1
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Noël M, Guez T, Thillier Y, Vasseur JJ, Debart F. Access to High-Purity 7m G-cap RNA in Substantial Quantities by a Convenient All-Chemical Solid-Phase Method. Chembiochem 2023; 24:e202300544. [PMID: 37666794 DOI: 10.1002/cbic.202300544] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 08/02/2023] [Revised: 08/24/2023] [Accepted: 09/04/2023] [Indexed: 09/06/2023]
Abstract
Given the importance of mRNA with 5'-cap, easy access to RNA substrates with different 7m G caps, of high quality and in large quantities is essential to elucidate the roles of RNA and the regulation of underlying processes. In addition to existing synthetic routes to 5'-cap RNA based on enzymatic, chemical or chemo-enzymatic methods, we present here an all-chemical method for synthetic RNA capping. The novelty of this study lies in the fact that the capping reaction is performed on solid-support after automated RNA assembly using commercial 2'-O-propionyloxymethyl ribonucleoside phosphoramidites, which enable final RNA deprotection under mild conditions while preserving both 7m G-cap and RNA integrity. The capping reaction is efficiently carried out between a 5'-phosphoroimidazolide RNA anchored on the support and 7m GDP in DMF in the presence of zinc chloride. Substantial amounts of 7m G-cap RNA (from 1 to 28 nucleotides in length and of any sequence with or without internal methylations) containing various cap structures (7m GpppA, 7m GpppAm , 7m Gpppm6 A, 7m Gpppm6 Am , 7m GpppG, 7m GpppGm ) were obtained with high purity after IEX-HPLC purification. This capping method using solid-phase chemistry is convenient to perform and provides access to valuable RNA substrates as useful research tools to unravel specific issues regarding cap-related processes.
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Affiliation(s)
- Mathieu Noël
- Institut des Biomolécules Max Mousseron, UMR 5247 CNRS-University of Montpellier-ENSCM, Equipe ChemBioNAC, Pôle Chimie Balard Recherche, 1919 Route de Mende, 34293, Montpellier Cedex 5, France
| | - Theo Guez
- Institut des Biomolécules Max Mousseron, UMR 5247 CNRS-University of Montpellier-ENSCM, Equipe ChemBioNAC, Pôle Chimie Balard Recherche, 1919 Route de Mende, 34293, Montpellier Cedex 5, France
| | - Yann Thillier
- Institut des Biomolécules Max Mousseron, UMR 5247 CNRS-University of Montpellier-ENSCM, Equipe ChemBioNAC, Pôle Chimie Balard Recherche, 1919 Route de Mende, 34293, Montpellier Cedex 5, France
- Present address: Chemgenes, 900 Middlesex Turnpike, Billerica, MA 01821, USA
| | - Jean-Jacques Vasseur
- Institut des Biomolécules Max Mousseron, UMR 5247 CNRS-University of Montpellier-ENSCM, Equipe ChemBioNAC, Pôle Chimie Balard Recherche, 1919 Route de Mende, 34293, Montpellier Cedex 5, France
| | - Françoise Debart
- Institut des Biomolécules Max Mousseron, UMR 5247 CNRS-University of Montpellier-ENSCM, Equipe ChemBioNAC, Pôle Chimie Balard Recherche, 1919 Route de Mende, 34293, Montpellier Cedex 5, France
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2
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Hariharan VN, Shin M, Chang CW, O’Reilly D, Biscans A, Yamada K, Guo Z, Somasundaran M, Tang Q, Monopoli K, Krishnamurthy PM, Devi G, McHugh N, Cooper DA, Echeverria D, Cruz J, Chan IL, Liu P, Lim SY, McConnell J, Singh SP, Hildebrand S, Sousa J, Davis SM, Kennedy Z, Ferguson C, Godinho BMDC, Thillier Y, Caiazzi J, Ly S, Muhuri M, Kelly K, Humphries F, Cousineau A, Parsi KM, Li Q, Wang Y, Maehr R, Gao G, Korkin D, McDougall WM, Finberg RW, Fitzgerald KA, Wang JP, Watts JK, Khvorova A. Divalent siRNAs are bioavailable in the lung and efficiently block SARS-CoV-2 infection. Proc Natl Acad Sci U S A 2023; 120:e2219523120. [PMID: 36893269 PMCID: PMC10089225 DOI: 10.1073/pnas.2219523120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [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: 11/28/2022] [Accepted: 02/05/2023] [Indexed: 03/11/2023] Open
Abstract
The continuous evolution of SARS-CoV-2 variants complicates efforts to combat the ongoing pandemic, underscoring the need for a dynamic platform for the rapid development of pan-viral variant therapeutics. Oligonucleotide therapeutics are enhancing the treatment of numerous diseases with unprecedented potency, duration of effect, and safety. Through the systematic screening of hundreds of oligonucleotide sequences, we identified fully chemically stabilized siRNAs and ASOs that target regions of the SARS-CoV-2 genome conserved in all variants of concern, including delta and omicron. We successively evaluated candidates in cellular reporter assays, followed by viral inhibition in cell culture, with eventual testing of leads for in vivo antiviral activity in the lung. Previous attempts to deliver therapeutic oligonucleotides to the lung have met with only modest success. Here, we report the development of a platform for identifying and generating potent, chemically modified multimeric siRNAs bioavailable in the lung after local intranasal and intratracheal delivery. The optimized divalent siRNAs showed robust antiviral activity in human cells and mouse models of SARS-CoV-2 infection and represent a new paradigm for antiviral therapeutic development for current and future pandemics.
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Affiliation(s)
- Vignesh N. Hariharan
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Minwook Shin
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Ching-Wen Chang
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Daniel O’Reilly
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Annabelle Biscans
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Ken Yamada
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Zhiru Guo
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Mohan Somasundaran
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Qi Tang
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Kathryn Monopoli
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | | | - Gitali Devi
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Nicholas McHugh
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - David A. Cooper
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - John Cruz
- Department of Pathology, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Io Long Chan
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Ping Liu
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Sun-Young Lim
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Jill McConnell
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Satya Prakash Singh
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Samuel Hildebrand
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Jacquelyn Sousa
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Sarah M. Davis
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Zachary Kennedy
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Chantal Ferguson
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Bruno M. D. C. Godinho
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Yann Thillier
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Jillian Caiazzi
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Socheata Ly
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Manish Muhuri
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA01655
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Karen Kelly
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Fiachra Humphries
- Program in Innate Immunity, Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Alyssa Cousineau
- Diabetes Center of Excellence and Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Krishna Mohan Parsi
- Diabetes Center of Excellence and Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Qi Li
- MassBiologics, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Yang Wang
- MassBiologics, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - René Maehr
- Diabetes Center of Excellence and Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Guangping Gao
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA01655
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA01655
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Dmitry Korkin
- Department of Computer Science, and Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA01609
| | - William M. McDougall
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Robert W. Finberg
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Katherine A. Fitzgerald
- Program in Innate Immunity, Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA01655
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Jennifer P. Wang
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Jonathan K. Watts
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
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3
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Jones Lipinski RA, Thillier Y, Morisseau C, Sebastiano CS, Smith BC, Hall CD, Katritzky AR. Molecular docking-guided synthesis of NSAID-glucosamine bioconjugates and their evaluation as COX-1/COX-2 inhibitors with potentially reduced gastric toxicity. Chem Biol Drug Des 2021; 98:102-113. [PMID: 33955172 DOI: 10.1111/cbdd.13855] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 03/21/2021] [Accepted: 04/05/2021] [Indexed: 12/23/2022]
Abstract
Non-steroidal anti-inflammatory drugs (NSAIDs) are a powerful class of inhibitors targeting two isoforms of the family of cyclooxygenase enzymes (COX-1 and COX-2). While NSAIDs are widely used in the management of pain, in particular as a treatment for osteo- and rheumatoid arthritis, their long-term use has been associated with numerous on- and off-target effects. As the carboxylic acid moiety present in common NSAIDs is responsible for some of their adverse effects, but is not required for their anti-inflammatory activity, we sought to mask this group through direct coupling to glucosamine, which is thought to prevent cartilage degradation. We report herein the conjugation of commonly prescribed NSAIDs to glucosamine hydrochloride and the use of molecular docking to show that addition of the carbohydrate moiety to the parent NSAID can enhance binding in the active site of COX-2. In a preliminary, in vitro screening assay, the diclofenac-glucosamine bioconjugate exhibited 10-fold greater activity toward COX-2, making it an ideal candidate for future in vivo studies. Furthermore, in an intriguing result, we observed that the mefenamic acid-glucosamine bioconjugate displayed enhanced activity toward COX-1 rather than COX-2.
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Affiliation(s)
- Rachel A Jones Lipinski
- Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, FL, USA.,Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA.,Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Yann Thillier
- Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - Christophe Morisseau
- Department of Entomology and Nematology, U.C. Davis Comprehensive Cancer Center, University of California Davis, Davis, CA, USA
| | - Christopher S Sebastiano
- Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - Brian C Smith
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA.,Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - C Dennis Hall
- Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - Alan R Katritzky
- Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, FL, USA.,Chemistry Department, Faculty of Science, King Adbulaziz University, Jeddah, Saudi Arabia
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4
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Maly J, Thillier Y, Or G, Lam K, Sack JT, Tian L, Yarov-Yarovoy V. Rational Engineering and Rosetta Design of a Genetically Encoded Fluorescent Reporter of Protein Conformational Change. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.2264] [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: 11/17/2022] Open
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5
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Tang Y, Thillier Y, Liu R, Li X, Lam KS, Gao T. Single-Bead Quantification of Peptide Loading Distribution for One-Bead One-Compound Library Synthesis Using Confocal Raman Spectroscopy. Anal Chem 2017; 89:7000-7008. [PMID: 28530391 DOI: 10.1021/acs.analchem.7b00516] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
We report an analytical method to determine peptide loading of "one-bead one-compound" (OBOC) combinatorial peptide libraries at single-bead level. The quantification is based on a linear relationship between the amount of N-terminal amino groups on individual peptide beads and the intensity of Raman signal obtained from a specifically designed reporter labeled on amino groups. Confocal Raman spectroscopy was employed to characterize peptide loading of beads with defined peptide sequences and from OBOC combinatorial peptide libraries. Although amine loading of blank TentaGel beads was found to be uniform, peptide loading among beads of OBOC peptide libraries varied substantially, particularly for those libraries with long sequences. Construction of OBOC libraries can be monitored with this novel analytical technique so that synthetic conditions can be optimized for the preparation of high-quality OBOC peptide libraries. As the variability of peptide loading of individual library beads can significantly influence the screening results, quantitative information obtained by this method will allow us to gain insight into the complexity and challenge of OBOC library synthesis and screening.
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Affiliation(s)
- Yuchen Tang
- College of Chemistry, Central China Normal University , Wuhan 430079, China.,China Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, Wuhan 430079, China.,Department of Biochemistry and Molecular Medicine, University of California at Davis , Sacramento, California 95817, United States
| | - Yann Thillier
- Department of Biochemistry and Molecular Medicine, University of California at Davis , Sacramento, California 95817, United States
| | - Ruiwu Liu
- Department of Biochemistry and Molecular Medicine, University of California at Davis , Sacramento, California 95817, United States
| | - Xiaocen Li
- Department of Biochemistry and Molecular Medicine, University of California at Davis , Sacramento, California 95817, United States
| | - Kit S Lam
- Department of Biochemistry and Molecular Medicine, University of California at Davis , Sacramento, California 95817, United States
| | - Tingjuan Gao
- College of Chemistry, Central China Normal University , Wuhan 430079, China.,China Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, Wuhan 430079, China
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6
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Carney RP, Thillier Y, Kiss Z, Sahabi A, Heleno Campos JC, Knudson A, Liu R, Olivos D, Saunders M, Tian L, Lam KS. Combinatorial Library Screening with Liposomes for Discovery of Membrane Active Peptides. ACS Comb Sci 2017; 19:299-307. [PMID: 28378995 DOI: 10.1021/acscombsci.6b00182] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Membrane active peptides (MAPs) represent a class of short biomolecules that have shown great promise in facilitating intracellular delivery without disrupting cellular plasma membranes. Yet their clinical application has been stalled by numerous factors: off-target delivery, a requirement for high local concentration near cells of interest, degradation en route to the target site, and in the case of cell-penetrating peptides, eventual entrapment in endolysosomal compartments. The current method of deriving MAPs from naturally occurring proteins has restricted the discovery of new peptides that may overcome these limitations. Here, we describe a new branch of assays featuring high-throughput functional screening capable of discovering new peptides with tailored cell uptake and endosomal escape capabilities. The one-bead-one-compound (OBOC) combinatorial method is used to screen libraries containing millions of potential MAPs for binding to synthetic liposomes, which can be adapted to mimic various aspects of limiting membranes. By incorporating unnatural and d-amino acids in the library, in addition to varying buffer conditions and liposome compositions, we have identified several new highly potent MAPs that improve on current standards and introduce motifs that were previously unknown or considered unsuitable. Since small variations in pH and lipid composition can be controlled during screening, peptides discovered using this methodology could aid researchers building drug delivery platforms with unique requirements, such as targeted intracellular localization.
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Affiliation(s)
- Randy P. Carney
- Department
of Biochemistry and Molecular Medicine, University of California Davis, 2700 Stockton Boulevard, Sacramento, California 95817, United States
| | - Yann Thillier
- Department
of Biochemistry and Molecular Medicine, University of California Davis, 2700 Stockton Boulevard, Sacramento, California 95817, United States
| | - Zsofia Kiss
- Department
of Biochemistry and Molecular Medicine, University of California Davis, 2700 Stockton Boulevard, Sacramento, California 95817, United States
| | - Amir Sahabi
- Department
of Biochemistry and Molecular Medicine, University of California Davis, 2700 Stockton Boulevard, Sacramento, California 95817, United States
| | - Jean Carlos Heleno Campos
- Department
of Biochemistry and Molecular Medicine, University of California Davis, 2700 Stockton Boulevard, Sacramento, California 95817, United States
| | - Alisha Knudson
- Department
of Biochemistry and Molecular Medicine, University of California Davis, 2700 Stockton Boulevard, Sacramento, California 95817, United States
| | - Ruiwu Liu
- Department
of Biochemistry and Molecular Medicine, University of California Davis, 2700 Stockton Boulevard, Sacramento, California 95817, United States
| | - David Olivos
- Department
of Biochemistry and Molecular Medicine, University of California Davis, 2700 Stockton Boulevard, Sacramento, California 95817, United States
| | - Mary Saunders
- Department
of Biochemistry and Molecular Medicine, University of California Davis, 2700 Stockton Boulevard, Sacramento, California 95817, United States
| | - Lin Tian
- Department
of Biochemistry and Molecular Medicine, University of California Davis, 2700 Stockton Boulevard, Sacramento, California 95817, United States
| | - Kit S. Lam
- Department
of Biochemistry and Molecular Medicine, University of California Davis, 2700 Stockton Boulevard, Sacramento, California 95817, United States
- Division
of Hematology/Oncology, University of California Davis Cancer Center, Sacramento, California United States
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7
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Thillier Y, Sallamand C, Baraguey C, Vasseur JJ, Debart F. Solid-Phase Synthesis of Oligonucleotide 5′-(α-P-Thio)triphosphates and 5′-(α-P-Thio)(β,γ-methylene)triphosphates. European J Org Chem 2014. [DOI: 10.1002/ejoc.201403381] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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8
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Jones RA, Thillier Y, Panda SS, Rivera Rosario N, Hall CD, Katritzky AR. Synthesis and characterisation of glucosamine–NSAID bioconjugates. Org Biomol Chem 2014; 12:8325-35. [DOI: 10.1039/c4ob01681e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Synthetic strategies to prepare non-steroidal anti-inflammatory drug–glucosamine bioconjugates.
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Affiliation(s)
- Rachel A. Jones
- Center for Heterocyclic Compounds
- Department of Chemistry
- University of Florida
- Gainesville, USA
| | - Yann Thillier
- Center for Heterocyclic Compounds
- Department of Chemistry
- University of Florida
- Gainesville, USA
| | - Siva S. Panda
- Center for Heterocyclic Compounds
- Department of Chemistry
- University of Florida
- Gainesville, USA
| | - Nicole Rivera Rosario
- Center for Heterocyclic Compounds
- Department of Chemistry
- University of Florida
- Gainesville, USA
| | - C. Dennis Hall
- Center for Heterocyclic Compounds
- Department of Chemistry
- University of Florida
- Gainesville, USA
| | - Alan R. Katritzky
- Center for Heterocyclic Compounds
- Department of Chemistry
- University of Florida
- Gainesville, USA
- Chemistry Department
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9
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Thillier Y, Stevens SK, Moy C, Taylor J, Vasseur JJ, Beigelman L, Debart F. Solid-phase synthesis of 5'-triphosphate 2'-5'-oligoadenylates analogs with 3'-O-biolabile groups and their evaluation as RNase L activators and antiviral drugs. Bioorg Med Chem 2013; 21:5461-9. [PMID: 23810677 DOI: 10.1016/j.bmc.2013.06.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 05/30/2013] [Accepted: 06/04/2013] [Indexed: 11/19/2022]
Abstract
5'-Triphosphate 2'-5'-oligoadenylate (2-5A) is the central player in the 2-5A system that is an innate immunity pathway in response to the presence of infectious agents. Intracellular endoribonuclease RNase L activated by 2-5A cleaves viral and cellular RNA resulting in apoptosis. The major limitations of 2-5A for therapeutic applications is the short biological half-life and poor cellular uptake. Modification of 2-5A with biolabile and lipophilic groups that facilitate its uptake, increase its in vivo stability and release the parent 2-5A drug in an intact form offer an alternative approach to therapeutic use of 2-5A. Here we have synthesized the trimeric and tetrameric 2-5A species bearing hydrophobic and enzymolabile pivaloyloxymethyl groups at 3'-positions and a triphosphate at the 5'-end. Both analogs were able to activate RNase L and the production of the trimer 2-5A (the most active) was scaled up to the milligram scale for antiviral evaluation in cells infected by influenza virus or respiratory syncytial virus. The trimer analog demonstrated some significant antiviral activity.
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Affiliation(s)
- Yann Thillier
- IBMM, UMR 5247, CNRS-UM1-UM2, Université Montpellier 2, Place Eugène Bataillon, 34095 Montpellier, France
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10
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Barral K, Sallamand C, Petzold C, Coutard B, Collet A, Thillier Y, Zimmermann J, Vasseur JJ, Canard B, Rohayem J, Debart F, Decroly E. Development of specific dengue virus 2'-O- and N7-methyltransferase assays for antiviral drug screening. Antiviral Res 2013; 99:292-300. [PMID: 23769894 DOI: 10.1016/j.antiviral.2013.06.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [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: 11/21/2012] [Revised: 05/31/2013] [Accepted: 06/03/2013] [Indexed: 12/16/2022]
Abstract
Dengue virus (DENV) protein NS5 carries two mRNA cap methyltransferase (MTase) activities involved in the synthesis of a cap structure, (7Me)GpppA(2'OMe)-RNA, at the 5'-end of the viral mRNA. The methylation of the cap guanine at its N7-position (N7-MTase, (7Me)GpppA-RNA) is essential for viral replication. The development of high throughput methods to identify specific inhibitors of N7-MTase is hampered by technical limitations in the large scale synthesis of long capped RNAs. In this work, we describe an efficient method to generate such capped RNA, GpppA(2'OMe)-RNA₇₄, by ligation of two RNA fragments. Then, we use GpppA(2'OMe)-RNA₇₄ as a substrate to assess DENV N7-MTase activity and to develop a robust and specific activity assay. We applied the same ligation procedure to generate (7Me)GpppA-RNA₇₄ in order to characterize the DENV 2'-O-MTase activity specifically on long capped RNA. We next compared the N7- and 2'-O-MTase inhibition effect of 18 molecules, previously proposed to affect MTase activities. These experiments allow the validation of a rapid and sensitive method easily adaptable for high-throughput inhibitor screening in anti-flaviviral drug development.
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Affiliation(s)
- K Barral
- AFMB, CNRS, Aix-Marseille Université, UMR 7257, Case 932, 163 Avenue de Luminy, 13288 Marseille Cedex 09, France.
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11
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Piton J, Larue V, Thillier Y, Dorléans A, Pellegrini O, Li de la Sierra-Gallay I, Vasseur JJ, Debart F, Tisné C, Condon C. Bacillus subtilis RNA deprotection enzyme RppH recognizes guanosine in the second position of its substrates. Proc Natl Acad Sci U S A 2013; 110:8858-63. [PMID: 23610407 PMCID: PMC3670357 DOI: 10.1073/pnas.1221510110] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The initiation of mRNA degradation often requires deprotection of its 5' end. In eukaryotes, the 5'-methylguanosine (cap) structure is principally removed by the Nudix family decapping enzyme Dcp2, yielding a 5'-monophosphorylated RNA that is a substrate for 5' exoribonucleases. In bacteria, the 5'-triphosphate group of primary transcripts is also converted to a 5' monophosphate by a Nudix protein called RNA pyrophosphohydrolase (RppH), allowing access to both endo- and 5' exoribonucleases. Here we present the crystal structures of Bacillus subtilis RppH (BsRppH) bound to GTP and to a triphosphorylated dinucleotide RNA. In contrast to Bdellovibrio bacteriovorus RppH, which recognizes the first nucleotide of its RNA targets, the B. subtilis enzyme has a binding pocket that prefers guanosine residues in the second position of its substrates. The identification of sequence specificity for RppH in an internal position was a highly unexpected result. NMR chemical shift mapping in solution shows that at least three nucleotides are required for unambiguous binding of RNA. Biochemical assays of BsRppH on RNA substrates with single-base-mutation changes in the first four nucleotides confirm the importance of guanosine in position two for optimal enzyme activity. Our experiments highlight important structural and functional differences between BsRppH and the RNA deprotection enzymes of distantly related bacteria.
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Affiliation(s)
- Jérémie Piton
- Centre National de la Recherche Scientifique (CNRS), Unité Propre de Recherche 9073 (affiliated with Université Paris Diderot, Sorbonne Paris Cité) Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - Valéry Larue
- Unité Mixte de Recherche (UMR) 8015, CNRS, Université Paris Descartes, Sorbonne Paris Cité, 75006 Paris, France; and
| | - Yann Thillier
- Institut des Biomolécules Max Mousseron, UMR 5247, CNRS–Université Montpellier 1–Université Montpellier 2, 34095 Montpellier Cedex 05, France
| | - Audrey Dorléans
- Centre National de la Recherche Scientifique (CNRS), Unité Propre de Recherche 9073 (affiliated with Université Paris Diderot, Sorbonne Paris Cité) Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - Olivier Pellegrini
- Centre National de la Recherche Scientifique (CNRS), Unité Propre de Recherche 9073 (affiliated with Université Paris Diderot, Sorbonne Paris Cité) Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - Inés Li de la Sierra-Gallay
- Centre National de la Recherche Scientifique (CNRS), Unité Propre de Recherche 9073 (affiliated with Université Paris Diderot, Sorbonne Paris Cité) Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - Jean-Jacques Vasseur
- Institut des Biomolécules Max Mousseron, UMR 5247, CNRS–Université Montpellier 1–Université Montpellier 2, 34095 Montpellier Cedex 05, France
| | - Françoise Debart
- Institut des Biomolécules Max Mousseron, UMR 5247, CNRS–Université Montpellier 1–Université Montpellier 2, 34095 Montpellier Cedex 05, France
| | - Carine Tisné
- Unité Mixte de Recherche (UMR) 8015, CNRS, Université Paris Descartes, Sorbonne Paris Cité, 75006 Paris, France; and
| | - Ciarán Condon
- Centre National de la Recherche Scientifique (CNRS), Unité Propre de Recherche 9073 (affiliated with Université Paris Diderot, Sorbonne Paris Cité) Institut de Biologie Physico-Chimique, 75005 Paris, France
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Thillier Y, Losfeld G, Escande V, Dupouy C, Vasseur JJ, Debart F, Grison C. Metallophyte wastes and polymetallic catalysis: a promising combination in green chemistry. The illustrative synthesis of 5′-capped RNA. RSC Adv 2013. [DOI: 10.1039/c3ra23115a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Selisko B, Potisopon S, Agred R, Priet S, Varlet I, Thillier Y, Sallamand C, Debart F, Vasseur JJ, Canard B. Molecular basis for nucleotide conservation at the ends of the dengue virus genome. PLoS Pathog 2012; 8:e1002912. [PMID: 23028313 PMCID: PMC3441707 DOI: 10.1371/journal.ppat.1002912] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [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] [Received: 07/06/2012] [Accepted: 08/03/2012] [Indexed: 12/02/2022] Open
Abstract
The dengue virus (DV) is an important human pathogen from the Flavivirus genus, whose genome- and antigenome RNAs start with the strictly conserved sequence pppAG. The RNA-dependent RNA polymerase (RdRp), a product of the NS5 gene, initiates RNA synthesis de novo, i.e., without the use of a pre-existing primer. Very little is known about the mechanism of this de novo initiation and how conservation of the starting adenosine is achieved. The polymerase domain NS5PolDV of NS5, upon initiation on viral RNA templates, synthesizes mainly dinucleotide primers that are then elongated in a processive manner. We show here that NS5PolDV contains a specific priming site for adenosine 5′-triphosphate as the first transcribed nucleotide. Remarkably, in the absence of any RNA template the enzyme is able to selectively synthesize the dinucleotide pppAG when Mn2+ is present as catalytic ion. The T794 to A799 priming loop is essential for initiation and provides at least part of the ATP-specific priming site. The H798 loop residue is of central importance for the ATP-specific initiation step. In addition to ATP selection, NS5PolDV ensures the conservation of the 5′-adenosine by strongly discriminating against viral templates containing an erroneous 3′-end nucleotide in the presence of Mg2+. In the presence of Mn2+, NS5PolDV is remarkably able to generate and elongate the correct pppAG primer on these erroneous templates. This can be regarded as a genomic/antigenomic RNA end repair mechanism. These conservational mechanisms, mediated by the polymerase alone, may extend to other RNA virus families having RdRps initiating RNA synthesis de novo. The 5′- and 3′-ends of RNA virus genomes have evolved towards efficient replication, translation, and escape from defense mechanisms of the host cell. Little is known about how RNA viruses conserve or restore the correct ends of their genomes. The Flavivirus genus of positive-strand RNA viruses contains important human pathogens such as yellow fever virus, West Nile virus, Japanese encephalitis virus and dengue virus (DV). The Flavivirus genome ends are strictly conserved as 5′-AG…CU-3′. We demonstrate here the primary role of the DV polymerase in the conservation of the first and last genomic residue. We show that DV polymerase contains an ATP-specific priming site, which imposes a strong preference for the de novo synthesis of a dinucleotide primer starting with an ATP. Furthermore, the polymerase is able to indirectly correct erroneous sequences by producing the correct primer in the absence of template and on templates containing incorrect nucleotides at the 3′-end. The correct primer is productively elongated on either correct or incorrect templates. Our findings provide a direct demonstration of the implication of a viral RNA polymerase in the conservation and repair of genome ends. Other polymerases from other RNA virus families are likely to employ similar mechanisms.
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Affiliation(s)
- Barbara Selisko
- Aix-Marseille Université, CNRS, AFMB UMR 7257, 163, Marseille, France.
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Thillier Y, Decroly E, Morvan F, Canard B, Vasseur JJ, Debart F. Synthesis of 5' cap-0 and cap-1 RNAs using solid-phase chemistry coupled with enzymatic methylation by human (guanine-N⁷)-methyl transferase. RNA 2012; 18:856-68. [PMID: 22334760 PMCID: PMC3312571 DOI: 10.1261/rna.030932.111] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Accepted: 11/19/2011] [Indexed: 05/19/2023]
Abstract
The 5' end of eukaryotic mRNA carries a N(7)-methylguanosine residue linked by a 5'-5' triphosphate bond. This cap moiety ((7m)GpppN) is an essential RNA structural modification allowing its efficient translation, limiting its degradation by cellular 5' exonucleases and avoiding its recognition as "nonself" by the innate immunity machinery. In vitro synthesis of capped RNA is an important bottleneck for many biological studies. Moreover, the lack of methods allowing the synthesis of large amounts of RNA starting with a specific 5'-end sequence have hampered biological and structural studies of proteins recognizing the cap structure or involved in the capping pathway. Due to the chemical nature of N(7)-methylguanosine, the synthesis of RNAs possessing a cap structure at the 5' end is still a significant challenge. In the present work, we combined a chemical synthesis method and an enzymatic methylation assay in order to produce large amounts of RNA oligonucleotides carrying a cap-0 or cap-1. Short RNAs were synthesized on solid support by the phosphoramidite 2'-O-pivaloyloxymethyl chemistry. The cap structure was then coupled by the addition of GDP after phosphorylation of the terminal 5'-OH and activation by imidazole. After deprotection and release from the support, GpppN-RNAs or GpppN(2'-Om)-RNAs were purified before the N(7)-methyl group was added by enzymatic means using the human (guanine-N(7))-methyl transferase to yield (7m)GpppN-RNAs (cap-0) or (7m)GpppN(2'-Om)-RNAs (cap-1). The RNAs carrying different cap structures (cap, cap-0 or, cap-1) act as bona fide substrates mimicking cellular capped RNAs and can be used for biochemical and structural studies.
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Affiliation(s)
- Yann Thillier
- IBMM, UMR 5247 CNRS-UM1-UM2, Université Montpellier 2, 34095 Montpellier cedex 05, France
| | - Etienne Decroly
- AFMB, UMR 6098 CNRS-Universités d'Aix-Marseille I et II, 13288 Marseille cedex 9, France
| | - François Morvan
- IBMM, UMR 5247 CNRS-UM1-UM2, Université Montpellier 2, 34095 Montpellier cedex 05, France
| | - Bruno Canard
- AFMB, UMR 6098 CNRS-Universités d'Aix-Marseille I et II, 13288 Marseille cedex 9, France
| | - Jean-Jacques Vasseur
- IBMM, UMR 5247 CNRS-UM1-UM2, Université Montpellier 2, 34095 Montpellier cedex 05, France
| | - Françoise Debart
- IBMM, UMR 5247 CNRS-UM1-UM2, Université Montpellier 2, 34095 Montpellier cedex 05, France
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