drugs have been approved by the US FDA and over 100 oligonucleotides drugs are currently at different stages of human trials. Several of these oligonucleotide drugs are modified using the phosphorothioate (PS) backbone modification where one of the nonbridging oxygen atoms of the phosphodiester linkage is replaced with sulfur. In this review, we summarize our knowledge on receptor-mediated uptake of PS antisense oligonucleotides (ASOs) within different cell types of the liver-a privileged organ for the discovery of oligonucleotide-based therapeutics.
Collapse
Affiliation(s)
- Colton M Miller
- 1 Department of Biochemistry, University of Nebraska , Lincoln, Nebraska
| | | | | | | | | | - Edward N Harris
- 1 Department of Biochemistry, University of Nebraska , Lincoln, Nebraska
| | | |
Collapse
|
21
|
Li L, Shen X, Liu Z, Norrbom M, Prakash TP, O'Reilly D, Sharma VK, Damha MJ, Watts JK, Rigo F, Corey DR. Activation of Frataxin Protein Expression by Antisense Oligonucleotides Targeting the Mutant Expanded Repeat. Nucleic Acid Ther 2018; 28:23-33. [PMID: 29341839 PMCID: PMC5790436 DOI: 10.1089/nat.2017.0703] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 11/28/2017] [Indexed: 12/31/2022] Open
Abstract
Friedreich's Ataxia (FA) is an inherited neurologic disorder caused by an expanded GAA repeat within intron 1 of the frataxin (FXN) gene that reduces expression of FXN protein. Agents that increase expression of FXN have the potential to alleviate the disease. We previously reported that duplex RNAs (dsRNAs) and antisense oligonucleotides (ASOs) complementary to the GAA repeat could enhance expression of FXN protein. We now explore the potential of a diverse group of chemically modified dsRNAs and ASOs to define the breadth of repeat-targeted synthetic nucleic acids as a platform for therapeutic development for FA. ASOs and dsRNAs can activate FXN protein expression in FA patient-derived cell lines that possess varied numbers of GAA repeats. Increased FXN protein expression was achieved by ASOs incorporating diverse chemical modifications with low nanomolar potencies, suggesting substantial flexibility in choosing compounds for further chemical optimization and animal studies. Our data encourage further development of ASOs as agents to treat FA.
Collapse
Affiliation(s)
- Liande Li
- 1 Department of Pharmacology, UT Southwestern Medical Center at Dallas , Dallas, Texas
- 2 Department of Biochemistry, UT Southwestern Medical Center at Dallas , Dallas, Texas
| | - Xiulong Shen
- 1 Department of Pharmacology, UT Southwestern Medical Center at Dallas , Dallas, Texas
- 2 Department of Biochemistry, UT Southwestern Medical Center at Dallas , Dallas, Texas
| | - Zhongtian Liu
- 1 Department of Pharmacology, UT Southwestern Medical Center at Dallas , Dallas, Texas
- 2 Department of Biochemistry, UT Southwestern Medical Center at Dallas , Dallas, Texas
| | | | | | - Daniel O'Reilly
- 4 Department of Chemistry, McGill University , Montreal, Canada
| | - Vivek K Sharma
- 5 RNA Therapeutics Institute and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School , Worcester, Massachusetts
| | - Masad J Damha
- 4 Department of Chemistry, McGill University , Montreal, Canada
| | - Jonathan K Watts
- 5 RNA Therapeutics Institute and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School , Worcester, Massachusetts
| | - Frank Rigo
- 3 Ionis Pharmaceuticals , Carlsbad, California
| | - David R Corey
- 1 Department of Pharmacology, UT Southwestern Medical Center at Dallas , Dallas, Texas
- 2 Department of Biochemistry, UT Southwestern Medical Center at Dallas , Dallas, Texas
| |
Collapse
|
22
|
Tanowitz M, Hettrick L, Revenko A, Kinberger GA, Prakash TP, Seth PP. Asialoglycoprotein receptor 1 mediates productive uptake of N-acetylgalactosamine-conjugated and unconjugated phosphorothioate antisense oligonucleotides into liver hepatocytes. Nucleic Acids Res 2017; 45:12388-12400. [PMID: 29069408 PMCID: PMC5716100 DOI: 10.1093/nar/gkx960] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 10/11/2017] [Indexed: 01/13/2023] Open
Abstract
Antisense oligonucleotide (ASO) therapeutics show tremendous promise for the treatment of previously intractable human diseases but to exert their effects on cellular RNA processing they must first cross the plasma membrane by endocytosis. The conjugation of ASOs to a receptor ligand can dramatically increase their entry into certain cells and tissues, as demonstrated by the implementation of N-acetylgalactosamine (GalNAc)-conjugated ASOs for Asialoglycoprotein Receptor (ASGR)-mediated uptake into liver hepatocytes. We compared the internalization and activity of GalNAc-conjugated ASOs and their parents in endogenous ASGR-expressing cells and were able to recapitulate hepatocyte ASO uptake and activity in cells engineered to heterologously express the receptor. We found that the minor receptor subunit, ASGR2, is not required for effective in vitro or in vivo uptake of GalNAc-conjugated ASO and that the major subunit, ASGR1, plays a small but significant role in the uptake of unconjugated phosphorothioate ASOs into hepatocytes. Moreover, our data demonstrates there is a large excess capacity of liver ASGR for the effective uptake of GalNAc–ASO conjugates, suggesting broad opportunities to exploit receptors with relatively moderate levels of expression.
Collapse
Affiliation(s)
- Michael Tanowitz
- Department of Medicinal Chemistry, Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Lisa Hettrick
- Department of Antisense Drug Discovery, Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Alexey Revenko
- Department of Antisense Drug Discovery, Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Garth A Kinberger
- Department of Medicinal Chemistry, Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Thazha P Prakash
- Department of Medicinal Chemistry, Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Punit P Seth
- Department of Medicinal Chemistry, Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| |
Collapse
|
23
|
Schmidt K, Prakash TP, Donner AJ, Kinberger GA, Gaus HJ, Low A, Østergaard ME, Bell M, Swayze EE, Seth PP. Characterizing the effect of GalNAc and phosphorothioate backbone on binding of antisense oligonucleotides to the asialoglycoprotein receptor. Nucleic Acids Res 2017; 45:2294-2306. [PMID: 28158620 PMCID: PMC5389643 DOI: 10.1093/nar/gkx060] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 02/01/2017] [Indexed: 11/14/2022] Open
Abstract
Targeted delivery of antisense oligonucleotides (ASO) to hepatocytes via the asialoglycoprotein receptor (ASGR) has improved the potency of ASO drugs ∼30-fold in the clinic (1). In order to fully characterize the effect of GalNAc valency, oligonucleotide length, flexibility and chemical composition on ASGR binding, we tested and validated a fluorescence polarization competition binding assay. The ASGR binding, and in vitro and in vivo activities of 1, 2 and 3 GalNAc conjugated single stranded and duplexed ASOs were studied. Two and three GalNAc conjugated single stranded ASOs bind the ASGR with the strongest affinity and display optimal in vitro and in vivo activities. 1 GalNAc conjugated ASOs showed 10-fold reduced ASGR binding affinity relative to three GalNAc ASOs but only 2-fold reduced activity in mice. An unexpected observation was that the ASGR also appears to play a role in the uptake of unconjugated phosphorothioate modified ASOs in the liver as evidenced by the loss of activity of GalNAc conjugated and unconjugated ASOs in ASGR knockout mice. Our results provide insights into how backbone charge and chemical composition assist in the binding and internalization of highly polar anionic single stranded oligonucleotides into cells and tissues.
Collapse
Affiliation(s)
- Karsten Schmidt
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Thazha P Prakash
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Aaron J Donner
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Garth A Kinberger
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Hans J Gaus
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Audrey Low
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | | | - Melanie Bell
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Eric E Swayze
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Punit P Seth
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| |
Collapse
|
24
|
Mullick AE, Yeh ST, Graham MJ, Engelhardt JA, Prakash TP, Crooke RM. Blood Pressure Lowering and Safety Improvements With Liver Angiotensinogen Inhibition in Models of Hypertension and Kidney Injury. Hypertension 2017; 70:566-576. [PMID: 28716988 DOI: 10.1161/hypertensionaha.117.09755] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 06/04/2017] [Accepted: 06/07/2017] [Indexed: 01/16/2023]
Abstract
Uncontrolled hypertension is an important contributor to cardiovascular disease. Despite the armamentarium of antihypertensive treatments, there remains a need for novel agents effective in individuals who cannot reach acceptable blood pressure levels. Inhibitors targeting the renin-angiotensin-aldosterone system (RAAS) are widely used but may not optimally inhibit RAAS and demonstrate an acceptable safety profile. Experiments were conducted to characterize a series of AGT (angiotensinogen) antisense oligonucleotides (ASOs) and compare their efficacy and tolerability to traditional RAAS blockade. AGT ASOs which target multiple systemic sites of AGT versus an N-acetylgalactosamine-conjugated AGT ASO that targets the liver were compared with captopril and losartan. Spontaneously hypertensive rats fed an 8% NaCl diet, a model of malignant hypertension resistant to standard RAAS inhibitors, demonstrated robust and durable blood pressure reductions with AGT ASO treatments, which was not observed with standard RAAS blockade. Studies in rat models of acute kidney injury produced by salt deprivation revealed kidney injury with ASO treatment that reduced kidney-expressed AGT, but not in animals treated with the N-acetylgalactosamine AGT ASO despite comparable plasma AGT reductions. Administration of either captopril or losartan also produced acute kidney injury during salt deprivation. Thus, intrarenal RAAS derived from kidney AGT, and inhibited by the standard of care, contributes to the maintenance of renal function during severe RAAS challenge. Such improvements in efficacy and tolerability by a liver-selective AGT inhibitor could be desirable in individuals not at their blood pressure goal with existing RAAS blockade.
Collapse
Affiliation(s)
| | - Steve T Yeh
- From the Ionis Pharmaceuticals, Inc, Carlsbad, CA
| | | | | | | | | |
Collapse
|
25
|
Prakash TP, Lima WF, Murray HM, Li W, Kinberger GA, Chappell AE, Gaus H, Seth PP, Bhat B, Crooke ST, Swayze EE. Identification of metabolically stable 5΄-phosphate analogs that support single-stranded siRNA activity. Nucleic Acids Res 2017; 45:6994. [PMID: 28472515 PMCID: PMC5499767 DOI: 10.1093/nar/gkx381] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Thazha P Prakash
- Isis Pharmaceuticals Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, USA
| | - Walt F Lima
- Isis Pharmaceuticals Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, USA
| | - Heather M Murray
- Isis Pharmaceuticals Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, USA
| | - Wenyu Li
- Isis Pharmaceuticals Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, USA
| | | | | | - Hans Gaus
- Isis Pharmaceuticals Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, USA
| | - Punit P Seth
- Isis Pharmaceuticals Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, USA
| | - Balkrishen Bhat
- Isis Pharmaceuticals Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, USA
| | - Stanley T Crooke
- Isis Pharmaceuticals Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, USA
| | - Eric E Swayze
- Isis Pharmaceuticals Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, USA
| |
Collapse
|
26
|
Hu J, Rigo F, Prakash TP, Corey DR. Recognition of c9orf72 Mutant RNA by Single-Stranded Silencing RNAs. Nucleic Acid Ther 2017; 27:87-94. [PMID: 28005462 PMCID: PMC5372765 DOI: 10.1089/nat.2016.0655] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 11/15/2016] [Indexed: 01/09/2023] Open
Abstract
Mutations within the chromosome 9 open reading frame 72 (c9orf72) gene are associated with both familial amyotrophic lateral sclerosis and frontotemporal dementia. The mutation leads to an expanded GGGGCC hexanucleotide repeat within the first intron of c9orf72 and an expanded CCCCGG repeat within a corresponding antisense transcript. Both the mutant intronic and antisense RNAs have been implicated in disease. We have previously reported that duplex RNAs complementary to the repeats can recognize disease-causing RNA and block detection of nuclear foci formed by the mutant transcripts. Here, we test the hypothesis that inhibition can also be achieved by single-stranded silencing RNAs (ss-siRNAs). ss-siRNAs are single-stranded antisense oligonucleotides (ASOs) that function through RNAi interference (RNAi) to silence gene expression. ss-siRNAs can block the expanded repeats within both intronic RNA and the antisense transcripts. Inhibition is more potent than by analogous duplex RNAs. Our data suggest that the potent effects on foci are caused by a combination of mechanisms including RNAi and direct binding of the ss-siRNA to the target transcripts. These findings reinforce the suggestion that ss-siRNAs combine the favorable properties of duplex RNA and single-stranded ASOs.
Collapse
Affiliation(s)
- Jiaxin Hu
- 1 Department of Pharmacology, UT Southwestern Medical Center at Dallas , Dallas, Texas
- 2 Department of Biochemistry, UT Southwestern Medical Center at Dallas , Dallas, Texas
| | - Frank Rigo
- 3 Ionis Pharmaceuticals , Carlsbad, California
| | | | - David R Corey
- 1 Department of Pharmacology, UT Southwestern Medical Center at Dallas , Dallas, Texas
- 2 Department of Biochemistry, UT Southwestern Medical Center at Dallas , Dallas, Texas
| |
Collapse
|
27
|
Pallan PS, Prakash TP, de Leon AR, Egli M. Limits of RNA 2′-OH Mimicry by Fluorine: Crystal Structure of Bacillus halodurans RNase H Bound to a 2′-FRNA:DNA Hybrid. Biochemistry 2016; 55:5321-5. [DOI: 10.1021/acs.biochem.6b00849] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Pradeep S. Pallan
- Department
of Biochemistry, Vanderbilt University, School of Medicine, Nashville, Tennessee 37232, United States
| | - Thazha P. Prakash
- Department
of Medicinal Chemistry, Ionis Pharmaceuticals Inc., Carlsbad, California 92010, United States
| | - Arnie R. de Leon
- Department
of Biochemistry, Vanderbilt University, School of Medicine, Nashville, Tennessee 37232, United States
| | - Martin Egli
- Department
of Biochemistry, Vanderbilt University, School of Medicine, Nashville, Tennessee 37232, United States
| |
Collapse
|
28
|
Yu RZ, Gunawan R, Post N, Zanardi T, Hall S, Burkey J, Kim TW, Graham MJ, Prakash TP, Seth PP, Swayze EE, Geary RS, Henry SP, Wang Y. Disposition and Pharmacokinetics of a GalNAc3-Conjugated Antisense Oligonucleotide Targeting Human Lipoprotein (a) in Monkeys. Nucleic Acid Ther 2016; 26:372-380. [PMID: 27500733 DOI: 10.1089/nat.2016.0623] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Triantennary N-acetyl galactosamine (GalNAc3)-conjugated antisense oligonucleotides (ASOs) have greatly improved potency due to receptor-mediated uptake into hepatocyte. The disposition and pharmacokinetics of ISIS 681257, a GalNAc3-conjugated ASO, were studied in monkeys. Following subcutaneous (SC) injection, ISIS 681257 was rapidly absorbed into the systemic circulation, with peak plasma levels observed within hours after dosing. After reaching Cmax, plasma concentrations rapidly declined in a multiexponential manner and were characterized by a dominant initial rapid distribution phase in which drug transferred to tissues from circulation, followed by a much slower terminal elimination phase (half-life of 4 weeks). Intact ISIS 681257 is the major full-length oligonucleotide species in plasma (≥70%). In tissues, the conjugated-GalNAc sugar moiety was rapidly metabolized, leaving the fully unconjugated form as the only full-length oligonucleotide detected at 48 h after dosing. Unconjugated ISIS 681257 cleared slowly from tissues with a half-life of 4 weeks. ISIS 681257 was highly bound to plasma proteins (>97% bound), which limited its urinary excretion. Disposition of ISIS 681257 in plasma and liver appeared nonlinear over the 1-40 mg/kg dose range studied. The plasma and liver tissue concentration data were well described by a population based mixed-effects modeling approach with Michaelis-Menten uptake from plasma to liver. Safety data from the study and the good exposure, as well as the extended half-life of the unconjugated ASO in the liver, support further development and less frequent dosing in Phase I clinical study.
Collapse
Affiliation(s)
- Rosie Z Yu
- Ionis Pharmaceuticals, Inc. , Carlsbad, California
| | - Rudy Gunawan
- Ionis Pharmaceuticals, Inc. , Carlsbad, California
| | - Noah Post
- Ionis Pharmaceuticals, Inc. , Carlsbad, California
| | | | - Shannon Hall
- Ionis Pharmaceuticals, Inc. , Carlsbad, California
| | | | - Tae-Won Kim
- Ionis Pharmaceuticals, Inc. , Carlsbad, California
| | | | | | - Punit P Seth
- Ionis Pharmaceuticals, Inc. , Carlsbad, California
| | | | | | | | - Yanfeng Wang
- Ionis Pharmaceuticals, Inc. , Carlsbad, California
| |
Collapse
|
29
|
Abstract
Incorporation of chemical modifications into small interfering RNAs (siRNAs) increases their metabolic stability and improves their tissue distribution. However, how these modifications impact interactions with Argonaute-2 (Ago2), the molecular target of siRNAs, is not known. Herein we present the crystal structure of human Ago2 bound to a metabolically stable siRNA containing extensive backbone modifications. Comparison to the structure of an equivalent unmodified-siRNA complex indicates that the structure of Ago2 is relatively unaffected by chemical modifications in the bound siRNA. In contrast, the modified siRNA appears to be much more plastic and shifts, relative to the unmodified siRNA, to optimize contacts with Ago2. Structure-activity analysis reveals that even major conformational perturbations in the 3' half of the siRNA seed region have a relatively modest effect on knockdown potency. These findings provide an explanation for a variety of modification patterns tolerated in siRNAs and a structural basis for advancing therapeutic siRNA design.
Collapse
Affiliation(s)
- Nicole T. Schirle
- Department of Integrative Computational and Structural Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Garth A. Kinberger
- Ionis Pharmaceuticals Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, United States
| | - Heather F. Murray
- Ionis Pharmaceuticals Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, United States
| | - Walt F. Lima
- Ionis Pharmaceuticals Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, United States
| | - Thazha P. Prakash
- Ionis Pharmaceuticals Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, United States
| | - Ian J. MacRae
- Department of Integrative Computational and Structural Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| |
Collapse
|
30
|
Kinberger GA, Prakash TP, Yu J, Vasquez G, Low A, Chappell A, Schmidt K, Murray HM, Gaus H, Swayze EE, Seth PP. Conjugation of mono and di-GalNAc sugars enhances the potency of antisense oligonucleotides via ASGR mediated delivery to hepatocytes. Bioorg Med Chem Lett 2016; 26:3690-3. [PMID: 27268307 DOI: 10.1016/j.bmcl.2016.05.084] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 05/24/2016] [Accepted: 05/27/2016] [Indexed: 11/29/2022]
Abstract
Antisense oligonucleotides (ASOs) conjugated to trivalent GalNAc ligands show 10-fold enhanced potency for suppressing gene targets expressed in hepatocytes. Trivalent GalNAc is a high affinity ligand for the asialoglycoprotein receptor (ASGR)-a C-type lectin expressed almost exclusively on hepatocytes in the liver. In this communication, we show that conjugation of two and even one GalNAc sugar to single stranded chemically modified ASOs can enhance potency 5-10 fold in mice. Evaluation of the mono- and di-GalNAc ASO conjugates in an ASGR binding assay suggested that chemical features of the ASO enhance binding to the receptor and provide a rationale for the enhanced potency.
Collapse
Affiliation(s)
- Garth A Kinberger
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, United States
| | - Thazha P Prakash
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, United States
| | - Jinghua Yu
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, United States
| | - Guillermo Vasquez
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, United States
| | - Audrey Low
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, United States
| | - Alfred Chappell
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, United States
| | - Karsten Schmidt
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, United States
| | - Heather M Murray
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, United States
| | - Hans Gaus
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, United States
| | - Eric E Swayze
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, United States
| | - Punit P Seth
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, United States.
| |
Collapse
|
31
|
Prakash TP, Kinberger GA, Murray HM, Chappell A, Riney S, Graham MJ, Lima WF, Swayze EE, Seth PP. Synergistic effect of phosphorothioate, 5'-vinylphosphonate and GalNAc modifications for enhancing activity of synthetic siRNA. Bioorg Med Chem Lett 2016; 26:2817-2820. [PMID: 27161280 DOI: 10.1016/j.bmcl.2016.04.063] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 04/20/2016] [Accepted: 04/21/2016] [Indexed: 12/30/2022]
Abstract
Chemical modifications are essential to improve metabolic stability and pharmacokinetic properties of siRNA to enable their systemic delivery. We investigated the effect of combing the phosphorothioate (PS) modification with metabolically stable phosphate analog (E)-5'-vinylphosphonate and GalNAc cluster conjugation on the activity of fully 2'-modified siRNA in cell culture and mice. Our data suggest that integrating multiple chemical approaches in one siRNA molecule improved potency 5-10 fold and provide a roadmap for developing more efficient siRNA drugs.
Collapse
Affiliation(s)
- Thazha P Prakash
- Ionis Pharmaceuticals Inc., 2855 Gazelle Ct., Carlsbad, CA 92010, United States.
| | - Garth A Kinberger
- Ionis Pharmaceuticals Inc., 2855 Gazelle Ct., Carlsbad, CA 92010, United States
| | - Heather M Murray
- Ionis Pharmaceuticals Inc., 2855 Gazelle Ct., Carlsbad, CA 92010, United States
| | - Alfred Chappell
- Ionis Pharmaceuticals Inc., 2855 Gazelle Ct., Carlsbad, CA 92010, United States
| | - Stan Riney
- Ionis Pharmaceuticals Inc., 2855 Gazelle Ct., Carlsbad, CA 92010, United States
| | - Mark J Graham
- Ionis Pharmaceuticals Inc., 2855 Gazelle Ct., Carlsbad, CA 92010, United States
| | - Walt F Lima
- Ionis Pharmaceuticals Inc., 2855 Gazelle Ct., Carlsbad, CA 92010, United States
| | - Eric E Swayze
- Ionis Pharmaceuticals Inc., 2855 Gazelle Ct., Carlsbad, CA 92010, United States
| | - Punit P Seth
- Ionis Pharmaceuticals Inc., 2855 Gazelle Ct., Carlsbad, CA 92010, United States
| |
Collapse
|
32
|
Migawa MT, Prakash TP, Vasquez G, Wan WB, Yu J, Kinberger GA, Østergaard ME, Swayze EE, Seth PP. A convenient synthesis of 5'-triantennary N-acetyl-galactosamine clusters based on nitromethanetrispropionic acid. Bioorg Med Chem Lett 2016; 26:2194-7. [PMID: 27025342 DOI: 10.1016/j.bmcl.2016.03.070] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 03/15/2016] [Accepted: 03/16/2016] [Indexed: 10/22/2022]
Abstract
A convenient method for the synthesis of several triantennary GalNAc clusters based on a nitromethanetrispropionic acid core was developed. The synthetic approach involves pentafluorophenolic ester intermediates which can be used in a one-pot, seven reaction procedure to quickly prepare a variety of triantennary GalNAc conjugated ASOs. The GalNAc clusters were conjugated to the 5'-end of an antisense oligonucleotide and evaluated for activity in primary mouse hepatocytes where they showed ∼10-fold improvement in activity.
Collapse
Affiliation(s)
- Michael T Migawa
- Medicinal Chemistry, Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, United States.
| | - Thazha P Prakash
- Medicinal Chemistry, Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, United States
| | - Guillermo Vasquez
- Medicinal Chemistry, Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, United States
| | - W Brad Wan
- Medicinal Chemistry, Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, United States
| | - Jinghua Yu
- Medicinal Chemistry, Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, United States
| | - Garth A Kinberger
- Medicinal Chemistry, Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, United States
| | - Michael E Østergaard
- Medicinal Chemistry, Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, United States
| | - Eric E Swayze
- Medicinal Chemistry, Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, United States
| | - Punit P Seth
- Medicinal Chemistry, Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, United States
| |
Collapse
|
33
|
Prakash TP, Yu J, Migawa MT, Kinberger GA, Wan WB, Østergaard ME, Carty RL, Vasquez G, Low A, Chappell A, Schmidt K, Aghajan M, Crosby J, Murray HM, Booten SL, Hsiao J, Soriano A, Machemer T, Cauntay P, Burel SA, Murray SF, Gaus H, Graham MJ, Swayze EE, Seth PP. Comprehensive Structure-Activity Relationship of Triantennary N-Acetylgalactosamine Conjugated Antisense Oligonucleotides for Targeted Delivery to Hepatocytes. J Med Chem 2016; 59:2718-33. [PMID: 26914862 DOI: 10.1021/acs.jmedchem.5b01948] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The comprehensive structure-activity relationships of triantennary GalNAc conjugated ASOs for enhancing potency via ASGR mediated delivery to hepatocytes is reported. Seventeen GalNAc clusters were assembled from six distinct scaffolds and attached to ASOs. The resulting ASO conjugates were evaluated in ASGR binding assays, in primary hepatocytes, and in mice. Five structurally distinct GalNAc clusters were chosen for more extensive evaluation using ASOs targeting SRB-1, A1AT, FXI, TTR, and ApoC III mRNAs. GalNAc-ASO conjugates exhibited excellent potencies (ED50 0.5-2 mg/kg) for reducing the targeted mRNAs and proteins. This work culminated in the identification of a simplified tris-based GalNAc cluster (THA-GN3), which can be efficiently assembled using readily available starting materials and conjugated to ASOs using a solution phase conjugation strategy. GalNAc-ASO conjugates thus represent a viable approach for enhancing potency of ASO drugs in the clinic without adding significant complexity or cost to existing protocols for manufacturing oligonucleotide drugs.
Collapse
Affiliation(s)
- Thazha P Prakash
- Ionis Pharmaceuticals Inc. , 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Jinghua Yu
- Ionis Pharmaceuticals Inc. , 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Michael T Migawa
- Ionis Pharmaceuticals Inc. , 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Garth A Kinberger
- Ionis Pharmaceuticals Inc. , 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - W Brad Wan
- Ionis Pharmaceuticals Inc. , 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Michael E Østergaard
- Ionis Pharmaceuticals Inc. , 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Recaldo L Carty
- Ionis Pharmaceuticals Inc. , 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Guillermo Vasquez
- Ionis Pharmaceuticals Inc. , 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Audrey Low
- Ionis Pharmaceuticals Inc. , 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Alfred Chappell
- Ionis Pharmaceuticals Inc. , 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Karsten Schmidt
- Ionis Pharmaceuticals Inc. , 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Mariam Aghajan
- Ionis Pharmaceuticals Inc. , 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Jeff Crosby
- Ionis Pharmaceuticals Inc. , 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Heather M Murray
- Ionis Pharmaceuticals Inc. , 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Sheri L Booten
- Ionis Pharmaceuticals Inc. , 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Jill Hsiao
- Ionis Pharmaceuticals Inc. , 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Armand Soriano
- Ionis Pharmaceuticals Inc. , 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Todd Machemer
- Ionis Pharmaceuticals Inc. , 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Patrick Cauntay
- Ionis Pharmaceuticals Inc. , 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Sebastien A Burel
- Ionis Pharmaceuticals Inc. , 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Susan F Murray
- Ionis Pharmaceuticals Inc. , 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Hans Gaus
- Ionis Pharmaceuticals Inc. , 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Mark J Graham
- Ionis Pharmaceuticals Inc. , 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Eric E Swayze
- Ionis Pharmaceuticals Inc. , 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Punit P Seth
- Ionis Pharmaceuticals Inc. , 2855 Gazelle Court, Carlsbad, California 92010, United States
| |
Collapse
|
34
|
Liang XH, Shen W, Sun H, Kinberger GA, Prakash TP, Nichols JG, Crooke ST. Hsp90 protein interacts with phosphorothioate oligonucleotides containing hydrophobic 2'-modifications and enhances antisense activity. Nucleic Acids Res 2016; 44:3892-907. [PMID: 26945041 PMCID: PMC4856991 DOI: 10.1093/nar/gkw144] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 02/25/2016] [Indexed: 02/05/2023] Open
Abstract
RNase H1-dependent antisense oligonucleotides (ASOs) are chemically modified to enhance pharmacological properties. Major modifications include phosphorothioate (PS) backbone and different 2′-modifications in 2–5 nucleotides at each end (wing) of an ASO. Chemical modifications can affect protein binding and understanding ASO-protein interactions is important for better drug design. Recently we identified many intracellular ASO-binding proteins and found that protein binding could affect ASO potency. Here, we analyzed the structure-activity-relationships of ASO-protein interactions and found 2′-modifications significantly affected protein binding, including La, P54nrb and NPM. PS-ASOs containing more hydrophobic 2′-modifications exhibit higher affinity for proteins in general, although certain proteins, e.g. Ku70/Ku80 and TCP1, are less affected by 2′-modifications. We found that Hsp90 protein binds PS-ASOs containing locked-nucleic-acid (LNA) or constrained-ethyl-bicyclic-nucleic-acid ((S)-cEt) modifications much more avidly than 2′-O-methoxyethyl (MOE). ASOs bind the mid-domain of Hsp90 protein. Hsp90 interacts with more hydrophobic 2′ modifications, e.g. (S)-cEt or LNA, in the 5′-wing of the ASO. Reduction of Hsp90 protein decreased activity of PS-ASOs with 5′-LNA or 5′-cEt wings, but not with 5′-MOE wing. Together, our results indicate Hsp90 protein enhances the activity of PS/LNA or PS/(S)-cEt ASOs, and imply that altering protein binding of ASOs using different chemical modifications can improve therapeutic performance of PS-ASOs.
Collapse
Affiliation(s)
- Xue-Hai Liang
- Department of Core Antisense Research, IONIS Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Wen Shen
- Department of Core Antisense Research, IONIS Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Hong Sun
- Department of Core Antisense Research, IONIS Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Garth A Kinberger
- Department of Medicinal Chemistry, IONIS Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Thazha P Prakash
- Department of Medicinal Chemistry, IONIS Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Joshua G Nichols
- Department of Core Antisense Research, IONIS Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Stanley T Crooke
- Department of Core Antisense Research, IONIS Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| |
Collapse
|
35
|
Abstract
Genome editing with the clustered, regularly interspaced, short palindromic repeats (CRISPR)-Cas9 nuclease system is a powerful technology for manipulating genomes, including introduction of gene disruptions or corrections. Here we develop a chemically modified, 29-nucleotide synthetic CRISPR RNA (scrRNA), which in combination with unmodified transactivating crRNA (tracrRNA) is shown to functionally replace the natural guide RNA in the CRISPR-Cas9 nuclease system and to mediate efficient genome editing in human cells. Incorporation of rational chemical modifications known to protect against nuclease digestion and stabilize RNA-RNA interactions in the tracrRNA hybridization region of CRISPR RNA (crRNA) yields a scrRNA with enhanced activity compared with the unmodified crRNA and comparable gene disruption activity to the previously published single guide RNA. Taken together, these findings provide a platform for therapeutic applications, especially for nervous system disease, using successive application of cell-permeable, synthetic CRISPR RNAs to activate and then silence Cas9 nuclease activity.
Collapse
Affiliation(s)
| | - Moira A McMahon
- Ludwig Institute for Cancer Research and Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093
| | | | | | | | - Don W Cleveland
- Ludwig Institute for Cancer Research and Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093
| |
Collapse
|
36
|
Burel SA, Hart CE, Cauntay P, Hsiao J, Machemer T, Katz M, Watt A, Bui HH, Younis H, Sabripour M, Freier SM, Hung G, Dan A, Prakash TP, Seth PP, Swayze EE, Bennett CF, Crooke ST, Henry SP. Hepatotoxicity of high affinity gapmer antisense oligonucleotides is mediated by RNase H1 dependent promiscuous reduction of very long pre-mRNA transcripts. Nucleic Acids Res 2015; 44:2093-109. [PMID: 26553810 PMCID: PMC4797265 DOI: 10.1093/nar/gkv1210] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 10/27/2015] [Indexed: 12/24/2022] Open
Abstract
High affinity antisense oligonucleotides (ASOs) containing bicylic modifications (BNA) such as locked nucleic acid (LNA) designed to induce target RNA cleavage have been shown to have enhanced potency along with a higher propensity to cause hepatotoxicity. In order to understand the mechanism of this hepatotoxicity, transcriptional profiles were collected from the livers of mice treated with a panel of highly efficacious hepatotoxic or non-hepatotoxic LNA ASOs. We observed highly selective transcript knockdown in mice treated with non-hepatotoxic LNA ASOs, while the levels of many unintended transcripts were reduced in mice treated with hepatotoxic LNA ASOs. This transcriptional signature was concurrent with on-target RNA reduction and preceded transaminitis. Remarkably, the mRNA transcripts commonly reduced by toxic LNA ASOs were generally not strongly associated with any particular biological process, cellular component or functional group. However, they tended to have much longer pre-mRNA transcripts. We also demonstrate that the off-target RNA knockdown and hepatotoxicity is attenuated by RNase H1 knockdown, and that this effect can be generalized to high affinity modifications beyond LNA. This suggests that for a certain set of ASOs containing high affinity modifications such as LNA, hepatotoxicity can occur as a result of unintended off-target RNase H1 dependent RNA degradation.
Collapse
Affiliation(s)
| | | | | | - Jill Hsiao
- Isis Pharmaceuticals, Carlsbad, CA 921010, USA
| | | | | | - Andy Watt
- Isis Pharmaceuticals, Carlsbad, CA 921010, USA
| | | | | | | | | | - Gene Hung
- Isis Pharmaceuticals, Carlsbad, CA 921010, USA
| | - Amy Dan
- Isis Pharmaceuticals, Carlsbad, CA 921010, USA
| | - T P Prakash
- Isis Pharmaceuticals, Carlsbad, CA 921010, USA
| | | | | | | | | | | |
Collapse
|
37
|
Prakash TP, Brad Wan W, Low A, Yu J, Chappell AE, Gaus H, Kinberger GA, Østergaard ME, Migawa MT, Swayze EE, Seth PP. Solid-phase synthesis of 5'-triantennary N-acetylgalactosamine conjugated antisense oligonucleotides using phosphoramidite chemistry. Bioorg Med Chem Lett 2015; 25:4127-30. [PMID: 26299345 DOI: 10.1016/j.bmcl.2015.08.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 07/30/2015] [Accepted: 08/06/2015] [Indexed: 11/20/2022]
Abstract
A convenient solid-phase synthetic method was developed for assembling a triantennary N-acetylgalactosamine (GalNAc) cluster on the 5'-end of antisense oligonucleotide using phosphoramidite chemistry. Conjugation of the 5'-triantennary GalNAc cluster improved potency of the 14 mer ASO 7-fold in mice and more than 50 fold in hepatocytes. The synthetic approach described in this Letter simplifies the synthesis of 5'-triantennary GalNAc cluster conjugated ASOs and helps understand the structure-activity relationship for targeting hepatocytes with oligonucleotide therapeutics.
Collapse
Affiliation(s)
- Thazha P Prakash
- Medicinal Chemistry, Isis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, United States.
| | - W Brad Wan
- Medicinal Chemistry, Isis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, United States
| | - Audrey Low
- Medicinal Chemistry, Isis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, United States
| | - Jinghua Yu
- Medicinal Chemistry, Isis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, United States
| | - Alfred E Chappell
- Medicinal Chemistry, Isis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, United States
| | - Hans Gaus
- Medicinal Chemistry, Isis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, United States
| | - Garth A Kinberger
- Medicinal Chemistry, Isis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, United States
| | - Michael E Østergaard
- Medicinal Chemistry, Isis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, United States
| | - Michael T Migawa
- Medicinal Chemistry, Isis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, United States
| | - Eric E Swayze
- Medicinal Chemistry, Isis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, United States
| | - Punit P Seth
- Medicinal Chemistry, Isis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, United States
| |
Collapse
|
38
|
Østergaard ME, Yu J, Kinberger GA, Wan WB, Migawa MT, Vasquez G, Schmidt K, Gaus HJ, Murray HM, Low A, Swayze EE, Prakash TP, Seth PP. Efficient Synthesis and Biological Evaluation of 5'-GalNAc Conjugated Antisense Oligonucleotides. Bioconjug Chem 2015; 26:1451-5. [PMID: 26011654 DOI: 10.1021/acs.bioconjchem.5b00265] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Conjugation of triantennary N-acetyl galactosamine (GalNAc) to oligonucleotide therapeutics results in marked improvement in potency for reducing gene targets expressed in hepatocytes. In this report we describe a robust and efficient solution-phase conjugation strategy to attach triantennary GalNAc clusters (mol. wt. ∼2000) activated as PFP (pentafluorophenyl) esters onto 5'-hexylamino modified antisense oligonucleotides (5'-HA ASOs, mol. wt. ∼8000 Da). The conjugation reaction is efficient and was used to prepare GalNAc conjugated ASOs from milligram to multigram scale. The solution phase method avoids loading of GalNAc clusters onto solid-support for automated synthesis and will facilitate evaluation of GalNAc clusters for structure activity relationship (SAR) studies. Furthermore, we show that transfer of the GalNAc cluster from the 3'-end of an ASO to the 5'-end results in improved potency in cells and animals.
Collapse
Affiliation(s)
- Michael E Østergaard
- Isis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Jinghua Yu
- Isis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Garth A Kinberger
- Isis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - W Brad Wan
- Isis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Michael T Migawa
- Isis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Guillermo Vasquez
- Isis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Karsten Schmidt
- Isis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Hans J Gaus
- Isis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Heather M Murray
- Isis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Audrey Low
- Isis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Eric E Swayze
- Isis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Thazha P Prakash
- Isis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Punit P Seth
- Isis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| |
Collapse
|
39
|
Prakash TP, Lima WF, Murray HM, Li W, Kinberger GA, Chappell AE, Gaus H, Seth PP, Bhat B, Crooke ST, Swayze EE. Identification of metabolically stable 5'-phosphate analogs that support single-stranded siRNA activity. Nucleic Acids Res 2015; 43:2993-3011. [PMID: 25753666 PMCID: PMC4381071 DOI: 10.1093/nar/gkv162] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 02/16/2015] [Accepted: 02/19/2015] [Indexed: 12/23/2022] Open
Abstract
The ss-siRNA activity in vivo requires a metabolically stable 5'-phosphate analog. In this report we used crystal structure of the 5'-phosphate binding pocket of Ago-2 bound with guide strand to design and synthesize ss-siRNAs containing various 5'-phosphate analogs. Our results indicate that the electronic and spatial orientation of the 5'-phosphate analog was critical for ss-siRNA activity. Chemically modified ss-siRNA targeting human apoC III mRNA demonstrated good potency for inhibiting ApoC III mRNA and protein in transgenic mice. Moreover, ApoC III ss-siRNAs were able to reduce the triglyceride and LDL cholesterol in transgenic mice demonstrating pharmacological effect of ss-siRNA. Our study provides guidance to develop surrogate phosphate analog for ss-siRNA and demonstrates that ss-siRNA provides an alternative strategy for therapeutic gene silencing.
Collapse
Affiliation(s)
- Thazha P Prakash
- Isis Pharmaceuticals Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, USA
| | - Walt F Lima
- Isis Pharmaceuticals Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, USA
| | - Heather M Murray
- Isis Pharmaceuticals Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, USA
| | - Wenyu Li
- Isis Pharmaceuticals Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, USA
| | | | | | - Hans Gaus
- Isis Pharmaceuticals Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, USA
| | - Punit P Seth
- Isis Pharmaceuticals Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, USA
| | - Balkrishen Bhat
- Isis Pharmaceuticals Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, USA
| | - Stanley T Crooke
- Isis Pharmaceuticals Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, USA
| | - Eric E Swayze
- Isis Pharmaceuticals Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, USA
| |
Collapse
|
40
|
Abstract
Single-stranded silencing RNAs (ss-siRNAs) are chemically modified single-stranded oligonucleotides that can function through the cellular RNA interference (RNAi) machinery to modulate gene expression. Because their invention is recent, few studies have appeared describing their use and the potential of ss-siRNAs as a platform for controlling gene expression remains largely unknown. Using oligonucleotides to modulate splicing is an important area for therapeutic development and we tested the hypothesis that ss-siRNAs targeting splice sites might also be capable of directing increased production of therapeutically promising protein isoforms. Here we observe that ss-siRNAs alter splicing of dystrophin. Altered splicing requires a seed sequence complementarity to the target and expression of the RNAi factor argonaute 2. These results demonstrate that ss-siRNAs can be used to modulate splicing, providing another option for therapeutic development programs that aim to increase production of key protein isoforms. Splicing is a classical nuclear process and our data showing that it can be modulated through the action of RNA and RNAi factors offers further evidence that RNAi can take place in mammalian cell nuclei.
Collapse
Affiliation(s)
- Jing Liu
- 1Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas.,2Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
| | - Jiaxin Hu
- 1Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas.,2Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
| | - Jessica A Hicks
- 1Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas.,2Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
| | | | - David R Corey
- 1Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas.,2Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
| |
Collapse
|
41
|
Pandey SK, Nowak A, Perkins J, Ferng A, Prakash TP. Effect of 2'-O-[2-[2-(N,N-dimethylamino)ethoxy]ethyl] modification on activity of gapmer antisense oligonucleotides containing 2',4'-constrained 2'-O-ethyl nucleic acid. Bioorg Med Chem Lett 2015; 25:1688-1691. [PMID: 25804718 DOI: 10.1016/j.bmcl.2015.03.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 02/26/2015] [Accepted: 03/02/2015] [Indexed: 01/30/2023]
Abstract
We evaluated the effect of combining 2'-O-[2-[2-(N,N-dimethylamino)ethoxy]ethyl] (2'-O-DMAEOE), a 2'-cationic modification, with a 2',4'-constrained 2'-O-ethyl nucleic acid (cEt BNA) on the activity of an antisense oligonucleotide (ASO) using PTEN as a model target. Our results suggest that replacing one cEt BNA nucleotide with 2'-O-DMAEOE nucleotide at the 5'-end of a 2-10-2 gapmer ASO maintained the potency relative to parent ASO in liver. The cationic 2'-O-DMAEOE modification did not improve the activity of ASO in extra-hepatic tissues. Results from this study provide guidance to design improved antisense oligonucleotide drugs.
Collapse
Affiliation(s)
- Sanjay K Pandey
- Antisense Drug Discovery, Isis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, United States.
| | - Anna Nowak
- Antisense Drug Discovery, Isis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, United States
| | - Jake Perkins
- Medicinal Chemistry, Isis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, United States
| | - Annie Ferng
- Antisense Drug Discovery, Isis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, United States
| | - Thazha P Prakash
- Medicinal Chemistry, Isis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, United States
| |
Collapse
|
42
|
Hu J, Liu J, Narayanannair KJ, Lackey JG, Kuchimanchi S, Rajeev KG, Manoharan M, Swayze EE, Lima WF, Prakash TP, Xiang Q, Martinez C, Corey DR. Allele-selective inhibition of mutant atrophin-1 expression by duplex and single-stranded RNAs. Biochemistry 2014; 53:4510-8. [PMID: 24981774 PMCID: PMC4108179 DOI: 10.1021/bi500610r] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
![]()
Dentatorubral-pallidoluysian
atrophy (DRPLA) is a progressive neurodegenerative
disorder that currently has no curative treatments. DRPLA is caused
by an expansion of a CAG trinucleotide repeat region within the protein-encoding
sequence of the atrophin-1 (ATN-1) gene. Inhibition
of mutant ATN-1 protein expression is one strategy for treating DRPLA,
and allele-selective gene silencing agents that block mutant expression
over wild-type expression would be lead compounds for therapeutic
development. Here we develop an assay for distinguishing mutant from
wild-type ATN-1 protein by gel electrophoresis. We use this assay
to evaluate duplex RNAs and single-stranded silencing RNAs (ss-siRNAs)
for allele-selective inhibition of ATN-1 protein expression. We observed
potent and allele-selective inhibition by RNA duplexes that contain
mismatched bases relative to the CAG target and have the potential
to form miRNA-like complexes. ss-siRNAs that contained mismatches
were as selective as mismatch-containing duplexes. We also report
allele-selective inhibition by duplex RNAs containing unlocked nucleic
acids or abasic substitutions, although selectivities are not as high.
Five compounds that showed >8-fold allele selectivity for mutant ATN-1 were also selective for inhibiting the expression
of two other trinucleotide repeat disease genes, ataxin-3 (ATXN-3) and huntingtin (HTT). These data
demonstrate that the expanded trinucleotide repeat within ATN-1 mRNA is a potential target for compounds designed
to achieve allele-selective inhibition of ATN-1 protein, and one agent
may allow the targeting of multiple disease genes.
Collapse
Affiliation(s)
- Jiaxin Hu
- Departments of Pharmacology and Biochemistry, University of Texas Southwestern Medical Center , 6001 Forest Park Road, Dallas, Texas 75390-9041, United States
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
43
|
Prakash TP, Graham MJ, Yu J, Carty R, Low A, Chappell A, Schmidt K, Zhao C, Aghajan M, Murray HF, Riney S, Booten SL, Murray SF, Gaus H, Crosby J, Lima WF, Guo S, Monia BP, Swayze EE, Seth PP. Targeted delivery of antisense oligonucleotides to hepatocytes using triantennary N-acetyl galactosamine improves potency 10-fold in mice. Nucleic Acids Res 2014; 42:8796-807. [PMID: 24992960 PMCID: PMC4117763 DOI: 10.1093/nar/gku531] [Citation(s) in RCA: 405] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Triantennary N-acetyl galactosamine (GalNAc, GN3: ), a high-affinity ligand for the hepatocyte-specific asialoglycoprotein receptor (ASGPR), enhances the potency of second-generation gapmer antisense oligonucleotides (ASOs) 6-10-fold in mouse liver. When combined with next-generation ASO designs comprised of short S-cEt (S-2'-O-Et-2',4'-bridged nucleic acid) gapmer ASOs, ∼ 60-fold enhancement in potency relative to the parent MOE (2'-O-methoxyethyl RNA) ASO was observed. GN3: -conjugated ASOs showed high affinity for mouse ASGPR, which results in enhanced ASO delivery to hepatocytes versus non-parenchymal cells. After internalization into cells, the GN3: -ASO conjugate is metabolized to liberate the parent ASO in the liver. No metabolism of the GN3: -ASO conjugate was detected in plasma suggesting that GN3: acts as a hepatocyte targeting prodrug that is detached from the ASO by metabolism after internalization into the liver. GalNAc conjugation also enhanced potency and duration of the effect of two ASOs targeting human apolipoprotein C-III and human transthyretin (TTR) in transgenic mice. The unconjugated ASOs are currently in late stage clinical trials for the treatment of familial chylomicronemia and TTR-mediated polyneuropathy. The ability to translate these observations in humans offers the potential to improve therapeutic index, reduce cost of therapy and support a monthly dosing schedule for therapeutic suppression of gene expression in the liver using ASOs.
Collapse
Affiliation(s)
- Thazha P Prakash
- Isis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Mark J Graham
- Isis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Jinghua Yu
- Isis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Rick Carty
- Isis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Audrey Low
- Isis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Alfred Chappell
- Isis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Karsten Schmidt
- Isis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Chenguang Zhao
- Isis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Mariam Aghajan
- Isis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Heather F Murray
- Isis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Stan Riney
- Isis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Sheri L Booten
- Isis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Susan F Murray
- Isis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Hans Gaus
- Isis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Jeff Crosby
- Isis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Walt F Lima
- Isis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Shuling Guo
- Isis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Brett P Monia
- Isis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Eric E Swayze
- Isis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Punit P Seth
- Isis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| |
Collapse
|
44
|
Yu J, Pandey SK, Khatri H, Prakash TP, Swayze EE, Seth PP. Synthesis and antisense properties of 2'-O-(2S-methoxypropyl)-RNA-modified gapmer antisense oligonucleotides. ChemMedChem 2014; 9:2040-4. [PMID: 24891270 DOI: 10.1002/cmdc.201402099] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Indexed: 11/06/2022]
Abstract
To ascertain whether increasing hydrophobicity can enhance the activity of second-generation antisense oligonucleotides (ASOs) in muscle, we investigated the antisense properties of 2'-O-(2S-methoxypropyl)-RNA (2S-MOP)-modified ASOs. Synthesis of the 2S-MOP 5-methyl uridine phosphoramidite was accomplished on a multi-gram scale by Lewis-acid-catalyzed ring opening of 5'-O-tert-butyldiphenylsilyl ether-protected 2,2'-anhydro-5-methyl uridine with 2S-methoxy-1-propanol. Synthesis of the 2S-MOP 5-methyl cytidine nucleoside from the corresponding 5-methyl uridine nucleoside was accomplished by formation and displacement of a 4-triazolide intermediate with aqueous ammonia. 2S-MOP-modified oligonucleotides were prepared on an automated DNA synthesizer and showed similar enhancements in duplex thermal stability as 2'-O-methoxyethyl RNA (MOE)-modified oligonucleotides. 2S-MOP-containing antisense oligonucleotides were evaluated in Balb-c mice and showed good activity for decreasing the expression levels of scavenger receptor B1 (Srb1) and phosphatase and tensin homologue (PTEN) mRNA in liver and muscle tissue.
Collapse
Affiliation(s)
- Jinghua Yu
- Isis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010 (USA)
| | | | | | | | | | | |
Collapse
|
45
|
Liang XH, Shen W, Sun H, Prakash TP, Crooke ST. TCP1 complex proteins interact with phosphorothioate oligonucleotides and can co-localize in oligonucleotide-induced nuclear bodies in mammalian cells. Nucleic Acids Res 2014; 42:7819-32. [PMID: 24861627 PMCID: PMC4081088 DOI: 10.1093/nar/gku484] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Phosphorothioate (PS) antisense oligonucleotides (ASOs) have been successfully developed as drugs to reduce the expression of disease-causing genes. PS-ASOs can be designed to induce degradation of complementary RNAs via the RNase H pathway and much is understood about that process. However, interactions of PS-ASOs with other cellular proteins are not well characterized. Here we report that in cells transfected with PS-ASOs, the chaperonin T-complex 1 (TCP1) proteins interact with PS-ASOs and enhance antisense activity. The TCP1-β subunit co-localizes with PS-ASOs in distinct nuclear structures, termed phosphorothioate bodies or PS-bodies. Upon Ras-related nuclear protein (RAN) depletion, cytoplasmic PS-body-like structures were observed and nuclear concentrations of PS-ASOs were reduced, suggesting that TCP1-β can interact with PS-ASOs in the cytoplasm and that the nuclear import of PS-ASOs is at least partially through the RAN-mediated pathway. Upon free uptake, PS-ASOs co-localize with TCP1 proteins in cytoplasmic foci related to endosomes/lysosomes. Together, our results indicate that the TCP1 complex binds oligonucleotides with TCP1-β subunit being a nuclear PS-body component and suggest that the TCP1 complex may facilitate PS-ASO uptake and/or release from the endocytosis pathway.
Collapse
Affiliation(s)
- Xue-hai Liang
- Department of Core Antisense Research, ISIS Pharmaceuticals, Inc., Carlsbad, CA 92010, USA
| | - Wen Shen
- Department of Core Antisense Research, ISIS Pharmaceuticals, Inc., Carlsbad, CA 92010, USA
| | - Hong Sun
- Department of Core Antisense Research, ISIS Pharmaceuticals, Inc., Carlsbad, CA 92010, USA
| | - Thazha P Prakash
- Department of Medicinal Chemistry, ISIS Pharmaceuticals, Inc., Carlsbad, CA 92010, USA
| | - Stanley T Crooke
- Department of Core Antisense Research, ISIS Pharmaceuticals, Inc., Carlsbad, CA 92010, USA
| |
Collapse
|
46
|
Hu J, Liu J, Yu D, Aiba Y, Lee S, Pendergraff H, Boubaker J, Artates JW, Lagier-Tourenne C, Lima WF, Swayze EE, Prakash TP, Corey DR. Exploring the effect of sequence length and composition on allele-selective inhibition of human huntingtin expression by single-stranded silencing RNAs. Nucleic Acid Ther 2014; 24:199-209. [PMID: 24694346 DOI: 10.1089/nat.2013.0476] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Mutant huntingtin (HTT) protein is the cause of Huntington's disease (HD), an incurable neurological disorder. Almost all patients are heterozygous for mutant HTT and approaches that reduce levels of mutant HTT while leaving expression of wild-type HTT intact might be ideal options for therapeutic development. We have developed several allele-selective strategies for silencing HTT, including single-stranded silencing RNAs (ss-siRNAs). ss-siRNAs are oligonucleotides containing chemical modifications that permit action through the RNA interference (RNAi) pathway. Modified ss-siRNAs chosen to test the effects of varying oligomer length, lipid modification, the introduction of mismatched bases, and variation of chemical modification. We find that several modified ss-siRNA are potent and allele-selective inhibitors of HTT expression. An ss-siRNA with three mismatched bases relative to the CAG repeat was an allele-selective inhibitor of HTT expression in the HdhQ175 mouse model. Multiple allele-selective ss-siRNAs provide a wide platform of modifications to draw on for further optimization and therapeutic development. Our data provide insights into how ss-siRNAs can be modified to improve their properties and facilitate the discovery of the lead compounds necessary for further development.
Collapse
Affiliation(s)
- Jiaxin Hu
- 1 Departments of Pharmacology and Biochemistry, University of Texas Southwestern Medical Center at Dallas , Dallas, Texas
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
47
|
Migawa MT, Prakash TP, Vasquez G, Seth PP, Swayze EE. Synthesis and biophysical properties of constrained D-altritol nucleic acids (cANA). Org Lett 2013; 15:4316-9. [PMID: 23937264 DOI: 10.1021/ol401730d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The first synthesis of constrained altritol nucleic acids (cANA) containing antisense oligonucleotides (ASOs) was carried out to ascertain how conformationally restricting the D-altritol backbone-containing ASO (Me-ANA) would affect their ability to form duplexes with RNA. It was found that the thermal stability was reduced (cANA/RNA -1.1 °C/modification) compared to DNA/RNA, suggesting the constrained system results in a small destabilizing perturbation in the duplex structure.
Collapse
Affiliation(s)
- Michael T Migawa
- Department of Medicinal Chemistry, Isis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, California 92010, USA.
| | | | | | | | | |
Collapse
|
48
|
Liu J, Yu D, Aiba Y, Pendergraff H, Swayze EE, Lima WF, Hu J, Prakash TP, Corey DR. ss-siRNAs allele selectively inhibit ataxin-3 expression: multiple mechanisms for an alternative gene silencing strategy. Nucleic Acids Res 2013; 41:9570-83. [PMID: 23935115 PMCID: PMC3814390 DOI: 10.1093/nar/gkt693] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Single-stranded silencing RNAs (ss-siRNAs) provide an alternative approach to gene silencing. ss-siRNAs combine the simplicity and favorable biodistribution of antisense oligonucleotides with robust silencing through RNA interference (RNAi). Previous studies reported potent and allele-selective inhibition of human huntingtin expression by ss-siRNAs that target the expanded CAG repeats within the mutant allele. Mutant ataxin-3, the genetic cause of Machado-Joseph Disease, also contains an expanded CAG repeat. We demonstrate here that ss-siRNAs are allele-selective inhibitors of ataxin-3 expression and then redesign ss-siRNAs to optimize their selectivity. We find that both RNAi-related and non-RNAi-related mechanisms affect gene expression by either blocking translation or affecting alternative splicing. These results have four broad implications: (i) ss-siRNAs will not always behave similarly to analogous RNA duplexes; (ii) the sequences surrounding CAG repeats affect allele-selectivity of anti-CAG oligonucleotides; (iii) ss-siRNAs can function through multiple mechanisms and; and (iv) it is possible to use chemical modification to optimize ss-siRNA properties and improve their potential for drug discovery.
Collapse
Affiliation(s)
- Jing Liu
- Departments of Pharmacology and Biochemistry, UT Southwestern Medical Center at Dallas, Dallas, TX 75390, USA and Department of Medicinal Chemistry and Core Antisense Research, ISIS Pharmaceuticals, Carlsbad, CA 92010, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
49
|
Prakash TP, Lima WF, Murray HM, Elbashir S, Cantley W, Foster D, Jayaraman M, Chappell AE, Manoharan M, Swayze EE, Crooke ST. Lipid nanoparticles improve activity of single-stranded siRNA and gapmer antisense oligonucleotides in animals. ACS Chem Biol 2013; 8:1402-6. [PMID: 23614580 DOI: 10.1021/cb4001316] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We evaluated the abilities of an antisense oligonucleotide (ASO), a small interfering RNA (siRNA), and a single-stranded siRNA (ss-siRNA) to inhibit expression from the PTEN gene in mice when formulated identically with lipid nanoparticles (LNPs). Significantly greater reductions in levels of PTEN mRNA were observed for LNP-formulated agents compared to unformulated drugs when gene silencing was evaluated after a single dose in the livers of mice. An unformulated ss-siRNA modified with a metabolically stable phosphate mimic 5'-(E)-vinylphosphonate showed dose-dependent reduction of PTEN mRNA in mice, albeit at doses significantly higher than those observed for formulated ss-siRNA. These results demonstrate that LNPs can be used to deliver functional antisense and ss-siRNA therapeutics to the liver, indicating that progress in the field of siRNA delivery is transferable to other classes of nucleic acid-based drugs.
Collapse
Affiliation(s)
- Thazha P. Prakash
- Department of Medicinal Chemistry, Isis Pharmaceuticals, Inc., 1896 Rutherford Road, Carlsbad,
California 92008, United States
| | - Walt F. Lima
- Department of Medicinal Chemistry, Isis Pharmaceuticals, Inc., 1896 Rutherford Road, Carlsbad,
California 92008, United States
| | - Heather M. Murray
- Department of Medicinal Chemistry, Isis Pharmaceuticals, Inc., 1896 Rutherford Road, Carlsbad,
California 92008, United States
| | - Sayda Elbashir
- Alnylam Pharmaceuticals, 300 Third Street,
Cambridge, Massachusetts 02142, United States
| | - William Cantley
- Alnylam Pharmaceuticals, 300 Third Street,
Cambridge, Massachusetts 02142, United States
| | - Don Foster
- Alnylam Pharmaceuticals, 300 Third Street,
Cambridge, Massachusetts 02142, United States
| | - Muthusamy Jayaraman
- Alnylam Pharmaceuticals, 300 Third Street,
Cambridge, Massachusetts 02142, United States
| | - Alfred E. Chappell
- Department of Medicinal Chemistry, Isis Pharmaceuticals, Inc., 1896 Rutherford Road, Carlsbad,
California 92008, United States
| | - Muthiah Manoharan
- Alnylam Pharmaceuticals, 300 Third Street,
Cambridge, Massachusetts 02142, United States
| | - Eric E. Swayze
- Department of Medicinal Chemistry, Isis Pharmaceuticals, Inc., 1896 Rutherford Road, Carlsbad,
California 92008, United States
| | - Stanley T. Crooke
- Department of Medicinal Chemistry, Isis Pharmaceuticals, Inc., 1896 Rutherford Road, Carlsbad,
California 92008, United States
| |
Collapse
|
50
|
Egli M, Minasov G, Tereshko V, Pallan PS, Teplova M, Inamati GB, Lesnik EA, Owens SR, Ross BS, Prakash TP, Manoharan M. Correction to Probing the Influence of Stereoelectronic Effects on the Biophysical Properties of Oligonucleotides: Comprehensive Analysis of the RNA Affinity, Nuclease Resistance, and Crystal Structure of Ten 2′- O-Ribonucleic Acid Modifications. Biochemistry 2013. [DOI: 10.1021/bi4002166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|