1
|
Ahmed-Belkacem R, Troussier J, Delpal A, Canard B, Vasseur JJ, Decroly E, Debart F. N-Arylsulfonamide-based adenosine analogues to target RNA cap N7-methyltransferase nsp14 of SARS-CoV-2. RSC Med Chem 2024; 15:839-847. [PMID: 38516599 PMCID: PMC10953473 DOI: 10.1039/d3md00737e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 01/25/2024] [Indexed: 03/23/2024] Open
Abstract
RNA cap methylations have been shown to be crucial for the life cycle, replication, and infection of ssRNA viruses, as well as for evading the host's innate immune system. Viral methyltransferases (MTases) therefore represent an attractive target for the development of compounds as tools and inhibitors. In coronaviruses, N7-methyltransferase function is localized in nsp14, which has become an increasingly important therapeutic target with the COVID-19 pandemic. In recent years, we have been developing SAH-derived bisubstrates with adenosine and an N-arylsulfonamide moiety targeting both SAM and RNA binding sites in nsp14. We report here the synthesis of 31 SAH analogues with the N-arylsulfonamide attached to the 5'-position of adenosine via different linkers such as N-ethylthioether, N-ethylsulfone, N-ethylamino or N-methyltriazole. The compounds were obtained efficiently by amine sulfonylation or click chemistry. Their ability to inhibit SARS-CoV-2 N7-MTase was evaluated and the best inhibitors showed a submicromolar inhibitory activity against N7-MTase nsp14.
Collapse
Affiliation(s)
| | - Joris Troussier
- IBMM, University of Montpellier CNRS, ENSCM Montpellier France
| | - Adrien Delpal
- AFMB, University of Aix-Marseille CNRS Marseille France
| | - Bruno Canard
- AFMB, University of Aix-Marseille CNRS Marseille France
| | | | | | | |
Collapse
|
2
|
Fiorucci D, Meaccini M, Poli G, Stincarelli MA, Vagaggini C, Giannecchini S, Sutto-Ortiz P, Canard B, Decroly E, Dreassi E, Brai A, Botta M. Identification of Novel Non-Nucleoside Inhibitors of Zika Virus NS5 Protein Targeting MTase Activity. Int J Mol Sci 2024; 25:2437. [PMID: 38397115 PMCID: PMC10888717 DOI: 10.3390/ijms25042437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/13/2024] [Accepted: 02/15/2024] [Indexed: 02/25/2024] Open
Abstract
Zika virus (ZIKV) is a positive-sense single-stranded virus member of the Flaviviridae family. Among other arboviruses, ZIKV can cause neurological disorders such as Guillain Barré syndrome, and it can have congenital neurological manifestations and affect fertility. ZIKV nonstructural protein 5 (NS5) is essential for viral replication and limiting host immune detection. Herein, we performed virtual screening to identify novel small-molecule inhibitors of the ZIKV NS5 methyltransferase (MTase) domain. Compounds were tested against the MTases of both ZIKV and DENV, demonstrating good inhibitory activities against ZIKV MTase. Extensive molecular dynamic studies conducted on the series led us to identify other derivatives with improved activity against the MTase and limiting ZIKV infection with an increased selectivity index. Preliminary pharmacokinetic parameters have been determined, revealing excellent stability over time. Preliminary in vivo toxicity studies demonstrated that the hit compound 17 is well tolerated after acute administration. Our results provide the basis for further optimization studies on novel non-nucleoside MTase inhibitors.
Collapse
Affiliation(s)
- Diego Fiorucci
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Micaela Meaccini
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Giulio Poli
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Maria Alfreda Stincarelli
- Department of Experimental and Clinical Medicine, University of Florence, Viale Morgagni 48, 50134 Florence, Italy; (M.A.S.); (S.G.)
| | - Chiara Vagaggini
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Simone Giannecchini
- Department of Experimental and Clinical Medicine, University of Florence, Viale Morgagni 48, 50134 Florence, Italy; (M.A.S.); (S.G.)
| | - Priscila Sutto-Ortiz
- AFMB, Aix-Marseille University, CNRS, UMR 7257, Case 925, 163 Avenue de Luminy, Cedex 09, 13288 Marseille, France; (P.S.-O.)
| | - Bruno Canard
- AFMB, Aix-Marseille University, CNRS, UMR 7257, Case 925, 163 Avenue de Luminy, Cedex 09, 13288 Marseille, France; (P.S.-O.)
| | - Etienne Decroly
- AFMB, Aix-Marseille University, CNRS, UMR 7257, Case 925, 163 Avenue de Luminy, Cedex 09, 13288 Marseille, France; (P.S.-O.)
| | - Elena Dreassi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Annalaura Brai
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Maurizio Botta
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
| |
Collapse
|
3
|
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] [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.
Collapse
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
| |
Collapse
|
4
|
Shen S, Zhang LS. The regulation of antiviral innate immunity through non-m 6A RNA modifications. Front Immunol 2023; 14:1286820. [PMID: 37915585 PMCID: PMC10616867 DOI: 10.3389/fimmu.2023.1286820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 10/04/2023] [Indexed: 11/03/2023] Open
Abstract
The post-transcriptional RNA modifications impact the dynamic regulation of gene expression in diverse biological and physiological processes. Host RNA modifications play an indispensable role in regulating innate immune responses against virus infection in mammals. Meanwhile, the viral RNAs can be deposited with RNA modifications to interfere with the host immune responses. The N6-methyladenosine (m6A) has boosted the recent emergence of RNA epigenetics, due to its high abundance and a transcriptome-wide widespread distribution in mammalian cells, proven to impact antiviral innate immunity. However, the other types of RNA modifications are also involved in regulating antiviral responses, and the functional roles of these non-m6A RNA modifications have not been comprehensively summarized. In this Review, we conclude the regulatory roles of 2'-O-methylation (Nm), 5-methylcytidine (m5C), adenosine-inosine editing (A-to-I editing), pseudouridine (Ψ), N1-methyladenosine (m1A), N7-methylguanosine (m7G), N6,2'-O-dimethyladenosine (m6Am), and N4-acetylcytidine (ac4C) in antiviral innate immunity. We provide a systematic introduction to the biogenesis and functions of these non-m6A RNA modifications in viral RNA, host RNA, and during virus-host interactions, emphasizing the biological functions of RNA modification regulators in antiviral responses. Furthermore, we discussed the recent research progress in the development of antiviral drugs through non-m6A RNA modifications. Collectively, this Review conveys knowledge and inspiration to researchers in multiple disciplines, highlighting the challenges and future directions in RNA epitranscriptome, immunology, and virology.
Collapse
Affiliation(s)
- Shenghai Shen
- Division of Life Science, The Hong Kong University of Science and Technology (HKUST), Kowloon, Hong Kong SAR, China
| | - Li-Sheng Zhang
- Division of Life Science, The Hong Kong University of Science and Technology (HKUST), Kowloon, Hong Kong SAR, China
- Department of Chemistry, The Hong Kong University of Science and Technology (HKUST), Kowloon, Hong Kong SAR, China
| |
Collapse
|
5
|
Hausdorff M, Delpal A, Barelier S, Nicollet L, Canard B, Touret F, Colmant A, Coutard B, Vasseur JJ, Decroly E, Debart F. Structure-guided optimization of adenosine mimetics as selective and potent inhibitors of coronavirus nsp14 N7-methyltransferases. Eur J Med Chem 2023; 256:115474. [PMID: 37192550 DOI: 10.1016/j.ejmech.2023.115474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 05/05/2023] [Accepted: 05/08/2023] [Indexed: 05/18/2023]
Abstract
The COVID-19 pandemic reveals the urgent need to develop new therapeutics targeting the SARS-CoV-2 replication machinery. The first antiviral drugs were nucleoside analogues targeting RdRp and protease inhibitors active on nsp5 Mpro. In addition to these common antiviral targets, SARS-CoV-2 codes for the highly conserved protein nsp14 harbouring N7-methyltransferase (MTase) activity. Nsp14 is involved in cap N7-methylation of viral RNA and its inhibition impairs viral RNA translation and immune evasion, making it an attractive new antiviral target. In this work, we followed a structure-guided drug design approach to design bisubstrates mimicking the S-adenosylmethionine methyl donor and RNA cap. We developed adenosine mimetics with an N-arylsulfonamide moiety in the 5'-position, recently described as a guanine mimicking the cap structure in a potent adenosine-derived nsp14 inhibitor. Here, the adenine moiety was replaced by hypoxanthine, N6-methyladenine, or C7-substituted 7-deaza-adenine. 26 novel adenosine mimetics were synthesized, one of which selectively inhibits nsp14 N7-MTase activity with a subnanomolar IC50 (and seven with a single-digit nanomolar IC50). In the most potent inhibitors, adenine was replaced by two different 7-deaza-adenines bearing either a phenyl or a 3-quinoline group at the C7-position via an ethynyl linker. These more complex compounds are barely active on the cognate human N7-MTase and docking experiments reveal that their selectivity of inhibition might result from the positioning of their C7 substitution in a SAM entry tunnel present in the nsp14 structure and absent in the hN7-MTase. These compounds show moderate antiviral activity against SARS-CoV-2 replication in cell culture, suggesting delivery or stability issue.
Collapse
Affiliation(s)
- Marcel Hausdorff
- IBMM, CNRS, University of Montpellier, ENSCM, Montpellier, France
| | - Adrien Delpal
- AFMB, CNRS, Aix-Marseille University, UMR 7257, 163 Avenue de Luminy, Marseille, France
| | - Sarah Barelier
- AFMB, CNRS, Aix-Marseille University, UMR 7257, 163 Avenue de Luminy, Marseille, France
| | - Laura Nicollet
- IBMM, CNRS, University of Montpellier, ENSCM, Montpellier, France
| | - Bruno Canard
- AFMB, CNRS, Aix-Marseille University, UMR 7257, 163 Avenue de Luminy, Marseille, France
| | - Franck Touret
- IHU Méditerranée Infection, Unité Virus Emergents, University of Aix-Marseille, 13005, Marseille, France
| | - Agathe Colmant
- IHU Méditerranée Infection, Unité Virus Emergents, University of Aix-Marseille, 13005, Marseille, France
| | - Bruno Coutard
- IHU Méditerranée Infection, Unité Virus Emergents, University of Aix-Marseille, 13005, Marseille, France
| | | | - Etienne Decroly
- AFMB, CNRS, Aix-Marseille University, UMR 7257, 163 Avenue de Luminy, Marseille, France.
| | - Françoise Debart
- IBMM, CNRS, University of Montpellier, ENSCM, Montpellier, France.
| |
Collapse
|
6
|
Decombe A, El Kazzi P, Decroly E. Interplay of RNA 2'-O-methylations with viral replication. Curr Opin Virol 2023; 59:101302. [PMID: 36764118 DOI: 10.1016/j.coviro.2023.101302] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/06/2022] [Accepted: 12/19/2022] [Indexed: 02/11/2023]
Abstract
Viral RNAs (vRNAs) are decorated by post-transcriptional modifications, including methylation of nucleotides. Methylations regulate biological functions linked to the sequence, structure, and protein interactome of RNA. Several RNA viruses were found to harbor 2'-O-methylations, affecting the ribose moiety of RNA. This mark was initially shown to target the first and second nucleotides of the 5'-end cap structure of mRNA. More recently, nucleotides within vRNA were also reported to carry 2'-O-methylations. The consequences of such methylations are still puzzling since they were associated with both proviral and antiviral effects. Here, we focus on the mechanisms governing vRNA 2'-O-methylation and we explore the possible roles of this epitranscriptomic modification for viral replication.
Collapse
Affiliation(s)
- Alice Decombe
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288 Marseille Cedex 09, France
| | - Priscila El Kazzi
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288 Marseille Cedex 09, France
| | - Etienne Decroly
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288 Marseille Cedex 09, France.
| |
Collapse
|
7
|
Bobileva O, Bobrovs R, Sirma EE, Kanepe I, Bula AL, Patetko L, Ramata-Stunda A, Grinberga S, Jirgensons A, Jaudzems K. 3-(Adenosylthio)benzoic Acid Derivatives as SARS-CoV-2 Nsp14 Methyltransferase Inhibitors. Molecules 2023; 28:molecules28020768. [PMID: 36677825 PMCID: PMC9862586 DOI: 10.3390/molecules28020768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/06/2023] [Accepted: 01/10/2023] [Indexed: 01/13/2023] Open
Abstract
SARS-CoV-2 nsp14 guanine-N7-methyltransferase plays an important role in the viral RNA translation process by catalyzing the transfer of a methyl group from S-adenosyl-methionine (SAM) to viral mRNA cap. We report a structure-guided design and synthesis of 3-(adenosylthio)benzoic acid derivatives as nsp14 methyltransferase inhibitors resulting in compound 5p with subnanomolar inhibitory activity and improved cell membrane permeability in comparison with the parent inhibitor. Compound 5p acts as a bisubstrate inhibitor targeting both SAM and mRNA-binding pockets of nsp14. While the selectivity of 3-(adenosylthio)benzoic acid derivatives against human glycine N-methyltransferase was not improved, the discovery of phenyl-substituted analogs 5p,t may contribute to further development of SARS-CoV-2 nsp14 bisubstrate inhibitors.
Collapse
Affiliation(s)
- Olga Bobileva
- Latvian Institute of Organic Synthesis, LV-1006 Riga, Latvia
- Correspondence:
| | - Raitis Bobrovs
- Latvian Institute of Organic Synthesis, LV-1006 Riga, Latvia
| | | | - Iveta Kanepe
- Latvian Institute of Organic Synthesis, LV-1006 Riga, Latvia
| | - Anna L. Bula
- Latvian Institute of Organic Synthesis, LV-1006 Riga, Latvia
| | - Liene Patetko
- Faculty of Biology, University of Latvia, LV-1004 Riga, Latvia
| | | | | | | | | |
Collapse
|
8
|
Kazzi PE, Rabah N, Chamontin C, Poulain L, Ferron F, Debart F, Canard B, Missé D, Coutard B, Nisole S, Decroly E. Internal RNA 2′O-methylation in the HIV-1 genome counteracts ISG20 nuclease-mediated antiviral effect. Nucleic Acids Res 2022; 51:2501-2515. [PMID: 36354007 PMCID: PMC10085690 DOI: 10.1093/nar/gkac996] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 09/16/2022] [Accepted: 10/19/2022] [Indexed: 11/11/2022] Open
Abstract
Abstract
RNA 2′O-methylation is a ‘self’ epitranscriptomic modification allowing discrimination between host and pathogen. Indeed, human immunodeficiency virus 1 (HIV-1) induces 2′O-methylation of its genome by recruiting the cellular FTSJ3 methyltransferase, thereby impairing detection by RIG-like receptors. Here, we show that RNA 2′O-methylations interfere with the antiviral activity of interferon-stimulated gene 20-kDa protein (ISG20). Biochemical experiments showed that ISG20-mediated degradation of 2′O-methylated RNA pauses two nucleotides upstream of and at the methylated residue. Structure-function analysis indicated that this inhibition is due to steric clash between ISG20 R53 and D90 residues and the 2′O-methylated nucleotide. We confirmed that hypomethylated HIV-1 genomes produced in FTSJ3-KO cells were more prone to in vitro degradation by ISG20 than those produced in cells expressing FTSJ3. Finally, we found that reverse-transcription of hypomethylated HIV-1 was impaired in T cells by interferon-induced ISG20, demonstrating the direct antagonist effect of 2′O-methylation on ISG20-mediated antiviral activity.
Collapse
Affiliation(s)
- Priscila El Kazzi
- AFMB, CNRS, Aix-Marseille University , UMR 7257, Case 925, 163 Avenue de Luminy , 13288 Marseille Cedex 09, France
| | - Nadia Rabah
- AFMB, CNRS, Aix-Marseille University , UMR 7257, Case 925, 163 Avenue de Luminy , 13288 Marseille Cedex 09, France
- Université de Toulon , 83130 La Garde , France
| | - Célia Chamontin
- IRIM, CNRS UMR9004, Université de Montpellier , Montpellier , France
| | - Lina Poulain
- AFMB, CNRS, Aix-Marseille University , UMR 7257, Case 925, 163 Avenue de Luminy , 13288 Marseille Cedex 09, France
| | - François Ferron
- AFMB, CNRS, Aix-Marseille University , UMR 7257, Case 925, 163 Avenue de Luminy , 13288 Marseille Cedex 09, France
- European Virus Bioinformatics Center , Leutragraben 1, 07743 Jena , Germany
| | - Françoise Debart
- IBMM, UMR 5247 CNRS, Université de Montpellier , ENSCM, Montpellier , France
| | - Bruno Canard
- AFMB, CNRS, Aix-Marseille University , UMR 7257, Case 925, 163 Avenue de Luminy , 13288 Marseille Cedex 09, France
| | - Dorothée Missé
- MIVEGEC, Univ. Montpellier, CNRS , IRD, Montpellier, France
| | - Bruno Coutard
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207) , Marseille , France
| | - Sébastien Nisole
- IRIM, CNRS UMR9004, Université de Montpellier , Montpellier , France
| | - Etienne Decroly
- AFMB, CNRS, Aix-Marseille University , UMR 7257, Case 925, 163 Avenue de Luminy , 13288 Marseille Cedex 09, France
| |
Collapse
|
9
|
Ahmed-Belkacem R, Hausdorff M, Delpal A, Sutto-Ortiz P, Colmant AMG, Touret F, Ogando NS, Snijder EJ, Canard B, Coutard B, Vasseur JJ, Decroly E, Debart F. Potent Inhibition of SARS-CoV-2 nsp14 N7-Methyltransferase by Sulfonamide-Based Bisubstrate Analogues. J Med Chem 2022; 65:6231-6249. [PMID: 35439007 PMCID: PMC9045040 DOI: 10.1021/acs.jmedchem.2c00120] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Indexed: 12/15/2022]
Abstract
Enzymes involved in RNA capping of SARS-CoV-2 are essential for the stability of viral RNA, translation of mRNAs, and virus evasion from innate immunity, making them attractive targets for antiviral agents. In this work, we focused on the design and synthesis of nucleoside-derived inhibitors against the SARS-CoV-2 nsp14 (N7-guanine)-methyltransferase (N7-MTase) that catalyzes the transfer of the methyl group from the S-adenosyl-l-methionine (SAM) cofactor to the N7-guanosine cap. Seven compounds out of 39 SAM analogues showed remarkable double-digit nanomolar inhibitory activity against the N7-MTase nsp14. Molecular docking supported the structure-activity relationships of these inhibitors and a bisubstrate-based mechanism of action. The three most potent inhibitors significantly stabilized nsp14 (ΔTm ≈ 11 °C), and the best inhibitor demonstrated high selectivity for nsp14 over human RNA N7-MTase.
Collapse
Affiliation(s)
| | - Marcel Hausdorff
- IBMM,
University of Montpellier, CNRS, ENSCM, 34293 Montpellier, cedex 5, France
| | - Adrien Delpal
- AFMB,
University of Aix-Marseille, CNRS, 13288 Marseille, cedex 9, France
| | | | - Agathe M. G. Colmant
- IHU
Méditerranée Infection, Unité Virus Emergents, University of Aix-Marseille, IRD 190, INSERM 1207, 13005 Marseille, France
| | - Franck Touret
- IHU
Méditerranée Infection, Unité Virus Emergents, University of Aix-Marseille, IRD 190, INSERM 1207, 13005 Marseille, France
| | - Natacha S. Ogando
- Department
of Medical Microbiology, Leiden University
Medical Center, 2333 ZA Leiden, The Netherlands
| | - Eric J. Snijder
- Department
of Medical Microbiology, Leiden University
Medical Center, 2333 ZA Leiden, The Netherlands
| | - Bruno Canard
- AFMB,
University of Aix-Marseille, CNRS, 13288 Marseille, cedex 9, France
| | - Bruno Coutard
- IHU
Méditerranée Infection, Unité Virus Emergents, University of Aix-Marseille, IRD 190, INSERM 1207, 13005 Marseille, France
| | - Jean-Jacques Vasseur
- IBMM,
University of Montpellier, CNRS, ENSCM, 34293 Montpellier, cedex 5, France
| | - Etienne Decroly
- AFMB,
University of Aix-Marseille, CNRS, 13288 Marseille, cedex 9, France
| | - Françoise Debart
- IBMM,
University of Montpellier, CNRS, ENSCM, 34293 Montpellier, cedex 5, France
| |
Collapse
|
10
|
Burgess HM, Vink EI, Mohr I. Minding the message: tactics controlling RNA decay, modification, and translation in virus-infected cells. Genes Dev 2022; 36:108-132. [PMID: 35193946 PMCID: PMC8887129 DOI: 10.1101/gad.349276.121] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
With their categorical requirement for host ribosomes to translate mRNA, viruses provide a wealth of genetically tractable models to investigate how gene expression is remodeled post-transcriptionally by infection-triggered biological stress. By co-opting and subverting cellular pathways that control mRNA decay, modification, and translation, the global landscape of post-transcriptional processes is swiftly reshaped by virus-encoded factors. Concurrent host cell-intrinsic countermeasures likewise conscript post-transcriptional strategies to mobilize critical innate immune defenses. Here we review strategies and mechanisms that control mRNA decay, modification, and translation in animal virus-infected cells. Besides settling infection outcomes, post-transcriptional gene regulation in virus-infected cells epitomizes fundamental physiological stress responses in health and disease.
Collapse
Affiliation(s)
- Hannah M Burgess
- Department of Microbial Sciences, School of Biosciences and Medicine, University of Surrey, Guildford GU2 7XH, United Kingdom
| | - Elizabeth I Vink
- Department of Microbiology, New York University School of Medicine, New York, New York 10016, USA
| | - Ian Mohr
- Department of Microbiology, New York University School of Medicine, New York, New York 10016, USA.,Laura and Isaac Perlmutter Cancer Institute, New York University School of Medicine, New York, New York 10016, USA
| |
Collapse
|
11
|
Dwivedy A, Mariadasse R, Ahmad M, Chakraborty S, Kar D, Tiwari S, Bhattacharyya S, Sonar S, Mani S, Tailor P, Majumdar T, Jeyakanthan J, Biswal BK. Characterization of the NiRAN domain from RNA-dependent RNA polymerase provides insights into a potential therapeutic target against SARS-CoV-2. PLoS Comput Biol 2021; 17:e1009384. [PMID: 34516563 PMCID: PMC8478224 DOI: 10.1371/journal.pcbi.1009384] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 09/28/2021] [Accepted: 08/26/2021] [Indexed: 12/14/2022] Open
Abstract
Apart from the canonical fingers, palm and thumb domains, the RNA dependent RNA polymerases (RdRp) from the viral order Nidovirales possess two additional domains. Of these, the function of the Nidovirus RdRp associated nucleotidyl transferase domain (NiRAN) remains unanswered. The elucidation of the 3D structure of RdRp from the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), provided the first ever insights into the domain organisation and possible functional characteristics of the NiRAN domain. Using in silico tools, we predict that the NiRAN domain assumes a kinase or phosphotransferase like fold and binds nucleoside triphosphates at its proposed active site. Additionally, using molecular docking we have predicted the binding of three widely used kinase inhibitors and five well characterized anti-microbial compounds at the NiRAN domain active site along with their drug-likeliness. For the first time ever, using basic biochemical tools, this study shows the presence of a kinase like activity exhibited by the SARS-CoV-2 RdRp. Interestingly, a well-known kinase inhibitor- Sorafenib showed a significant inhibition and dampened viral load in SARS-CoV-2 infected cells. In line with the current global COVID-19 pandemic urgency and the emergence of newer strains with significantly higher infectivity, this study provides a new anti-SARS-CoV-2 drug target and potential lead compounds for drug repurposing against SARS-CoV-2. The on-going coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is significantly affecting the world health. Unfortunately, over 180 million cases of COVID-19 resulting in nearly 4 million deaths have been reported till June, 2021. In this study, using a combination of bioinformatics, biochemical and mass spectrometry methods, we show that the Nidovirus RdRp associated Nucleotidyl transferase (NiRAN) domain of the RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 exhibits a kinase like activity. Additionally, we also show that few broad spectrum anti-cancer and anti-microbial drugs dampen this kinase like activity. Of note, Sorafenib, an FDA approved anti-cancer kinase inhibiting drug significantly reduces the SARS-CoV-2 load in cell lines. Our study suggests that NiRAN domain of the SARS-CoV-2 RdRp is indispensible for the successful viral life cycle and shows that abolishing this enzymatic function of RdRp by small molecule inhibitors may open novel avenues for COVID-19 therapeutics.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Sudipta Sonar
- Translational Health Science and Technology Institute, Faridabad, India
| | - Shailendra Mani
- Translational Health Science and Technology Institute, Faridabad, India
| | | | - Tanmay Majumdar
- National Institute of Immunology, New Delhi, India
- * E-mail: (TM); (JJ); (BKB)
| | - Jeyaraman Jeyakanthan
- Department of Bioinformatics, Alagappa University, Tamil Nadu, India
- * E-mail: (TM); (JJ); (BKB)
| | | |
Collapse
|
12
|
Dwivedy A, Mariadasse R, Ahmad M, Chakraborty S, Kar D, Tiwari S, Bhattacharyya S, Sonar S, Mani S, Tailor P, Majumdar T, Jeyakanthan J, Biswal BK. Characterization of the NiRAN domain from RNA-dependent RNA polymerase provides insights into a potential therapeutic target against SARS-CoV-2. PLoS Comput Biol 2021. [DOI: https://doi.org/10.1371/journal.pcbi.1009384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Apart from the canonical fingers, palm and thumb domains, the RNA dependent RNA polymerases (RdRp) from the viral order Nidovirales possess two additional domains. Of these, the function of the Nidovirus RdRp associated nucleotidyl transferase domain (NiRAN) remains unanswered. The elucidation of the 3D structure of RdRp from the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), provided the first ever insights into the domain organisation and possible functional characteristics of the NiRAN domain. Using in silico tools, we predict that the NiRAN domain assumes a kinase or phosphotransferase like fold and binds nucleoside triphosphates at its proposed active site. Additionally, using molecular docking we have predicted the binding of three widely used kinase inhibitors and five well characterized anti-microbial compounds at the NiRAN domain active site along with their drug-likeliness. For the first time ever, using basic biochemical tools, this study shows the presence of a kinase like activity exhibited by the SARS-CoV-2 RdRp. Interestingly, a well-known kinase inhibitor- Sorafenib showed a significant inhibition and dampened viral load in SARS-CoV-2 infected cells. In line with the current global COVID-19 pandemic urgency and the emergence of newer strains with significantly higher infectivity, this study provides a new anti-SARS-CoV-2 drug target and potential lead compounds for drug repurposing against SARS-CoV-2.
Collapse
|
13
|
Abstract
The OC43 coronavirus is a human pathogen that usually causes only the common cold. One of its key enzymes, similar to other coronaviruses, is the 2'-O-RNA methyltransferase (MTase), which is essential for viral RNA stability and expression. Here, we report the crystal structure of the 2'-O-RNA MTase in a complex with the pan-methyltransferase inhibitor sinefungin solved at 2.2-Å resolution. The structure reveals an overall fold consistent with the fold observed in other coronaviral MTases. The major differences are in the conformation of the C terminus of the nsp16 subunit and an additional helix in the N terminus of the nsp10 subunits. The structural analysis also revealed very high conservation of the S-adenosyl methionine (SAM) binding pocket, suggesting that the SAM pocket is a suitable spot for the design of antivirals effective against all human coronaviruses. IMPORTANCE Some coronaviruses are dangerous pathogens, while some cause only common colds. The reasons are not understood, although the spike proteins probably play an important role. However, to understand the coronaviral biology in sufficient detail, we need to compare the key enzymes from different coronaviruses. We solved the crystal structure of 2'-O-RNA methyltransferase of the OC43 coronavirus, a virus that usually causes mild colds. The structure revealed some differences in the overall fold but also revealed that the SAM binding site is conserved, suggesting that development of antivirals against multiple coronaviruses is feasible.
Collapse
|
14
|
Sutto-Ortiz P, Tcherniuk S, Ysebaert N, Abeywickrema P, Noël M, Decombe A, Debart F, Vasseur JJ, Canard B, Roymans D, Rigaux P, Eléouët JF, Decroly E. The methyltransferase domain of the Respiratory Syncytial Virus L protein catalyzes cap N7 and 2'-O-methylation. PLoS Pathog 2021; 17:e1009562. [PMID: 33956914 PMCID: PMC8130918 DOI: 10.1371/journal.ppat.1009562] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 05/18/2021] [Accepted: 04/15/2021] [Indexed: 12/15/2022] Open
Abstract
Respiratory syncytial virus (RSV) is a negative sense single-stranded RNA virus and one of the main causes of severe lower respiratory tract infections in infants and young children. RSV RNA replication/transcription and capping are ensured by the viral Large (L) protein. The L protein contains a polymerase domain associated with a polyribonucleotidyl transferase domain in its N-terminus, and a methyltransferase (MTase) domain followed by the C-terminal domain (CTD) enriched in basic amino acids at its C-terminus. The MTase-CTD of Mononegavirales forms a clamp to accommodate RNA that is subsequently methylated on the cap structure and depending on the virus, on internal positions. These enzymatic activities are essential for efficient viral mRNA translation into proteins, and to prevent the recognition of uncapped viral RNA by innate immunity sensors. In this work, we demonstrated that the MTase-CTD of RSV, as well as the full-length L protein in complex with phosphoprotein (P), catalyzes the N7- and 2’-O-methylation of the cap structure of a short RNA sequence that corresponds to the 5’ end of viral mRNA. Using different experimental systems, we showed that the RSV MTase-CTD methylates the cap structure with a preference for N7-methylation as first reaction. However, we did not observe cap-independent internal methylation, as recently evidenced for the Ebola virus MTase. We also found that at μM concentrations, sinefungin, a S-adenosylmethionine analogue, inhibits the MTase activity of the RSV L protein and of the MTase-CTD domain. Altogether, these results suggest that the RSV MTase domain specifically recognizes viral RNA decorated by a cap structure and catalyzes its methylation, which is required for translation and innate immune system subversion. Respiratory syncytial virus (RSV) is responsible of infant bronchiolitis and severe lower respiratory tract infections in infants and young children, and the leading cause of hospitalization in children under one year of age. However, we still lack a vaccine and therapeutics against this important pathogen. The main enzymatic activities involved in RSV propagation are embedded in the Large (L) protein that contains the polymerase domain and also all the activities required for RNA cap structure synthesis and methylation. These post-transcriptional RNA modifications play a key role in virus replication because cap N7-methylation is required for viral RNA translation into proteins, and 2’-O-methylation hides viral RNA from innate immunity detection. Viral methyltransferase (MTase) activities are now considered potential antiviral targets because their inhibition might limit the virus production and strengthen early virus detection by innate immunity sensors. In this work, we compared the enzymatic activities of the MTase expressed as a single domain or in the context of the full-length L protein. We demonstrated that the MTase protein catalyzes the specific methylation of the cap structure at both N7- and 2’-O-positions, and we obtained the proof of concept that a S-adenosylmethionine analogue can inhibit the MTase activity of the L protein.
Collapse
Affiliation(s)
| | - Sergey Tcherniuk
- Unité de Virologie et Immunologie Moléculaires, INRAE, Université Paris Saclay, Jouy en Josas, France
| | - Nina Ysebaert
- Janssen Infectious Diseases and Vaccines, Beerse, Belgium
| | | | - Mathieu Noël
- IBMM, Université de Montpellier, ENSCM, CNRS, UMR 5247, Montpellier, France
| | - Alice Decombe
- Aix Marseille Université, CNRS, AFMB UMR 7257, Marseille, France
| | - Françoise Debart
- IBMM, Université de Montpellier, ENSCM, CNRS, UMR 5247, Montpellier, France
| | | | - Bruno Canard
- Aix Marseille Université, CNRS, AFMB UMR 7257, Marseille, France
| | - Dirk Roymans
- Janssen Infectious Diseases and Vaccines, Beerse, Belgium
| | - Peter Rigaux
- Janssen Infectious Diseases and Vaccines, Beerse, Belgium
| | - Jean-François Eléouët
- Unité de Virologie et Immunologie Moléculaires, INRAE, Université Paris Saclay, Jouy en Josas, France
| | - Etienne Decroly
- Aix Marseille Université, CNRS, AFMB UMR 7257, Marseille, France
- * E-mail:
| |
Collapse
|
15
|
Markiewicz L, Drazkowska K, Sikorski PJ. Tricks and threats of RNA viruses - towards understanding the fate of viral RNA. RNA Biol 2021; 18:669-687. [PMID: 33618611 PMCID: PMC8078519 DOI: 10.1080/15476286.2021.1875680] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 12/22/2020] [Accepted: 01/09/2021] [Indexed: 12/24/2022] Open
Abstract
Human innate cellular defence pathways have evolved to sense and eliminate pathogens, of which, viruses are considered one of the most dangerous. Their relatively simple structure makes the identification of viral invasion a difficult task for cells. In the course of evolution, viral nucleic acids have become one of the strongest and most reliable early identifiers of infection. When considering RNA virus recognition, RNA sensing is the central mechanism in human innate immunity, and effectiveness of this sensing is crucial for triggering an appropriate antiviral response. Although human cells are armed with a variety of highly specialized receptors designed to respond only to pathogenic viral RNA, RNA viruses have developed an array of mechanisms to avoid being recognized by human interferon-mediated cellular defence systems. The repertoire of viral evasion strategies is extremely wide, ranging from masking pathogenic RNA through end modification, to utilizing sophisticated techniques to deceive host cellular RNA degrading enzymes, and hijacking the most basic metabolic pathways in host cells. In this review, we aim to dissect human RNA sensing mechanisms crucial for antiviral immune defences, as well as the strategies adopted by RNA viruses to avoid detection and degradation by host cells. We believe that understanding the fate of viral RNA upon infection, and detailing the molecular mechanisms behind virus-host interactions, may be helpful for developing more effective antiviral strategies; which are urgently needed to prevent the far-reaching consequences of widespread, highly pathogenic viral infections.
Collapse
|
16
|
Netzband R, Pager CT. Viral Epitranscriptomics. Virology 2021. [DOI: 10.1002/9781119818526.ch4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
17
|
Weixler L, Schäringer K, Momoh J, Lüscher B, Feijs KLH, Žaja R. ADP-ribosylation of RNA and DNA: from in vitro characterization to in vivo function. Nucleic Acids Res 2021; 49:3634-3650. [PMID: 33693930 PMCID: PMC8053099 DOI: 10.1093/nar/gkab136] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 02/11/2021] [Accepted: 02/17/2021] [Indexed: 12/12/2022] Open
Abstract
The functionality of DNA, RNA and proteins is altered dynamically in response to physiological and pathological cues, partly achieved by their modification. While the modification of proteins with ADP-ribose has been well studied, nucleic acids were only recently identified as substrates for ADP-ribosylation by mammalian enzymes. RNA and DNA can be ADP-ribosylated by specific ADP-ribosyltransferases such as PARP1-3, PARP10 and tRNA 2'-phosphotransferase (TRPT1). Evidence suggests that these enzymes display different preferences towards different oligonucleotides. These reactions are reversed by ADP-ribosylhydrolases of the macrodomain and ARH families, such as MACROD1, TARG1, PARG, ARH1 and ARH3. Most findings derive from in vitro experiments using recombinant components, leaving the relevance of this modification in cells unclear. In this Survey and Summary, we provide an overview of the enzymes that ADP-ribosylate nucleic acids, the reversing hydrolases, and the substrates' requirements. Drawing on data available for other organisms, such as pierisin1 from cabbage butterflies and the bacterial toxin-antitoxin system DarT-DarG, we discuss possible functions for nucleic acid ADP-ribosylation in mammals. Hypothesized roles for nucleic acid ADP-ribosylation include functions in DNA damage repair, in antiviral immunity or as non-conventional RNA cap. Lastly, we assess various methods potentially suitable for future studies of nucleic acid ADP-ribosylation.
Collapse
Affiliation(s)
- Lisa Weixler
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Pauwelsstrasse 30, Aachen, Germany
| | - Katja Schäringer
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Pauwelsstrasse 30, Aachen, Germany
| | - Jeffrey Momoh
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Pauwelsstrasse 30, Aachen, Germany
| | - Bernhard Lüscher
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Pauwelsstrasse 30, Aachen, Germany
| | - Karla L H Feijs
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Pauwelsstrasse 30, Aachen, Germany
| | - Roko Žaja
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Pauwelsstrasse 30, Aachen, Germany
| |
Collapse
|
18
|
Khalili Yazdi A, Li F, Devkota K, Perveen S, Ghiabi P, Hajian T, Bolotokova A, Vedadi M. A High-Throughput Radioactivity-Based Assay for Screening SARS-CoV-2 nsp10-nsp16 Complex. SLAS DISCOVERY 2021; 26:757-765. [PMID: 33874769 PMCID: PMC8216315 DOI: 10.1177/24725552211008863] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Frequent outbreaks of novel coronaviruses (CoVs), highlighted by the current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, necessitate the development of therapeutics that could be easily and effectively administered worldwide. The conserved mRNA-capping process enables CoVs to evade their host immune system and is a target for antiviral development. Nonstructural protein (nsp) 16 in complex with nsp10 catalyzes the final step of coronaviral mRNA capping through its 2'-O-methylation activity. Like other methyltransferases, the SARS-CoV-2 nsp10-nsp16 complex is druggable. However, the availability of an optimized assay for high-throughput screening (HTS) is an unmet need. Here, we report the development of a radioactivity-based assay for the methyltransferase activity of the nsp10-nsp16 complex in a 384-well format, kinetic characterization, and optimization of the assay for HTS (Z' factor = 0.83). Considering the high conservation of nsp16 across known CoV species, the potential inhibitors targeting the SARS-CoV-2 nsp10-nsp16 complex may also be effective against other emerging pathogenic CoVs.
Collapse
Affiliation(s)
| | - Fengling Li
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Kanchan Devkota
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Sumera Perveen
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Pegah Ghiabi
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Taraneh Hajian
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Albina Bolotokova
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
19
|
Ahmed-Belkacem R, Sutto-Ortiz P, Guiraud M, Canard B, Vasseur JJ, Decroly E, Debart F. Synthesis of adenine dinucleosides SAM analogs as specific inhibitors of SARS-CoV nsp14 RNA cap guanine-N7-methyltransferase. Eur J Med Chem 2020; 201:112557. [PMID: 32563813 PMCID: PMC7291971 DOI: 10.1016/j.ejmech.2020.112557] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 05/26/2020] [Accepted: 06/08/2020] [Indexed: 12/18/2022]
Abstract
The spreading of new viruses is known to provoke global human health threat. The current COVID-19 pandemic caused by the recently emerged coronavirus SARS-CoV-2 is one significant and unfortunate example of what the world will have to face in the future with emerging viruses in absence of appropriate treatment. The discovery of potent and specific antiviral inhibitors and/or vaccines to fight these massive outbreaks is an urgent research priority. Enzymes involved in the capping pathway of viruses and more specifically RNA N7- or 2′O-methyltransferases (MTases) are now admitted as potential targets for antiviral chemotherapy. We designed bisubstrate inhibitors by mimicking the transition state of the 2′-O-methylation of the cap RNA in order to block viral 2′-O MTases. This work resulted in the synthesis of 16 adenine dinucleosides with both adenosines connected by various nitrogen-containing linkers. Unexpectedly, all the bisubstrate compounds were barely active against 2′-O MTases of several flaviviruses or SARS-CoV but surprisingly, seven of them showed efficient and specific inhibition against SARS-CoV N7-MTase (nsp14) in the micromolar to submicromolar range. The most active nsp14 inhibitor identified is as potent as but particularly more specific than the broad-spectrum MTase inhibitor, sinefungin. Molecular docking suggests that the inhibitor binds to a pocket formed by the S-adenosyl methionine (SAM) and cap RNA binding sites, conserved among SARS-CoV nsp14. These dinucleoside SAM analogs will serve as starting points for the development of next inhibitors for SARS-CoV-2 nsp14 N7-MTase.
Collapse
Affiliation(s)
| | - Priscila Sutto-Ortiz
- AFMB, CNRS, Aix-Marseille University, UMR 7257, 163 Avenue de Luminy, Marseille, France
| | - Mathis Guiraud
- IBMM, CNRS, University of Montpellier, ENSCM, Montpellier, France
| | - Bruno Canard
- AFMB, CNRS, Aix-Marseille University, UMR 7257, 163 Avenue de Luminy, Marseille, France
| | | | - Etienne Decroly
- AFMB, CNRS, Aix-Marseille University, UMR 7257, 163 Avenue de Luminy, Marseille, France.
| | - Françoise Debart
- IBMM, CNRS, University of Montpellier, ENSCM, Montpellier, France.
| |
Collapse
|
20
|
Spizzichino S, Mattedi G, Lauder K, Valle C, Aouadi W, Canard B, Decroly E, Kaptein SJF, Neyts J, Graham C, Sule Z, Barlow DJ, Silvestri R, Castagnolo D. Design, Synthesis and Discovery of N,N'-Carbazoyl-aryl-urea Inhibitors of Zika NS5 Methyltransferase and Virus Replication. ChemMedChem 2020; 15:385-390. [PMID: 31805205 PMCID: PMC7106487 DOI: 10.1002/cmdc.201900533] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/05/2019] [Indexed: 12/18/2022]
Abstract
The recent outbreaks of Zika virus (ZIKV) infection worldwide make the discovery of novel antivirals against flaviviruses a research priority. This work describes the identification of novel inhibitors of ZIKV through a structure-based virtual screening approach using the ZIKV NS5-MTase. A novel series of molecules with a carbazoyl-aryl-urea structure has been discovered and a library of analogues has been synthesized. The new compounds inhibit ZIKV MTase with IC50 between 23-48 μM. In addition, carbazoyl-aryl-ureas also proved to inhibit ZIKV replication activity at micromolar concentration.
Collapse
Affiliation(s)
- Sharon Spizzichino
- School of Cancer and Pharmaceutical SciencesKing's College LondonLondonSE1 9NHUK
- Department of Drug Chemistry and TechnologiesSapienza University of RomeLaboratory Affiliated to Instituto Pasteur Italia – Fondazione Cenci BolognettiPiazzale Aldo Moro 500185RomaItaly
| | - Giulio Mattedi
- School of Cancer and Pharmaceutical SciencesKing's College LondonLondonSE1 9NHUK
| | - Kate Lauder
- School of Cancer and Pharmaceutical SciencesKing's College LondonLondonSE1 9NHUK
| | - Coralie Valle
- AFMB, CNRSAix-Marseille University UMR 7257, Case 925163 Avenue de Luminy13288Marseille Cedex 09France
| | - Wahiba Aouadi
- AFMB, CNRSAix-Marseille University UMR 7257, Case 925163 Avenue de Luminy13288Marseille Cedex 09France
| | - Bruno Canard
- AFMB, CNRSAix-Marseille University UMR 7257, Case 925163 Avenue de Luminy13288Marseille Cedex 09France
| | - Etienne Decroly
- AFMB, CNRSAix-Marseille University UMR 7257, Case 925163 Avenue de Luminy13288Marseille Cedex 09France
| | - Suzanne J. F. Kaptein
- Department of Microbiology, Immunology and Transplantation Rega Institute for Medical Research Laboratory of Virology and ChemotherapyKU LeuvenMinderbroedersstraat 103000LeuvenBelgium
| | - Johan Neyts
- Department of Microbiology, Immunology and Transplantation Rega Institute for Medical Research Laboratory of Virology and ChemotherapyKU LeuvenMinderbroedersstraat 103000LeuvenBelgium
| | - Carl Graham
- School of Cancer and Pharmaceutical SciencesKing's College LondonLondonSE1 9NHUK
| | - Zakary Sule
- School of Cancer and Pharmaceutical SciencesKing's College LondonLondonSE1 9NHUK
| | - David J. Barlow
- School of Cancer and Pharmaceutical SciencesKing's College LondonLondonSE1 9NHUK
| | - Romano Silvestri
- Department of Drug Chemistry and TechnologiesSapienza University of RomeLaboratory Affiliated to Instituto Pasteur Italia – Fondazione Cenci BolognettiPiazzale Aldo Moro 500185RomaItaly
| | - Daniele Castagnolo
- School of Cancer and Pharmaceutical SciencesKing's College LondonLondonSE1 9NHUK
| |
Collapse
|
21
|
Netzband R, Pager CT. Epitranscriptomic marks: Emerging modulators of RNA virus gene expression. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 11:e1576. [PMID: 31694072 PMCID: PMC7169815 DOI: 10.1002/wrna.1576] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 10/07/2019] [Accepted: 10/08/2019] [Indexed: 12/27/2022]
Abstract
Epitranscriptomics, the study of posttranscriptional chemical moieties placed on RNA, has blossomed in recent years. This is due in part to the emergence of high‐throughput detection methods as well as the burst of discoveries showing biological function of select chemical marks. RNA modifications have been shown to affect RNA structure, localization, and functions such as alternative splicing, stabilizing transcripts, nuclear export, cap‐dependent and cap‐independent translation, microRNA biogenesis and binding, RNA degradation, and immune regulation. As such, the deposition of chemical marks on RNA has the unique capability to spatially and temporally regulate gene expression. The goal of this article is to present the exciting convergence of the epitranscriptomic and virology fields, specifically the deposition and biological impact of N7‐methylguanosine, ribose 2′‐O‐methylation, pseudouridine, inosine, N6‐methyladenosine, and 5‐methylcytosine epitranscriptomic marks on gene expression of RNA viruses. This article is categorized under:RNA in Disease and Development > RNA in Disease RNA Interactions with Proteins and Other Molecules > Protein–RNA Interactions: Functional Implications
Collapse
Affiliation(s)
- Rachel Netzband
- Department of Biological Sciences, The RNA Institute, University at Albany-SUNY, Albany, New York
| | - Cara T Pager
- Department of Biological Sciences, The RNA Institute, University at Albany-SUNY, Albany, New York
| |
Collapse
|
22
|
Ahmed-Belkacem R, Sutto-Ortiz P, Decroly E, Vasseur JJ, Debart F. Synthesis of Adenine Dinucleosides 2′,5′-Bridged by Sulfur-Containing Linkers as Bisubstrate SAM Analogues for Viral RNA 2′- O
-Methyltransferases. European J Org Chem 2019. [DOI: 10.1002/ejoc.201901120] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
| | - Priscila Sutto-Ortiz
- AFMB, CNRS; Aix-Marseille University; UMR 7257; 163 avenue de Luminy Marseille France
| | - Etienne Decroly
- AFMB, CNRS; Aix-Marseille University; UMR 7257; 163 avenue de Luminy Marseille France
| | | | - Françoise Debart
- IBMM; UMR 5247, CNRS; University of Montpellier; ENSCM; Montpellier France
| |
Collapse
|
23
|
Mäkinen K, De S. The significance of methionine cycle enzymes in plant virus infections. CURRENT OPINION IN PLANT BIOLOGY 2019; 50:67-75. [PMID: 30959442 DOI: 10.1016/j.pbi.2019.03.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 02/25/2019] [Accepted: 03/05/2019] [Indexed: 05/22/2023]
Abstract
Both biotic and abiotic stresses cause changes in the activities of plant methionine cycle (MTC) enzymes. These changes contribute to the ability of the plant to manage stress. On the other hand, viruses utilize MTC enzymes to promote infection. Here, we review the growing but still limited knowledge of the interactions between plant viral proteins and MTC enzymes. Virus-induced changes in S-adenosyl methionine synthetase and S-adenosyl homocysteine hydrolase activities debilitate transcriptional and post-transcriptional RNA silencing and affect antiviral defense reactions connected to ethylene and polyamine biosynthesis pathways. Viral perturbations of host methionine homeostasis couple trans-sulfuration and gluthathione biosynthesis pathways to MTC functions. Large multiprotein complexes, which contain viral proteins and MTC enzymes, may represent metabolons assembled for specific viral functions or host defense responses. Proper understanding of the MTC-associated metabolic and regulatory interactions will reveal those with potential to create virus resistance in plants.
Collapse
Affiliation(s)
- Kristiina Mäkinen
- Faculty of Agriculture and Forestry, Department of Microbiology, Viikki Plant Sciences Center, P.O. Box 56, University of Helsinki, Finland.
| | - Swarnalok De
- Faculty of Agriculture and Forestry, Department of Microbiology, Viikki Plant Sciences Center, P.O. Box 56, University of Helsinki, Finland
| |
Collapse
|
24
|
|
25
|
Cross ST, Michalski D, Miller MR, Wilusz J. RNA regulatory processes in RNA virus biology. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1536. [PMID: 31034160 PMCID: PMC6697219 DOI: 10.1002/wrna.1536] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 04/02/2019] [Indexed: 12/13/2022]
Abstract
Numerous post‐transcriptional RNA processes play a major role in regulating the quantity, quality and diversity of gene expression in the cell. These include RNA processing events such as capping, splicing, polyadenylation and modification, but also aspects such as RNA localization, decay, translation, and non‐coding RNA‐associated regulation. The interface between the transcripts of RNA viruses and the various RNA regulatory processes in the cell, therefore, has high potential to significantly impact virus gene expression, regulation, cytopathology and pathogenesis. Furthermore, understanding RNA biology from the perspective of an RNA virus can shed considerable light on the broad impact of these post‐transcriptional processes in cell biology. Thus the goal of this article is to provide an overview of the richness of cellular RNA biology and how RNA viruses use, usurp and/or avoid the associated machinery to impact the outcome of infection. This article is categorized under:RNA in Disease and Development > RNA in Disease
Collapse
Affiliation(s)
- Shaun T Cross
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado
| | - Daniel Michalski
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado
| | - Megan R Miller
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado
| | - Jeffrey Wilusz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado
| |
Collapse
|
26
|
Unterholzner L, Almine JF. Camouflage and interception: how pathogens evade detection by intracellular nucleic acid sensors. Immunology 2018; 156:217-227. [PMID: 30499584 PMCID: PMC6376273 DOI: 10.1111/imm.13030] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 10/24/2018] [Accepted: 11/26/2018] [Indexed: 12/16/2022] Open
Abstract
Intracellular DNA and RNA sensors play a vital part in the innate immune response to viruses and other intracellular pathogens, causing the secretion of type I interferons, cytokines and chemokines from infected cells. Pathogen RNA can be detected by retinoic-acid inducible gene I-like receptors in the cytosol, whereas cytosolic DNA is recognized by DNA sensors such as cyclic GMP-AMP synthase (cGAS). The resulting local immune response, which is initiated within hours of infection, is able to eliminate many pathogens before they are able to establish an infection in the host. For this reason, all viruses, and some intracellular bacteria and protozoa, need to evade detection by nucleic acid sensors. Immune evasion strategies include the sequestration and modification of nucleic acids, and the inhibition or degradation of host factors involved in innate immune signalling. Large DNA viruses, such as herpesviruses, often use multiple viral proteins to inhibit signalling cascades at several different points; for instance herpes simplex virus 1 targets both DNA sensors cGAS and interferon-γ-inducible protein 16, as well as the adaptor protein STING (stimulator of interferon genes) and other signalling factors in the pathway. Viruses with a small genome encode only a few immunomodulatory proteins, but these are often multifunctional, such as the NS1 protein from influenza A virus, which inhibits RNA sensing in multiple ways. Intracellular bacteria and protozoa can also be detected by nucleic acid sensors. However, as the type I interferon response is not always beneficial for the host under these circumstances, some bacteria subvert, rather than evade, these signalling cascades for their own gain.
Collapse
Affiliation(s)
- Leonie Unterholzner
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, UK
| | - Jessica F Almine
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, UK
| |
Collapse
|
27
|
Shirokikh NE, Preiss T. Translation initiation by cap-dependent ribosome recruitment: Recent insights and open questions. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 9:e1473. [PMID: 29624880 DOI: 10.1002/wrna.1473] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 02/02/2018] [Accepted: 02/14/2018] [Indexed: 12/14/2022]
Abstract
Gene expression universally relies on protein synthesis, where ribosomes recognize and decode the messenger RNA template by cycling through translation initiation, elongation, and termination phases. All aspects of translation have been studied for decades using the tools of biochemistry and molecular biology available at the time. Here, we focus on the mechanism of translation initiation in eukaryotes, which is remarkably more complex than prokaryotic initiation and is the target of multiple types of regulatory intervention. The "consensus" model, featuring cap-dependent ribosome entry and scanning of mRNA leader sequences, represents the predominantly utilized initiation pathway across eukaryotes, although several variations of the model and alternative initiation mechanisms are also known. Recent advances in structural biology techniques have enabled remarkable molecular-level insights into the functional states of eukaryotic ribosomes, including a range of ribosomal complexes with different combinations of translation initiation factors that are thought to represent bona fide intermediates of the initiation process. Similarly, high-throughput sequencing-based ribosome profiling or "footprinting" approaches have allowed much progress in understanding the elongation phase of translation, and variants of them are beginning to reveal the remaining mysteries of initiation, as well as aspects of translation termination and ribosomal recycling. A current view on the eukaryotic initiation mechanism is presented here with an emphasis on how recent structural and footprinting results underpin axioms of the consensus model. Along the way, we further outline some contested mechanistic issues and major open questions still to be addressed. This article is categorized under: Translation > Translation Mechanisms Translation > Translation Regulation RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
Collapse
Affiliation(s)
- Nikolay E Shirokikh
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia
| | - Thomas Preiss
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia
| |
Collapse
|