1
|
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
|
2
|
Atdjian C, Iannazzo L, Braud E, Ethève-Quelquejeu M. Synthesis of SAM-Adenosine Conjugates for the Study of m 6
A-RNA Methyltransferases. European J Org Chem 2018. [DOI: 10.1002/ejoc.201800798] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Colette Atdjian
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques; Team “Chemistry of RNAs, nucleosides, peptides and heterocycles”; Université Paris Descartes; UMR 8601; 75005 Paris France
| | - Laura Iannazzo
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques; Team “Chemistry of RNAs, nucleosides, peptides and heterocycles”; Université Paris Descartes; UMR 8601; 75005 Paris France
| | - Emmanuelle Braud
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques; Team “Chemistry of RNAs, nucleosides, peptides and heterocycles”; Université Paris Descartes; UMR 8601; 75005 Paris France
| | - Mélanie Ethève-Quelquejeu
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques; Team “Chemistry of RNAs, nucleosides, peptides and heterocycles”; Université Paris Descartes; UMR 8601; 75005 Paris France
| |
Collapse
|
3
|
Misson L, Burn R, Vit A, Hildesheim J, Beliaeva MA, Blankenfeldt W, Seebeck FP. Inhibition and Regulation of the Ergothioneine Biosynthetic Methyltransferase EgtD. ACS Chem Biol 2018; 13:1333-1342. [PMID: 29658702 DOI: 10.1021/acschembio.8b00127] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Ergothioneine is an emerging factor in cellular redox homeostasis in bacteria, fungi, plants, and animals. Reports that ergothioneine biosynthesis may be important for the pathogenicity of bacteria and fungi raise the question as to how this pathway is regulated and whether the corresponding enzymes may be therapeutic targets. The first step in ergothioneine biosynthesis is catalyzed by the methyltransferase EgtD that converts histidine into N-α-trimethylhistidine. This report examines the kinetic, thermodynamic and structural basis for substrate, product, and inhibitor binding by EgtD from Mycobacterium smegmatis. This study reveals an unprecedented substrate binding mechanism and a fine-tuned affinity landscape as determinants for product specificity and product inhibition. Both properties are evolved features that optimize the function of EgtD in the context of cellular ergothioneine production. On the basis of these findings, we developed a series of simple histidine derivatives that inhibit methyltransferase activity at low micromolar concentrations. Crystal structures of inhibited complexes validate this structure- and mechanism-based design strategy.
Collapse
Affiliation(s)
- Laëtitia Misson
- Department for Chemistry, University of Basel, BPR 1096, Mattenstrasse 24a, Basel, Switzerland
| | - Reto Burn
- Department for Chemistry, University of Basel, BPR 1096, Mattenstrasse 24a, Basel, Switzerland
| | - Allegra Vit
- Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Julia Hildesheim
- Department for Chemistry, University of Basel, BPR 1096, Mattenstrasse 24a, Basel, Switzerland
| | - Mariia A. Beliaeva
- Department for Chemistry, University of Basel, BPR 1096, Mattenstrasse 24a, Basel, Switzerland
| | - Wulf Blankenfeldt
- Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, 38106 Braunschweig, Germany
| | - Florian P. Seebeck
- Department for Chemistry, University of Basel, BPR 1096, Mattenstrasse 24a, Basel, Switzerland
| |
Collapse
|
4
|
Krishna S, Shukla S, Lakra AD, Meeran SM, Siddiqi MI. Identification of potent inhibitors of DNA methyltransferase 1 (DNMT1) through a pharmacophore-based virtual screening approach. J Mol Graph Model 2017; 75:174-188. [PMID: 28582695 DOI: 10.1016/j.jmgm.2017.05.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 05/20/2017] [Accepted: 05/22/2017] [Indexed: 02/06/2023]
Abstract
DNA methylation is an epigenetic change that results in the addition of a methyl group at the carbon-5 position of cytosine residues. DNA methyltransferase (DNMT) inhibitors can suppress tumour growth and have significant therapeutic value. However, the established inhibitors are limited in their application due to their substantial cytotoxicity. Additionally, the standard drugs for DNMT inhibition are non-selective cytosine analogues with considerable cytotoxic side-effects. In the present study, we have designed a workflow by integrating various ligand-based and structure-based approaches to discover new agents active against DNMT1. We have derived a pharmacophore model with the help of available DNMT1 inhibitors. Utilising this model, we performed the virtual screening of Maybridge chemical library and the identified hits were then subsequently filtered based on the Naïve Bayesian classification model. The molecules that have returned from this classification model were subjected to ensemble based docking. We have selected 10 molecules for the biological assay by inspecting the interactions portrayed by these molecules. Three out of the ten tested compounds have shown DNMT1 inhibitory activity. These compounds were also found to demonstrate potential inhibition of cellular proliferation in human breast cancer MDA-MB-231 cells. In the present study, we have utilized a multi-step virtual screening protocol to identify inhibitors of DNMT1, which offers a starting point to develop more potent DNMT1 inhibitors as anti-cancer agents.
Collapse
Affiliation(s)
- Shagun Krishna
- Molecular & Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, 260031, India
| | - Samriddhi Shukla
- Endocrinology Division, CSIR-Central Drug Research Institute, Lucknow, 260031, India
| | - Amar Deep Lakra
- Endocrinology Division, CSIR-Central Drug Research Institute, Lucknow, 260031, India
| | - Syed Musthapa Meeran
- Endocrinology Division, CSIR-Central Drug Research Institute, Lucknow, 260031, India
| | - Mohammad Imran Siddiqi
- Molecular & Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, 260031, India.
| |
Collapse
|
5
|
Denny RA, Flick AC, Coe J, Langille J, Basak A, Liu S, Stock I, Sahasrabudhe P, Bonin P, Hay DA, Brennan PE, Pletcher M, Jones LH, Chekler ELP. Structure-Based Design of Highly Selective Inhibitors of the CREB Binding Protein Bromodomain. J Med Chem 2017; 60:5349-5363. [DOI: 10.1021/acs.jmedchem.6b01839] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- R. Aldrin Denny
- Medicine
Design, Pfizer, 610 Main Street, Cambridge Massachusetts 02139, United States
| | - Andrew C. Flick
- Medicine
Design, Pfizer, Eastern Point Road, Groton Connecticut 06340, United States
| | - Jotham Coe
- Medicine
Design, Pfizer, Eastern Point Road, Groton Connecticut 06340, United States
| | | | - Arindrajit Basak
- Medicine
Design, Pfizer, Eastern Point Road, Groton Connecticut 06340, United States
| | - Shenping Liu
- Structural
Biology and Biophysics, Medicine Design, Pfizer, Eastern Point
Road, Groton Connecticut 06340, United States
| | - Ingrid Stock
- Primary
Pharmacology Group, Pfizer, Eastern Point Road, Groton Connecticut 06340, United States
| | - Parag Sahasrabudhe
- Structural
Biology and Biophysics, Medicine Design, Pfizer, Eastern Point
Road, Groton Connecticut 06340, United States
| | - Paul Bonin
- Primary
Pharmacology Group, Pfizer, Eastern Point Road, Groton Connecticut 06340, United States
| | - Duncan A. Hay
- Evotec (UK) Ltd., 114 Innovation
Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, UK
- Structural
Genomics Consortium, Target Discovery Institute, ARUK Oxford Drug
Discovery Institute, University of Oxford, NDM Research Building, Roosevelt
Drive, Oxford OX3 7FZ, U.K
| | - Paul E. Brennan
- Structural
Genomics Consortium, Target Discovery Institute, ARUK Oxford Drug
Discovery Institute, University of Oxford, NDM Research Building, Roosevelt
Drive, Oxford OX3 7FZ, U.K
| | - Mathew Pletcher
- Rare
Disease Research Unit, Pfizer, 610 Main Street, Cambridge Massachusetts 02139, United States
| | - Lyn H. Jones
- Medicine
Design, Pfizer, 610 Main Street, Cambridge Massachusetts 02139, United States
| | | |
Collapse
|
6
|
Aranda J, Attana F, Tuñón I. Molecular Mechanism of Inhibition of DNA Methylation by Zebularine. ACS Catal 2017. [DOI: 10.1021/acscatal.6b03381] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Juan Aranda
- Departamento Química
Física, Universitat de València, 46100 Burjassot, Spain
| | - Fedaa Attana
- Departamento Química
Física, Universitat de València, 46100 Burjassot, Spain
| | - Iñaki Tuñón
- Departamento Química
Física, Universitat de València, 46100 Burjassot, Spain
| |
Collapse
|
7
|
A role for the bacterial GATC methylome in antibiotic stress survival. Nat Genet 2016; 48:581-6. [PMID: 26998690 PMCID: PMC4848143 DOI: 10.1038/ng.3530] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Accepted: 02/24/2016] [Indexed: 12/30/2022]
Abstract
Antibiotic resistance is an increasingly serious public health threat1. Understanding pathways allowing bacteria to survive antibiotic stress may unveil new therapeutic targets2–8. We explore the role of the bacterial epigenome in antibiotic stress survival using classical genetic tools and single-molecule real-time sequencing to characterize genomic methylation kinetics. We find that Escherichia coli survival under antibiotic pressure is severely compromised without adenine methylation at GATC sites. While the adenine methylome remains stable during drug stress, without GATC methylation, methyl-dependent mismatch repair (MMR) is deleterious, and fueled by the drug-induced error-prone polymerase PolIV, overwhelms cells with toxic DNA breaks. In multiple E. coli strains, including pathogenic and drug-resistant clinical isolates, DNA adenine methyltransferase deficiency potentiates antibiotics from the β-lactam and quinolone classes. This work indicates that the GATC methylome provides structural support for bacterial survival during antibiotics stress and suggests targeting bacterial DNA methylation as a viable approach to enhancing antibiotic activity.
Collapse
|
8
|
Abstract
S-Adenosyl-L-methionine (SAM) is a sulfonium molecule with a structural hybrid of methionine and adenosine. As the second largest cofactor in the human body, its major function is to serve as methyl donor for SAM-dependent methyltransferases (MTases). The resultant transmethylation of biomolecules constitutes a significant biochemical mechanism in epigenetic regulation, cellular signaling, and metabolite degradation. Recently, numerous SAM analogs have been developed as synthetic cofactors to transfer the activated groups on MTase substrates for downstream ligation and identification. Meanwhile, new compounds built upon or derived from the SAM scaffold have been designed and tested as selective inhibitors for important MTase targets. Here, we summarized the recent development and application of SAM analogs as chemical biology tools for MTases.
Collapse
Affiliation(s)
- Jing Zhang
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, The University of Georgia, Athens, Georgia 30602, United States
| | - Yujun George Zheng
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, The University of Georgia, Athens, Georgia 30602, United States
| |
Collapse
|
9
|
Abstract
The DNA of Escherichia coli contains 19,120 6-methyladenines and 12,045 5-methylcytosines in addition to the four regular bases, and these are formed by the postreplicative action of three DNA methyltransferases. The majority of the methylated bases are formed by the Dam and Dcm methyltransferases encoded by the dam (DNA adenine methyltransferase) and dcm (DNA cytosine methyltransferase) genes. Although not essential, Dam methylation is important for strand discrimination during the repair of replication errors, controlling the frequency of initiation of chromosome replication at oriC, and the regulation of transcription initiation at promoters containing GATC sequences. In contrast, there is no known function for Dcm methylation, although Dcm recognition sites constitute sequence motifs for Very Short Patch repair of T/G base mismatches. In certain bacteria (e.g., Vibrio cholerae, Caulobacter crescentus) adenine methylation is essential, and, in C. crescentus, it is important for temporal gene expression, which, in turn, is required for coordinating chromosome initiation, replication, and division. In practical terms, Dam and Dcm methylation can inhibit restriction enzyme cleavage, decrease transformation frequency in certain bacteria, and decrease the stability of short direct repeats and are necessary for site-directed mutagenesis and to probe eukaryotic structure and function.
Collapse
|
10
|
Leonard MT, Davis-Richardson AG, Ardissone AN, Kemppainen KM, Drew JC, Ilonen J, Knip M, Simell O, Toppari J, Veijola R, Hyöty H, Triplett EW. The methylome of the gut microbiome: disparate Dam methylation patterns in intestinal Bacteroides dorei. Front Microbiol 2014; 5:361. [PMID: 25101067 PMCID: PMC4101878 DOI: 10.3389/fmicb.2014.00361] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 06/26/2014] [Indexed: 12/02/2022] Open
Abstract
Despite the large interest in the human microbiome in recent years, there are no reports of bacterial DNA methylation in the microbiome. Here metagenomic sequencing using the Pacific Biosciences platform allowed for rapid identification of bacterial GATC methylation status of a bacterial species in human stool samples. For this work, two stool samples were chosen that were dominated by a single species, Bacteroides dorei. Based on 16S rRNA analysis, this species represented over 45% of the bacteria present in these two samples. The B. dorei genome sequence from these samples was determined and the GATC methylation sites mapped. The Bacteroides dorei genome from one subject lacked any GATC methylation and lacked the DNA adenine methyltransferase genes. In contrast, B. dorei from another subject contained 20,551 methylated GATC sites. Of the 4970 open reading frames identified in the GATC methylated B. dorei genome, 3184 genes were methylated as well as 1735 GATC methylations in intergenic regions. These results suggest that DNA methylation patterns are important to consider in multi-omic analyses of microbiome samples seeking to discover the diversity of bacterial functions and may differ between disease states.
Collapse
Affiliation(s)
- Michael T Leonard
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida Gainesville, FL, USA
| | - Austin G Davis-Richardson
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida Gainesville, FL, USA
| | - Alexandria N Ardissone
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida Gainesville, FL, USA
| | - Kaisa M Kemppainen
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida Gainesville, FL, USA
| | - Jennifer C Drew
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida Gainesville, FL, USA
| | - Jorma Ilonen
- Department of Clinical Microbiology, University of Eastern Finland Kuopio, Finland ; Immunogenetics Laboratory, University of Turku Turku, Finland
| | - Mikael Knip
- Children's Hospital, University of Helsinki and Helsinki University Central Hospital Helsinki, Finland ; Diabetes and Obesity Research Program, University of Helsinki Helsinki, Finland ; Department of Pediatrics, Tampere University Hospital Tampere, Finland
| | - Olli Simell
- Department of Pediatrics, Turku University Hospital, University of Turku Turku, Finland
| | - Jorma Toppari
- Department of Pediatrics, Turku University Hospital, University of Turku Turku, Finland
| | - Riitta Veijola
- Department of Pediatrics, Oulu University Hospital, University of Oulu Oulu, Finland
| | - Heikki Hyöty
- School of Medicine, University of Tampere Tampere, Finland
| | - Eric W Triplett
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida Gainesville, FL, USA
| |
Collapse
|
11
|
Emerging stem cell therapies: treatment, safety, and biology. Stem Cells Int 2012; 2012:521343. [PMID: 22919402 PMCID: PMC3419439 DOI: 10.1155/2012/521343] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Revised: 07/03/2012] [Accepted: 07/04/2012] [Indexed: 12/15/2022] Open
Abstract
Stem cells are the fundamental building blocks of life and contribute to the genesis and development of all higher organisms. The discovery of adult stem cells has led to an ongoing revolution of therapeutic and regenerative medicine and the proposal of novel therapies for previously terminal conditions. Hematopoietic stem cell transplantation was the first example of a successful stem cell therapy and is widely utilized for treating various diseases including adult T-cell leukemia-lymphoma and multiple myeloma. The autologous transplantation of mesenchymal stem cells is increasingly employed to catalyze the repair of mesenchymal tissue and others, including the lung and heart, and utilized in treating various conditions such as stroke, multiple sclerosis, and diabetes. There is also increasing interest in the therapeutic potential of other adult stem cells such as neural, mammary, intestinal, inner ear, and testicular stem cells. The discovery of induced pluripotent stem cells has led to an improved understanding of the underlying epigenetic keys of pluripotency and carcinogenesis. More in-depth studies of these epigenetic differences and the physiological changes that they effect will lead to the design of safer and more targeted therapies.
Collapse
|