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
|
Corbeski I, Vargas-Rosales PA, Bedi RK, Deng J, Coelho D, Braud E, Iannazzo L, Li Y, Huang D, Ethève-Quelquejeu M, Cui Q, Caflisch A. The catalytic mechanism of the RNA methyltransferase METTL3. eLife 2024; 12:RP92537. [PMID: 38470714 PMCID: PMC10932547 DOI: 10.7554/elife.92537] [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] [Indexed: 03/14/2024] Open
Abstract
The complex of methyltransferase-like proteins 3 and 14 (METTL3-14) is the major enzyme that deposits N6-methyladenosine (m6A) modifications on messenger RNA (mRNA) in humans. METTL3-14 plays key roles in various biological processes through its methyltransferase (MTase) activity. However, little is known about its substrate recognition and methyl transfer mechanism from its cofactor and methyl donor S-adenosylmethionine (SAM). Here, we study the MTase mechanism of METTL3-14 by a combined experimental and multiscale simulation approach using bisubstrate analogues (BAs), conjugates of a SAM-like moiety connected to the N6-atom of adenosine. Molecular dynamics simulations based on crystal structures of METTL3-14 with BAs suggest that the Y406 side chain of METTL3 is involved in the recruitment of adenosine and release of m6A. A crystal structure with a BA representing the transition state of methyl transfer shows a direct involvement of the METTL3 side chains E481 and K513 in adenosine binding which is supported by mutational analysis. Quantum mechanics/molecular mechanics (QM/MM) free energy calculations indicate that methyl transfer occurs without prior deprotonation of adenosine-N6. Furthermore, the QM/MM calculations provide further support for the role of electrostatic contributions of E481 and K513 to catalysis. The multidisciplinary approach used here sheds light on the (co)substrate binding mechanism, catalytic step, and (co)product release, and suggests that the latter step is rate-limiting for METTL3. The atomistic information on the substrate binding and methyl transfer reaction of METTL3 can be useful for understanding the mechanisms of other RNA MTases and for the design of transition state analogues as their inhibitors.
Collapse
Affiliation(s)
- Ivan Corbeski
- Department of Biochemistry, University of ZurichZurichSwitzerland
| | | | - Rajiv Kumar Bedi
- Department of Biochemistry, University of ZurichZurichSwitzerland
| | - Jiahua Deng
- Department of Chemistry, Boston UniversityBostonUnited States
| | - Dylan Coelho
- Université Paris Cité, CNRS, Laboratoire de Chimie et Biochimie Pharmacologiques et ToxicologiquesParisFrance
| | - Emmanuelle Braud
- Université Paris Cité, CNRS, Laboratoire de Chimie et Biochimie Pharmacologiques et ToxicologiquesParisFrance
| | - Laura Iannazzo
- Université Paris Cité, CNRS, Laboratoire de Chimie et Biochimie Pharmacologiques et ToxicologiquesParisFrance
| | - Yaozong Li
- Department of Biochemistry, University of ZurichZurichSwitzerland
| | - Danzhi Huang
- Department of Biochemistry, University of ZurichZurichSwitzerland
| | - Mélanie Ethève-Quelquejeu
- Université Paris Cité, CNRS, Laboratoire de Chimie et Biochimie Pharmacologiques et ToxicologiquesParisFrance
| | - Qiang Cui
- Department of Chemistry, Boston UniversityBostonUnited States
- Department of Physics, Boston UniversityBostonUnited States
- Department of Biomedical Engineering, Boston UniversityBostonUnited States
| | - Amedeo Caflisch
- Department of Biochemistry, University of ZurichZurichSwitzerland
| |
Collapse
|
3
|
Bourgery C, Mendoza DJ, Garnier G, Mouterde LMM, Allais F. Immobilization of Adenosine Derivatives onto Cellulose Nanocrystals via Click Chemistry for Biocatalysis Applications. ACS APPLIED MATERIALS & INTERFACES 2024; 16:11315-11323. [PMID: 38394235 DOI: 10.1021/acsami.3c19025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
Adenosine triphosphate (ATP) is a central molecule of organisms and is involved in many biological processes. It is also widely used in biocatalytic processes, especially as a substrate and precursor of many cofactors─such as nicotinamide adenine dinucleotide phosphate (NADP(H)), coenzyme A (CoA), and S-adenosylmethionine (SAM). Despite its great scientific interest and pivotal role, its use in industrial processes is impeded by its prohibitory cost. To overcome this limitation, we developed a greener synthesis of adenosine derivatives and efficiently selectively grafted them onto organic nanoparticles. In this study, cellulose nanocrystals were used as a model combined with click chemistry via a copper-catalyzed azide/alkyne cycloaddition reaction (CuAAC). The grafted adenosine triphosphate derivative fully retains its biocatalytic capability, enabling heterobiocatalysis for modern biochemical processes.
Collapse
Affiliation(s)
- Célestin Bourgery
- URD Agro-Biotechnologies Industrielles (ABI), CEBB, AgroParisTech, Pomacle 51110, France
| | - David Joram Mendoza
- Bioresource Processing Research Institute of Australia (BioPRIA), Department of Chemical and Biological Engineering, Monash University, Clayton, VIC 3800, Australia
| | - Gil Garnier
- URD Agro-Biotechnologies Industrielles (ABI), CEBB, AgroParisTech, Pomacle 51110, France
- Bioresource Processing Research Institute of Australia (BioPRIA), Department of Chemical and Biological Engineering, Monash University, Clayton, VIC 3800, Australia
| | - Louis M M Mouterde
- URD Agro-Biotechnologies Industrielles (ABI), CEBB, AgroParisTech, Pomacle 51110, France
| | - Florent Allais
- URD Agro-Biotechnologies Industrielles (ABI), CEBB, AgroParisTech, Pomacle 51110, France
- Bioresource Processing Research Institute of Australia (BioPRIA), Department of Chemical and Biological Engineering, Monash University, Clayton, VIC 3800, Australia
| |
Collapse
|
4
|
Ahmed-Belkacem R, Sutto-Ortiz P, Delpal A, Troussier J, Canard B, Vasseur JJ, Decroly E, Debart F. 5'-cap RNA/SAM mimetic conjugates as bisubstrate inhibitors of viral RNA cap 2'-O-methyltransferases. Bioorg Chem 2024; 143:107035. [PMID: 38199140 DOI: 10.1016/j.bioorg.2023.107035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/24/2023] [Accepted: 12/12/2023] [Indexed: 01/12/2024]
Abstract
Viral RNA cap 2'-O-methyltransferases are considered promising therapeutic targets for antiviral treatments, as they play a key role in the formation of viral RNA cap-1 structures to escape the host immune system. A better understanding of how they interact with their natural substrates (RNA and the methyl donor SAM) would enable the rational development of potent inhibitors. However, as few structures of 2'-O-MTases in complex with RNA have been described, little is known about substrate recognition by these MTases. For this, chemical tools mimicking the state in which the cap RNA substrate and SAM cofactor are bound in the enzyme's catalytic pocket may prove useful. In this work, we designed and synthesized over 30 RNA conjugates that contain a short oligoribonucleotide (ORN with 4 or 6 nucleotides) with the first nucleotide 2'-O-attached to an adenosine by linkers of different lengths and containing S or N-heteroatoms, or a 1,2,3-triazole ring. These ORN conjugates bearing or not a cap structure at 5'-extremity mimic the methylation transition state with RNA substrate/SAM complex as bisubstrates of 2'-O-MTases. The ORN conjugates were synthesized either by the incorporation of a dinucleoside phosphoramidite during RNA elongation or by click chemistry performed on solid-phase post-RNA elongation. Their ability to inhibit the activity of the nsp16/nsp10 complex of SARS-CoV-2 and the NS5 protein of dengue and Zika viruses was assessed. Significant submicromolar IC50 values and Kd values in the µM range were found, suggesting a possible interaction of some ORN conjugates with these viral 2'-O-MTases.
Collapse
Affiliation(s)
| | | | - Adrien Delpal
- AFMB, University of Aix-Marseille, CNRS, Marseille, France
| | - Joris Troussier
- IBMM, University of Montpellier, CNRS, ENSCM, Montpellier, France
| | - Bruno Canard
- AFMB, University of Aix-Marseille, CNRS, Marseille, France
| | | | | | - Françoise Debart
- IBMM, University of Montpellier, CNRS, ENSCM, Montpellier, France.
| |
Collapse
|
5
|
Corbeski I, Vargas-Rosales PA, Bedi RK, Deng J, Coelho D, Braud E, Iannazzo L, Li Y, Huang D, Etheve-Quelquejeu M, Cui Q, Caflisch A. The catalytic mechanism of the RNA methyltransferase METTL3. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.06.556513. [PMID: 37732228 PMCID: PMC10508762 DOI: 10.1101/2023.09.06.556513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
The complex of methyltransferase-like proteins 3 and 14 (METTL3-14) is the major enzyme that deposits N6-methyladenosine (m6A) modifications on mRNA in humans. METTL3-14 plays key roles in various biological processes through its methyltransferase (MTase) activity. However, little is known about its substrate recognition and methyl transfer mechanism from its cofactor and methyl donor S-adenosylmethionine (SAM). Here, we study the MTase mechanism of METTL3-14 by a combined experimental and multiscale simulation approach using bisubstrate analogues (BAs), conjugates of a SAM-like moiety connected to the N6-atom of adenosine. Molecular dynamics simulations based on crystal structures of METTL3-14 with BAs suggest that the Y406 side chain of METTL3 is involved in the recruitment of adenosine and release of m6A. A crystal structure with a bisubstrate analogue representing the transition state of methyl transfer shows a direct involvement of the METTL3 side chains E481 and K513 in adenosine binding which is supported by mutational analysis. Quantum mechanics/molecular mechanics (QM/MM) free energy calculations indicate that methyl transfer occurs without prior deprotonation of adenosine-N6. Furthermore, the QM/MM calculations provide further support for the role of electrostatic contributions of E481 and K513 to catalysis. The multidisciplinary approach used here sheds light on the (co)substrate binding mechanism, catalytic step, and (co)product release catalysed by METTL3, and suggests that the latter step is rate-limiting. The atomistic information on the substrate binding and methyl transfer reaction of METTL3 can be useful for understanding the mechanisms of other RNA MTases and for the design of transition state analogues as their inhibitors.
Collapse
|
6
|
Meynier V, Iannazzo L, Catala M, Oerum S, Braud E, Atdjian C, Barraud P, Fonvielle M, Tisné C, Ethève-Quelquejeu M. Synthesis of RNA-cofactor conjugates and structural exploration of RNA recognition by an m6A RNA methyltransferase. Nucleic Acids Res 2022; 50:5793-5806. [PMID: 35580049 PMCID: PMC9178011 DOI: 10.1093/nar/gkac354] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 04/22/2022] [Accepted: 05/10/2022] [Indexed: 11/14/2022] Open
Abstract
Chemical synthesis of RNA conjugates has opened new strategies to study enzymatic mechanisms in RNA biology. To gain insights into poorly understood RNA nucleotide methylation processes, we developed a new method to synthesize RNA-conjugates for the study of RNA recognition and methyl-transfer mechanisms of SAM-dependent m6A RNA methyltransferases. These RNA conjugates contain a SAM cofactor analogue connected at the N6-atom of an adenosine within dinucleotides, a trinucleotide or a 13mer RNA. Our chemical route is chemo- and regio-selective and allows flexible modification of the RNA length and sequence. These compounds were used in crystallization assays with RlmJ, a bacterial m6A rRNA methyltransferase. Two crystal structures of RlmJ in complex with RNA–SAM conjugates were solved and revealed the RNA-specific recognition elements used by RlmJ to clamp the RNA substrate in its active site. From these structures, a model of a trinucleotide bound in the RlmJ active site could be built and validated by methyltransferase assays on RlmJ mutants. The methyl transfer by RlmJ could also be deduced. This study therefore shows that RNA-cofactor conjugates are potent molecular tools to explore the active site of RNA modification enzymes.
Collapse
Affiliation(s)
- Vincent Meynier
- Expression Génétique Microbienne, UMR 8261, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique (IBPC), 75005, Paris, France
| | - Laura Iannazzo
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601, CNRS, Université Paris Cité, 75006, Paris, France
| | - Marjorie Catala
- Expression Génétique Microbienne, UMR 8261, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique (IBPC), 75005, Paris, France
| | - Stephanie Oerum
- Expression Génétique Microbienne, UMR 8261, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique (IBPC), 75005, Paris, France
| | - Emmanuelle Braud
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601, CNRS, Université Paris Cité, 75006, Paris, France
| | - Colette Atdjian
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601, CNRS, Université Paris Cité, 75006, Paris, France
| | - Pierre Barraud
- Expression Génétique Microbienne, UMR 8261, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique (IBPC), 75005, Paris, France
| | - Matthieu Fonvielle
- Sorbonne Université, Université Paris Cité, Centre de recherche des Cordeliers, 75006, Paris, France
| | - Carine Tisné
- Expression Génétique Microbienne, UMR 8261, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique (IBPC), 75005, Paris, France
| | - Mélanie Ethève-Quelquejeu
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601, CNRS, Université Paris Cité, 75006, Paris, France
| |
Collapse
|
7
|
Ahmed‐Belkacem R, Debart F, Vasseur J. Bisubstrate Strategies to Target Methyltransferases. European J Org Chem 2022. [DOI: 10.1002/ejoc.202101481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
8
|
Baraniak D, Boryski J. Triazole-Modified Nucleic Acids for the Application in Bioorganic and Medicinal Chemistry. Biomedicines 2021; 9:628. [PMID: 34073038 PMCID: PMC8229351 DOI: 10.3390/biomedicines9060628] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/26/2021] [Accepted: 05/26/2021] [Indexed: 02/07/2023] Open
Abstract
This review covers studies which exploit triazole-modified nucleic acids in the range of chemistry and biology to medicine. The 1,2,3-triazole unit, which is obtained via click chemistry approach, shows valuable and unique properties. For example, it does not occur in nature, constitutes an additional pharmacophore with attractive properties being resistant to hydrolysis and other reactions at physiological pH, exhibits biological activity (i.e., antibacterial, antitumor, and antiviral), and can be considered as a rigid mimetic of amide linkage. Herein, it is presented a whole area of useful artificial compounds, from the clickable monomers and dimers to modified oligonucleotides, in the field of nucleic acids sciences. Such modifications of internucleotide linkages are designed to increase the hybridization binding affinity toward native DNA or RNA, to enhance resistance to nucleases, and to improve ability to penetrate cell membranes. The insertion of an artificial backbone is used for understanding effects of chemically modified oligonucleotides, and their potential usefulness in therapeutic applications. We describe the state-of-the-art knowledge on their implications for synthetic genes and other large modified DNA and RNA constructs including non-coding RNAs.
Collapse
Affiliation(s)
- Dagmara Baraniak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland;
| | | |
Collapse
|