1
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Zewge D, Butora G, Sherer EC, Tellers DM, Sidler DR, Gouker J, Copeland G, Jadhav V, Li Z, Armstrong J, Davies IW. Post-Synthetic Modification of Oligonucleotides via Orthogonal Amidation and Copper Catalyzed Cycloaddition Reactions. Bioconjug Chem 2018; 29:1859-1865. [PMID: 29893553 DOI: 10.1021/acs.bioconjchem.8b00298] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
An efficient multicomponent orthogonal protocol was developed for post-synthetic oligonucleotide modification using commercially available 2'- O-methyl ester and 2'- O-propargyl nucleoside scaffolds. Amidation of methyl esters with primary amines was achieved in the presence of 2'-propargyl groups which were utilized for subsequent copper catalyzed cycloaddition with GalNAc-azide. The methodology was applied to generate siRNA composed of multiple amide and triazole conjugates. Computational methods were used to illustrate the impact of substitution at the 2'-position. This a powerful post-oligomerization technique for rapidly introducing diversity to oligonucleotide design.
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Affiliation(s)
- Daniel Zewge
- Department of Process Chemistry , Merck & Co. Inc. , Rahway , New Jersey 07065 , United States
| | - Gabor Butora
- Department of Process Chemistry , Merck & Co. Inc. , Rahway , New Jersey 07065 , United States
| | - Edward C Sherer
- Department of Process Chemistry , Merck & Co. Inc. , Rahway , New Jersey 07065 , United States
| | | | - Daniel R Sidler
- Department of Process Chemistry , Merck & Co. Inc. , Rahway , New Jersey 07065 , United States
| | - Joseph Gouker
- Department of Process Chemistry , Merck & Co. Inc. , Rahway , New Jersey 07065 , United States
| | - Greg Copeland
- Department of Process Chemistry , Merck & Co. Inc. , Rahway , New Jersey 07065 , United States
| | | | - Zhen Li
- Department of Process Chemistry , Merck & Co. Inc. , Rahway , New Jersey 07065 , United States
| | - Joseph Armstrong
- Department of Process Chemistry , Merck & Co. Inc. , Rahway , New Jersey 07065 , United States
| | - Ian W Davies
- Department of Process Chemistry , Merck & Co. Inc. , Rahway , New Jersey 07065 , United States
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2
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Gaus H, Miller CM, Seth PP, Harris EN. Structural Determinants for the Interactions of Chemically Modified Nucleic Acids with the Stabilin-2 Clearance Receptor. Biochemistry 2018; 57:2061-2064. [PMID: 29589907 PMCID: PMC5905987 DOI: 10.1021/acs.biochem.8b00126] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
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The Stabilin receptors
are systemic clearance receptors for some
classes of chemically modified nucleic acid therapeutics. In this
study, the recombinant human secreted ecto-domain of the small isoform
of Stabilin-2 (s190) was purified from cell culture and evaluated
for direct binding with a multitude of antisense oligonucleotides
(ASOs) using a fluorescence polarization-based assay. The tested ASOs
varied in their backbone composition, modification of the ribose 2′
position, overall length of the oligo, and sequence of the nucleotide
bases. A fully phosphorothioate (PS) ASO with a 5–10–5
pattern of flanking 2′-O-methoxyethyl modifications
was then used to test the effects of pH and salt concentration on
receptor binding. These tests concluded that the PS backbone was the
primary determinant for ASO binding and that decreasing pH and increasing
salt generally increased the rate of ligand dissociation and fit within
the biological parameters expected of a constitutive recycling receptor.
These results will be useful in the rational design of therapeutic
oligonucleotides for enhancing their affinity or avoidance of the
Stabilin receptors.
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Affiliation(s)
- Hans Gaus
- Department of Medicinal Chemistry , Ionis Pharmaceuticals , Carlsbad , California 92010 , United States
| | - Colton M Miller
- Department of Biochemistry , University of Nebraska , Lincoln , Nebraska 68588 , United States
| | - Punit P Seth
- Department of Medicinal Chemistry , Ionis Pharmaceuticals , Carlsbad , California 92010 , United States
| | - Edward N Harris
- Department of Biochemistry , University of Nebraska , Lincoln , Nebraska 68588 , United States
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3
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Willoughby JLS, Chan A, Sehgal A, Butler JS, Nair JK, Racie T, Shulga-Morskaya S, Nguyen T, Qian K, Yucius K, Charisse K, van Berkel TJC, Manoharan M, Rajeev KG, Maier MA, Jadhav V, Zimmermann TS. Evaluation of GalNAc-siRNA Conjugate Activity in Pre-clinical Animal Models with Reduced Asialoglycoprotein Receptor Expression. Mol Ther 2017; 26:105-114. [PMID: 28988716 PMCID: PMC5762979 DOI: 10.1016/j.ymthe.2017.08.019] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 08/21/2017] [Accepted: 08/24/2017] [Indexed: 02/04/2023] Open
Abstract
The hepatocyte-specific asialoglycoprotein receptor (ASGPR) is an ideal candidate for targeted drug delivery to the liver due to its high capacity for substrate clearance from circulation together with its well-conserved expression and function across species. The development of GalNAc-siRNA conjugates, in which a synthetic triantennary N-acetylgalactosamine-based ligand is conjugated to chemically modified siRNA, has enabled efficient, ASGPR-mediated delivery to hepatocytes. To investigate the potential impact of variations in receptor expression on the efficiency of GalNAc-siRNA conjugate delivery, we evaluated the pharmacokinetics and pharmacodynamics of GalNAc-siRNA conjugates in multiple pre-clinical models with reduced receptor expression. Despite greater than 50% reduction in ASGPR levels, GalNAc conjugate activity was retained, suggesting that the remaining receptor capacity was sufficient to mediate efficient uptake of potent GalNAc-siRNAs at pharmacologically relevant dose levels. Collectively, our data support a broad application of the GalNAc-siRNA technology for hepatic targeting, including disease states where ASGPR expression may be reduced.
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Affiliation(s)
| | - Amy Chan
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Alfica Sehgal
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | | | | | - Tim Racie
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | | | - Tuyen Nguyen
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Kun Qian
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | | | | | - Theo J C van Berkel
- Division of Biopharmaceutics, Leiden Academic Center for Drug Research, 2300 RA Leiden, the Netherlands
| | | | | | | | - Vasant Jadhav
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
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4
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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] [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.
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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
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5
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Liu K, Li Q, Wang Y, Liu R, Li Q, Liu S. Affinity-based fluorescence polarization assay for screening molecules acting on insect ryanodine receptors. RSC Adv 2016. [DOI: 10.1039/c6ra02244h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A fluorescence polarization assay was developed for studying affinity binding of active molecules to specific binding site on insect ryanodine receptor.
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Affiliation(s)
- Kechang Liu
- Department of Applied Chemistry
- College of Science
- China Agricultural University
- Beijing 100193
- China
| | - Qingyang Li
- Department of Applied Chemistry
- College of Science
- China Agricultural University
- Beijing 100193
- China
| | - Yi Wang
- Key Laboratory of Agri-food Safety of Anhui Province
- Lab of Quality & Safety and Risk Assessment for Agro-products on Storage and Preservation (Hefei)
- Ministry of Agriculture
- School of Resource and Environment
- Anhui Agricultural University
| | - Ruiquan Liu
- Department of Applied Chemistry
- College of Science
- China Agricultural University
- Beijing 100193
- China
| | - Qibo Li
- Department of Applied Chemistry
- College of Science
- China Agricultural University
- Beijing 100193
- China
| | - Shangzhong Liu
- Department of Applied Chemistry
- College of Science
- China Agricultural University
- Beijing 100193
- China
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6
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Biophysical characterization of lectin–glycan interactions for therapeutics, vaccines and targeted drug-delivery. Future Med Chem 2014; 6:2113-29. [DOI: 10.4155/fmc.14.130] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Lectin–glycan interactions play a role in biological processes, host–pathogen interactions and in disease. A more detailed understanding of these interactions is not only useful for the elucidation of their biological function but can also be applied in immunology, drug development and delivery and diagnostics. We review some commonly used biophysical techniques for studying lectin–glycan interactions; namely: frontal affinity chromatography, glycan/lectin microarray, surface plasmon resonance, electrochemical impedance spectroscopy, isothermal titration calorimetry, fluorescent assays, enzyme linked lectin sorbent assay and saturation transfer difference nuclear magnetic resonance spectroscopy. Each method is evaluated on efficiency, cost and throughput. We also consider the advantages and limitations of each technique and provide examples of their application in biology, drug discovery and delivery, immunology, glycoprofiling and biosensing.
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7
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Yoo B, Cheal SM, Torchon G, Dilhas A, Yang G, Pu J, Punzalan B, Larson SM, Ouerfelli O. N-acetylgalactosamino dendrons as clearing agents to enhance liver targeting of model antibody-fusion protein. Bioconjug Chem 2013; 24:2088-103. [PMID: 24147780 PMCID: PMC3900322 DOI: 10.1021/bc400333m] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Dendrimer clearing agents represent a unique class of compounds for use in multistep targeting (MST) in radioimmunotherapy and imaging. These compounds were developed to facilitate the removal of excess tumor-targeting monoclonal antibody (mAb) prior to administration of the radionuclide to minimize exposure of normal tissue to radiation. Clearing agents are designed to capture the circulating mAb, and target it to the liver for metabolism. Glycodendrons are ideally suited for MST applications as these highly branched compounds are chemically well-defined, thus advantageous over heterogeneous macromolecules. Previous studies have described glycodendron 3 as a clearing agent for use in three-step MST protocols, and early in vivo assessment of 3 showed promise. However, synthetic challenges have hampered its availability for further development. In this report we describe a new sequence of chemical steps which enables the straightforward synthesis and analytical characterization of this class of dendrons. With accessibility and analytical identification solved, we sought to evaluate both lower and higher generation dendrons for hepatocyte targeting as well as clearance of a model protein. We prepared a series of clearing agents where a single biotin is connected to glycodendrons displaying four, eight, sixteen or thirty-two α-thio-N-acetylgalactosamine (α-SGalNAc) units, resulting in compounds with molecular weights ranging from 2 to 17 kDa, respectively. These compounds were fully characterized by LCMS and NMR. We then evaluated the capacity of these agents to clear a model (131)I-labeled single chain variable fragment antibody-streptavidin ((131)I-scFv-SAv) fusion protein from blood and tissue in mice, and compared their clearing efficiencies to that of a 500 kDa dextran-biotin conjugate. Glycodendrons and dextran-biotin exhibited enhanced blood clearance of the scFv-SAv construct. Biodistribution analysis showed liver targeting/uptake of the scFv-SAv construct to be 2-fold higher for compounds 1 to 4, as well as for the 500 kDa dextran, over saline. Additionally, the data suggest the glycodendrons clear through the liver, whereas the dextran through reticuloendothelial system (RES) metabolism.
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Affiliation(s)
- Barney Yoo
- Organic Synthesis Core Facility, Memorial Sloan-Kettering Cancer Center, New York, New York, United States
- Molecular Pharmacology and Chemistry Program, Memorial Sloan-Kettering Cancer Center, New York, New York, United States
| | - Sarah M. Cheal
- Department of Radiology, Memorial Sloan-Kettering Cancer Center, New York, New York, United States
| | - Geralda Torchon
- Organic Synthesis Core Facility, Memorial Sloan-Kettering Cancer Center, New York, New York, United States
- Molecular Pharmacology and Chemistry Program, Memorial Sloan-Kettering Cancer Center, New York, New York, United States
| | - Anna Dilhas
- Organic Synthesis Core Facility, Memorial Sloan-Kettering Cancer Center, New York, New York, United States
- Molecular Pharmacology and Chemistry Program, Memorial Sloan-Kettering Cancer Center, New York, New York, United States
| | - Guangbin Yang
- Organic Synthesis Core Facility, Memorial Sloan-Kettering Cancer Center, New York, New York, United States
- Molecular Pharmacology and Chemistry Program, Memorial Sloan-Kettering Cancer Center, New York, New York, United States
| | - Jun Pu
- Organic Synthesis Core Facility, Memorial Sloan-Kettering Cancer Center, New York, New York, United States
- Molecular Pharmacology and Chemistry Program, Memorial Sloan-Kettering Cancer Center, New York, New York, United States
| | - Blesida Punzalan
- Department of Radiology, Memorial Sloan-Kettering Cancer Center, New York, New York, United States
| | - Steven M. Larson
- Molecular Pharmacology and Chemistry Program, Memorial Sloan-Kettering Cancer Center, New York, New York, United States
- Department of Radiology, Memorial Sloan-Kettering Cancer Center, New York, New York, United States
- Molecular Pharmacology and Therapy Service, Memorial Sloan-Kettering Cancer Center, New York, New York, United States
| | - Ouathek Ouerfelli
- Organic Synthesis Core Facility, Memorial Sloan-Kettering Cancer Center, New York, New York, United States
- Molecular Pharmacology and Chemistry Program, Memorial Sloan-Kettering Cancer Center, New York, New York, United States
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8
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Xin-feng Z, Jing-jing H, Qian L, Lu-sha W, Jian-bin Z, Xiao-hui Z, Zi-jian L, You-yi Z. Revealing binding interaction between seven drugs and immobilized β2-adrenoceptor by high-performance affinity chromatography using frontal analysis. J Mol Recognit 2013; 26:252-7. [PMID: 23526777 DOI: 10.1002/jmr.2271] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Revised: 12/23/2012] [Accepted: 01/29/2013] [Indexed: 02/02/2023]
Affiliation(s)
- Zhao Xin-feng
- College of Life Sciences; Northwest University; Xi'an; 710069; China
| | - Huang Jing-jing
- College of Life Sciences; Northwest University; Xi'an; 710069; China
| | - Li Qian
- College of Life Sciences; Northwest University; Xi'an; 710069; China
| | - Wei Lu-sha
- College of Life Sciences; Northwest University; Xi'an; 710069; China
| | - Zheng Jian-bin
- Institute of Analytical Science; Northwest University; Xi'an; 710069; China
| | - Zheng Xiao-hui
- College of Life Sciences; Northwest University; Xi'an; 710069; China
| | - Li Zi-jian
- Institute of Vascular Medicine; Peking University; Third Hospital and Key Laboratory of Molecular Cardiovascular Sciences, Ministry of Education; Beijing; 100083; China
| | - Zhang You-yi
- Institute of Vascular Medicine; Peking University; Third Hospital and Key Laboratory of Molecular Cardiovascular Sciences, Ministry of Education; Beijing; 100083; China
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9
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Kornilova AY, Algayer B, Breslin M, Addona GH, Uebele V. Development of a fluorescence polarization binding assay for folate receptor. Anal Biochem 2013; 432:59-62. [DOI: 10.1016/j.ab.2012.09.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 09/11/2012] [Accepted: 09/16/2012] [Indexed: 10/27/2022]
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