1
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Kurpiejewski K, Piecyk K, Lukaszewicz M, Kamel K, Chmurski K, Kmiecik S, Jankowska-Anyszka M. The Synergistic Effect of N2 and N7 Modifications on the Inhibitory Efficacy of mRNA Cap Analogues. Pharmaceuticals (Basel) 2024; 17:632. [PMID: 38794202 PMCID: PMC11123931 DOI: 10.3390/ph17050632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 04/30/2024] [Accepted: 05/02/2024] [Indexed: 05/26/2024] Open
Abstract
In the fight against cancer, researchers have turned their attention to the eukaryotic initiation factor eIF4E, a protein whose increased level is strongly correlated with the development and progression of various types of cancer. Among the numerous strategies devised to tackle eIF4E overexpression, the use of 5' end mRNA cap analogues has emerged as a promising approach. Here, we present new candidates as potent m7GMP analogues for inhibiting translation and interfacing with eIF4E. By employing an appropriate strategy, we synthesized doubly modified mono- and dinucleotide cap analogues, introducing simultaneous substituents at both the N7 and N2 positions of the guanine ring. This approach was identified as an effective and promising combination. Our findings reveal that these dual modifications increase the potency of the dinucleotide analogue, marking a significant advancement in the development of cancer therapeutics targeting the eIF4E pathway.
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Affiliation(s)
- Karol Kurpiejewski
- Faculty of Chemistry, University of Warsaw, 02-093 Warsaw, Poland; (K.K.); (K.P.); (K.C.)
| | - Karolina Piecyk
- Faculty of Chemistry, University of Warsaw, 02-093 Warsaw, Poland; (K.K.); (K.P.); (K.C.)
| | - Maciej Lukaszewicz
- Division of Biophysics, Institute of Experimental Physics, University of Warsaw, 02-093 Warsaw, Poland;
| | - Karol Kamel
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland;
| | - Kazimierz Chmurski
- Faculty of Chemistry, University of Warsaw, 02-093 Warsaw, Poland; (K.K.); (K.P.); (K.C.)
| | - Sebastian Kmiecik
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, 02-089 Warsaw, Poland;
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2
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Samykannu G, Mariyappan N, Natarajan J. Molecular interaction and MD-simulations: investigation of Sizofiran as a promising anti-cancer agent targeting eIF4E in colorectal cancer. In Silico Pharmacol 2024; 12:33. [PMID: 38655099 PMCID: PMC11033251 DOI: 10.1007/s40203-024-00206-3] [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: 02/24/2024] [Accepted: 03/28/2024] [Indexed: 04/26/2024] Open
Abstract
CRC has a major global health impact due to high mortality rates. CRC shows high expression of eukaryotic translation initiation factor (eIF4E) protein, the rapid development of lung, bladder, colon, prostate, breast, head, and neck cancer is attributed to the dysregulation of eIF4E making an important target for treatment. Targeting eIF4E-mediated translation is a promising anti-cancer strategy. Many organic compounds that inhibit eIF4E are being studied clinically. The compound Sizofiran has emerged as a promising eIF4E inhibitor candidate, but its exact mechanism of action is unclear. In an effort to close this discrepancy by clarifying the mechanism of the interactions between phytochemical substances and eIF4E, molecular docking and dynamics studies were conducted. Molecular docking studies found Sizofiran (- 12.513 kcal/mol) has the most affinity eIF4E binding energy out of 93 phytochemicals, 5 current drugs, and 4 known inhibitors. This positions it as a top eIF4E inhibitor candidate. An alignment of eIF4E protein sequences from multiple pathogens revealed that the glutamate103 interacting residues are evolutionarily conserved across the different eIF4E proteins. Further insights from 100 ns of MD simulations supported Sizofiran having superior stability and eIF4E inhibition compared to reference compounds. Designed Sizofiran-related compounds showed better activity than the current drugs such as Camptosar, Sorafenib, Regorafenib, Doxorubicin, and Kenpaullone, indicating strong potential to suppress CRC progression by targeting eIF4E. This research aims to significantly aid development of improved eIF4E-targeting drugs for cancer treatment. Graphical abstract Showing the Graphical abstract of the complete study. Supplementary Information The online version contains supplementary material available at 10.1007/s40203-024-00206-3.
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Affiliation(s)
- Gopinath Samykannu
- Data Mining and Text Mining Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore, TamilNadu India
| | - Nandhini Mariyappan
- Molecular Modelling and Designing Laboratory, Department of Physics, Bharathiar University, Coimbatore, TamilNadu India
| | - Jeyakumar Natarajan
- Data Mining and Text Mining Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore, TamilNadu India
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3
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Ratto A, Honek JF. Oxocarbon Acids and their Derivatives in Biological and Medicinal Chemistry. Curr Med Chem 2024; 31:1172-1213. [PMID: 36915986 DOI: 10.2174/0929867330666230313141452] [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: 09/29/2022] [Revised: 01/10/2023] [Accepted: 01/12/2023] [Indexed: 03/15/2023]
Abstract
The biological and medicinal chemistry of the oxocarbon acids 2,3- dihydroxycycloprop-2-en-1-one (deltic acid), 3,4-dihydroxycyclobut-3-ene-1,2-dione (squaric acid), 4,5-dihydroxy-4-cyclopentene-1,2,3-trione (croconic acid), 5,6-dihydroxycyclohex- 5-ene-1,2,3,4-tetrone (rhodizonic acid) and their derivatives is reviewed and their key chemical properties and reactions are discussed. Applications of these compounds as potential bioisosteres in biological and medicinal chemistry are examined. Reviewed areas include cell imaging, bioconjugation reactions, antiviral, antibacterial, anticancer, enzyme inhibition, and receptor pharmacology.
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Affiliation(s)
- Amanda Ratto
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
| | - John F Honek
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
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4
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Gao X, Jin Y, Zhu W, Wu X, Wang J, Guo C. Regulation of Eukaryotic Translation Initiation Factor 4E as a Potential Anticancer Strategy. J Med Chem 2023; 66:12678-12696. [PMID: 37725577 DOI: 10.1021/acs.jmedchem.3c00636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2023]
Abstract
Eukaryotic translation initiation factors (eIFs) are highly expressed in cancer cells, especially eIF4E, the central regulatory node driving cancer cell growth and a potential target for anticancer drugs. eIF4E-targeting strategies primarily focus on inhibiting eIF4E synthesis, interfering with eIF4E/eIF4G interactions, and targeting eIF4E phosphorylation and peptide inhibitors. Although some small-molecule inhibitors are in clinical trials, no eIF4E inhibitors are available for clinical use. We provide an overview of the regulatory mechanisms of eIF4E and summarize the progress in developing and discovering eIF4E inhibitor strategies. We propose that interference with eIF4E/eIF4G interactions will provide a new perspective for the design of eIF4E inhibitors and may be a preferred strategy.
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Affiliation(s)
- Xintao Gao
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Yonglong Jin
- The Affiliated Hospital of Qingdao University, Qingdao 266000, China
| | - Wenyong Zhu
- Department of Thoracic Surgery, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao, 266035, China
| | - Xiaochen Wu
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Jing Wang
- Department of Biology Science and Technology, Baotou Teacher's College, Baotou 014030, China
| | - Chuanlong Guo
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
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5
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Tang J, Ouyang H, Chen X, Jiang D, Tian Y, Huang Y, Shen X. Comparative Transcriptome Analyses of Leg Muscle during Early Growth between Geese ( Anser cygnoides) Breeds Differing in Body Size Characteristics. Genes (Basel) 2023; 14:genes14051048. [PMID: 37239409 DOI: 10.3390/genes14051048] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/02/2023] [Accepted: 05/04/2023] [Indexed: 05/28/2023] Open
Abstract
Goose is an important poultry commonly raised for meat. The early growth performance of geese significantly influences their market weight and slaughter weight, affecting the poultry industry's economic benefits. To identify the growth surge between the Shitou goose and the Wuzong goose, we collected the early growth body traits from 0 to 12 weeks. In addition, we investigated the transcriptomic changes in leg muscles at the high growth speed period to reveal the difference between the two geese breeds. We also estimated the growth curve parameters under three models, including the logistic, von Bertalanffy, and Gompertz models. The results showed that except for body length and keel length, the best-fitting model between the body weight and body size of the Shitou and Wuzong was the logistic model. The growth turning points of Shitou and Wuzong were 5.954 and 4.944 weeks, respectively, and the turning point of their body weight was 1459.01 g and 478.54 g, respectively. Growth surge occurred at 2-9 weeks in Shitou goose and at 1-7 weeks in Wuzong goose. The body size traits of the Shitou goose and Wuzong goose showed a trend of rapid growth in the early stage and slow growth in the later stage, and the Shitou goose growth was higher than the Wuzong goose. For transcriptome sequencing, a total of 87 differentially expressed genes (DEGs) were identified with a fold change ≥ 2 and a false discovery rate < 0.05. Many DEGs have a potential function for growth, such as CXCL12, SSTR4, FABP5, SLC2A1, MYLK4, and EIF4E3. KEGG pathway analysis identified that some DEGs were significantly enriched in the calcium signaling pathway, which may promote muscle growth. The gene-gene interaction network of DEGs was mainly related to the transmission of cell signals and substances, hematological system development, and functions. This study can provide theoretical guidance for the production and breeding management of the Shitou goose and Wuzong goose and help reveal the genetic mechanisms underlying diverse body sizes between two goose breeds.
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Affiliation(s)
- Jun Tang
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Waterfowl Healthy Breeding Engineering Research Center, Guangdong Higher Education Institutes, Guangzhou 510225, China
| | - Hongjia Ouyang
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Waterfowl Healthy Breeding Engineering Research Center, Guangdong Higher Education Institutes, Guangzhou 510225, China
| | - Xiaomei Chen
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Danli Jiang
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Waterfowl Healthy Breeding Engineering Research Center, Guangdong Higher Education Institutes, Guangzhou 510225, China
| | - Yunbo Tian
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Waterfowl Healthy Breeding Engineering Research Center, Guangdong Higher Education Institutes, Guangzhou 510225, China
| | - Yunmao Huang
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Waterfowl Healthy Breeding Engineering Research Center, Guangdong Higher Education Institutes, Guangzhou 510225, China
| | - Xu Shen
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Waterfowl Healthy Breeding Engineering Research Center, Guangdong Higher Education Institutes, Guangzhou 510225, China
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6
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Kumawat A, Namsani S, Pramanik D, Roy S, Singh JK. Integrated docking and enhanced sampling-based selection of repurposing drugs for SARS-CoV-2 by targeting host dependent factors. J Biomol Struct Dyn 2022; 40:9897-9908. [PMID: 34155961 PMCID: PMC8220434 DOI: 10.1080/07391102.2021.1937319] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Since the onset of global pandemic, the most focused research currently in progress is the development of potential drug candidates and clinical trials of existing FDA approved drugs for other relevant diseases, in order to repurpose them for the COVID-19. At the same time, several high throughput screenings of drugs have been reported to inhibit the viral components during the early course of infection but with little proven efficacies. Here, we investigate the drug repurposing strategies to counteract the coronavirus infection which involves several potential targetable host proteins involved in viral replication and disease progression. We report the high throughput analysis of literature-derived repurposing drug candidates that can be used to target the genetic regulators known to interact with viral proteins based on experimental and interactome studies. In this work we have performed integrated molecular docking followed by molecular dynamics (MD) simulations and free energy calculations through an expedite in silico process where the number of screened candidates reduces sequentially at every step based on physicochemical interactions. We elucidate that in addition to the pre-clinical and FDA approved drugs that targets specific regulatory proteins, a range of chemical compounds (Nafamostat, Chloramphenicol, Ponatinib) binds to the other gene transcription and translation regulatory proteins with higher affinity and may harbour potential for therapeutic uses. There is a rapid growing interest in the development of combination therapy for COVID-19 to target multiple enzymes/pathways. Our in silico approach would be useful in generating leads for experimental screening for rapid drug repurposing against SARS-CoV-2 interacting host proteins.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Amit Kumawat
- Prescience Insilico Private Limited, Bangalore, India,Department of Chemical Engineering, Indian Institute of Technology, Kanpur, India
| | | | - Debabrata Pramanik
- Department of Chemical Engineering, Indian Institute of Technology, Kanpur, India
| | - Sudip Roy
- Prescience Insilico Private Limited, Bangalore, India,CONTACT Sudip Roy ;
| | - Jayant K. Singh
- Prescience Insilico Private Limited, Bangalore, India,Department of Chemical Engineering, Indian Institute of Technology, Kanpur, India,Jayant K. Singh
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7
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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.
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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
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8
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Frosi Y, Ng S, Lin YC, Jiang S, Ramlan SR, Lama D, Verma CS, Asial I, Brown CJ. Development of a Novel Peptide Aptamer that Interacts with the eIF4E Capped-mRNA Binding Site using Peptide Epitope Linker Evolution (PELE). RSC Chem Biol 2022; 3:916-930. [PMID: 35866173 PMCID: PMC9257606 DOI: 10.1039/d2cb00099g] [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: 04/13/2022] [Accepted: 05/13/2022] [Indexed: 11/21/2022] Open
Abstract
Identifying new binding sites and poses that modify biological function are an important step towards drug discovery. We have identified a novel disulphide constrained peptide that interacts with the cap-binding site of eIF4E, an attractive therapeutic target that is commonly overexpressed in many cancers and plays a significant role in initiating a cancer specific protein synthesis program though binding the 5′cap (7′methyl-guanoisine) moiety found on mammalian mRNAs. The use of disulphide constrained peptides to explore intracellular biological targets is limited by their lack of cell permeability and the instability of the disulphide bond in the reducing environment of the cell, loss of which results in abrogation of binding. To overcome these challenges, the cap-binding site interaction motif was placed in a hypervariable loop on an VH domain, and then selections performed to select a molecule that could recapitulate the interaction of the peptide with the target of interest in a process termed Peptide Epitope Linker Evolution (PELE). A novel VH domain was identified that interacted with the eIF4E cap binding site with a nanomolar affinity and that could be intracellularly expressed in mammalian cells. Additionally, it was demonstrated to specifically modulate eIF4E function by decreasing cap-dependent translation and cyclin D1 expression, common effects of eIF4F complex disruption. Identifying new binding sites and poses that modify biological function are an important step towards drug discovery.![]()
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Affiliation(s)
- Yuri Frosi
- Disease Intervention Technology Lab (DITL), IMCB (ASTAR) 8A Biomedical Grove, #06-04/05, Neuros/Immunos 138648 Singapore
| | - Simon Ng
- Disease Intervention Technology Lab (DITL), IMCB (ASTAR) 8A Biomedical Grove, #06-04/05, Neuros/Immunos 138648 Singapore
| | - Yen-Chu Lin
- Insilico Medicine Taiwan Ltd. Suite 2013, No. 333, Sec.1, Keelung Rd., Xinyi Dist. 110 Taipei Taiwan
| | - Shimin Jiang
- Disease Intervention Technology Lab (DITL), IMCB (ASTAR) 8A Biomedical Grove, #06-04/05, Neuros/Immunos 138648 Singapore
| | - Siti Radhiah Ramlan
- Disease Intervention Technology Lab (DITL), IMCB (ASTAR) 8A Biomedical Grove, #06-04/05, Neuros/Immunos 138648 Singapore
| | - Dilraj Lama
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet Biomedicum Quarter 7B-C Solnavägen 9 17165 Solna Sweden
| | - Chandra S Verma
- Bioinformatics Institute (ASTAR) 30 Biopolis Street, #07-01 Matrix 138671 Singapore
| | - Ignacio Asial
- DotBio, 1 Research Link 117604 Singapore
- Nanyang Technological University, School of Biological Sciences Singapore
| | - Christopher J Brown
- Disease Intervention Technology Lab (DITL), IMCB (ASTAR) 8A Biomedical Grove, #06-04/05, Neuros/Immunos 138648 Singapore
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9
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Reichert D, Schepers H, Simke J, Lechner H, Dörner W, Höcker B, Ravoo BJ, Rentmeister A. Computational design and experimental characterization of a photo-controlled mRNA-cap guanine-N7 methyltransferase. RSC Chem Biol 2021; 2:1484-1490. [PMID: 34704053 PMCID: PMC8495969 DOI: 10.1039/d1cb00109d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 06/25/2021] [Indexed: 11/21/2022] Open
Abstract
The spatial and temporal control of gene expression at the post-transcriptional level is essential in eukaryotic cells and developing multicellular organisms. In recent years optochemical and optogenetic tools have enabled the manipulation and investigation of many steps in the involved processes. However, examples for light-mediated control of eukaryotic mRNA processing and the responsible enzymes are still rare. In particular, methylation of the 5′ cap of mRNA is required for ribosome assembly, and the responsible guanine-N7 methyltransferase (MTase) from E. cuniculi (Ecm1) proved suitable for activating translation. Here, we report on a photoswitchable MTase obtained by bridging the substrate-binding cleft of Ecm1 with a tetra-ortho-methoxy-azobenzene. This azobenzene derivative is characterized by efficient trans-to-cis isomerization using red light at 615 nm. Starting from a cysteine-free Ecm1 variant (ΔCys), we used a computational approach to identify suitable conjugation sites for the azobenzene moiety. We created and characterized the four best-ranked variants, each featuring two appropriately positioned cysteines close to the substrate-binding cleft. Conjugating and crosslinking the azobenzene between C149/C155 in a designed Ecm1 variant (VAR3-Az) enabled light-dependent modulation of the MTase activity and showed a 50% higher activity for the cis form than the trans-form of the azobenzene conjugated to VAR3-Az. Guided by computational design, we engineered a light-dependent 5' cap guanine-N7 methyltransferase by bridging the substrate-binding cleft with an azobenzene derivative.![]()
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Affiliation(s)
- Dennis Reichert
- Institute of Biochemistry, University of Münster, Correnstraße 36 Münster 48149 Germany .,Cells in Motion Interfaculty Center, University of Münster Münster 48149 Germany
| | - Helena Schepers
- Institute of Biochemistry, University of Münster, Correnstraße 36 Münster 48149 Germany
| | - Julian Simke
- Organic Chemistry Institute, University of Münster, Corrensstraße 36 Münster 48149 Germany
| | - Horst Lechner
- Department for Biochemistry, University of Bayreuth, Universitätsstraße 30 Bayreuth 95447 Germany.,Institute of Biochemistry, Graz University of Technology, Petersgasse 10-12/II Graz 8010 Austria
| | - Wolfgang Dörner
- Institute of Biochemistry, University of Münster, Correnstraße 36 Münster 48149 Germany
| | - Birte Höcker
- Department for Biochemistry, University of Bayreuth, Universitätsstraße 30 Bayreuth 95447 Germany
| | - Bart Jan Ravoo
- Cells in Motion Interfaculty Center, University of Münster Münster 48149 Germany.,Organic Chemistry Institute, University of Münster, Corrensstraße 36 Münster 48149 Germany
| | - Andrea Rentmeister
- Institute of Biochemistry, University of Münster, Correnstraße 36 Münster 48149 Germany .,Cells in Motion Interfaculty Center, University of Münster Münster 48149 Germany
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10
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Berdasco M, Esteller M. Towards a druggable epitranscriptome: Compounds that target RNA modifications in cancer. Br J Pharmacol 2021; 179:2868-2889. [PMID: 34185879 DOI: 10.1111/bph.15604] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 05/27/2021] [Accepted: 06/10/2021] [Indexed: 10/21/2022] Open
Abstract
Epitranscriptomics is an exciting emerging area that studies biochemical modifications of RNA. The field has been opened up by the technical efforts of the last decade to characterize and quantify RNA modifications, and this has led to a map of post-transcriptional RNA marks in normal cell fate and development. However, the scientific interest has been fuelled by the discovery of aberrant epitranscriptomes associated with human diseases, mainly cancer. The challenge is now to see whether epitrancriptomics offers mechanisms that can be effectively targeted by low MW compounds and are thus druggable. In this review, we will describe the principal RNA modifications (with a focus on mRNA), summarize the latest scientific evidence of their dysregulation in cancer and provide an overview of the state-of-the-art drug discovery to target the epitranscriptome. Finally, we will discuss the principal challenges in the field of chemical biology and drug development to increase the potential of targeted-RNA for clinical benefit.
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Affiliation(s)
- María Berdasco
- Epigenetic Therapies Group, Experimental and Clinical Hematology Program (PHEC), Josep Carreras Leukaemia Research Institute, Barcelona, Spain.,Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - Manel Esteller
- Cancer Epigenetics Group, Cancer and Leukemia Epigenetics and Biology Program (PEBCL), Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Spain.,Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain.,Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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11
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Wood S, Willbanks A, Cheng JX. The Role of RNA Modifications and RNA-modifying Proteins in Cancer Therapy and Drug Resistance. Curr Cancer Drug Targets 2021; 21:326-352. [PMID: 33504307 DOI: 10.2174/1568009621666210127092828] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 12/03/2020] [Accepted: 12/03/2020] [Indexed: 11/22/2022]
Abstract
The advent of new genome-wide sequencing technologies has uncovered abnormal RNA modifications and RNA editing in a variety of human cancers. The discovery of reversible RNA N6-methyladenosine (RNA: m6A) by fat mass and obesity-associated protein (FTO) demethylase has led to exponential publications on the pathophysiological functions of m6A and its corresponding RNA modifying proteins (RMPs) in the past decade. Some excellent reviews have summarized the recent progress in this field. Compared to the extent of research into RNA: m6A and DNA 5-methylcytosine (DNA: m5C), much less is known about other RNA modifications and their associated RMPs, such as the role of RNA: m5C and its RNA cytosine methyltransferases (RCMTs) in cancer therapy and drug resistance. In this review, we will summarize the recent progress surrounding the function, intramolecular distribution and subcellular localization of several major RNA modifications, including 5' cap N7-methylguanosine (m7G) and 2'-O-methylation (Nm), m6A, m5C, A-to-I editing, and the associated RMPs. We will then discuss dysregulation of those RNA modifications and RMPs in cancer and their role in cancer therapy and drug resistance.
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Affiliation(s)
- Shaun Wood
- Department of Pathology, Hematopathology Section, University of Chicago, Chicago, IL60637, United States
| | - Amber Willbanks
- Department of Pathology, Hematopathology Section, University of Chicago, Chicago, IL60637, United States
| | - Jason X Cheng
- Department of Pathology, Hematopathology Section, University of Chicago, Chicago, IL60637, United States
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12
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Reichert D, Mootz HD, Rentmeister A. Light-control of cap methylation and mRNA translation via genetic code expansion of Ecm1. Chem Sci 2021; 12:4383-4388. [PMID: 34163701 PMCID: PMC8179545 DOI: 10.1039/d1sc00159k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 02/04/2021] [Indexed: 12/24/2022] Open
Abstract
Gene expression is tightly regulated in all domains of life, with post-transcriptional regulation being more pronounced in higher eukaryotes. Optochemical and optogenetic approaches enable the actuation of many underlying processes by light, which is an excellent tool to exert spatio-temporal control. However, light-mediated control of eukaryotic mRNA processing and the respective enzymes has not been reported. We used genetic code expansion to install a photo-caged tyrosine (Y) in the active site of the cap methyltransferase Ecm1. This enzyme is responsible for guanine N7 methylation of the 5' cap, which is required for translation. Substituting Y284 with the photocaged ortho-nitrobenzyl-tyrosine (ONBY) almost completely abrogated the methylation activity of Ecm1. Irradiation with light removed the ONB group, restoring the native tyrosine and Ecm1 activity, yielding up to 97% conversion of the minimal substrate GpppA within 60 min after activation. Using luciferase- and eGFP-mRNAs as reporters, we could show that light actuates translation by inducing activation of Ecm1 ONBY284 in a eukaryotic in vitro translation system.
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Affiliation(s)
- Dennis Reichert
- Department of Chemistry, Institute of Biochemistry, University of Münster Correnstr. 36 48149 Münster Germany
- Cells in Motion Interfaculty Center, University of Münster 48149 Münster Germany
| | - Henning D Mootz
- Department of Chemistry, Institute of Biochemistry, University of Münster Correnstr. 36 48149 Münster Germany
| | - Andrea Rentmeister
- Department of Chemistry, Institute of Biochemistry, University of Münster Correnstr. 36 48149 Münster Germany
- Cells in Motion Interfaculty Center, University of Münster 48149 Münster Germany
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13
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Moya-Ramírez I, Bouton C, Kontoravdi C, Polizzi K. High resolution biosensor to test the capping level and integrity of mRNAs. Nucleic Acids Res 2021; 48:e129. [PMID: 33152073 PMCID: PMC7736790 DOI: 10.1093/nar/gkaa955] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 09/22/2020] [Accepted: 10/08/2020] [Indexed: 11/21/2022] Open
Abstract
5′ Cap structures are ubiquitous on eukaryotic mRNAs, essential for post-transcriptional processing, translation initiation and stability. Here we describe a biosensor designed to detect the presence of cap structures on mRNAs that is also sensitive to mRNA degradation, so uncapped or degraded mRNAs can be detected in a single step. The biosensor is based on a chimeric protein that combines the recognition and transduction roles in a single molecule. The main feature of this sensor is its simplicity, enabling semi-quantitative analyses of capping levels with minimal instrumentation. The biosensor was demonstrated to detect the capping level on several in vitro transcribed mRNAs. Its sensitivity and dynamic range remained constant with RNAs ranging in size from 250 nt to approximately 2700 nt and the biosensor was able to detect variations in the capping level in increments of at least 20%, with a limit of detection of 2.4 pmol. Remarkably, it also can be applied to more complex analytes, such mRNA vaccines and mRNAs transcribed in vivo. This biosensor is an innovative example of a technology able to detect analytically challenging structures such as mRNA caps. It could find application in a variety of scenarios, from quality analysis of mRNA-based products such as vaccines to optimization of in vitro capping reactions.
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Affiliation(s)
- Ignacio Moya-Ramírez
- Department of Chemical Engineering, Imperial College London, London SW7 2AZ, UK.,Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
| | - Clement Bouton
- Department of Infectious Disease, Imperial College London, London W2 1NY, UK
| | - Cleo Kontoravdi
- Department of Chemical Engineering, Imperial College London, London SW7 2AZ, UK
| | - Karen Polizzi
- Department of Chemical Engineering, Imperial College London, London SW7 2AZ, UK.,Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
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14
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Chasák J, Šlachtová V, Urban M, Brulíková L. Squaric acid analogues in medicinal chemistry. Eur J Med Chem 2020; 209:112872. [PMID: 33035923 DOI: 10.1016/j.ejmech.2020.112872] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/12/2020] [Accepted: 09/21/2020] [Indexed: 12/16/2022]
Abstract
In this review, we summarize the published data on squaric acid analogues with a special focus on their use in medicinal chemistry and as potential drugs. Squaric acid is an interesting small molecule with an almost perfectly square shape, and its analogues have a variety of biological activities that are enabled by the presence of significant H-bond donors and acceptors. Unfortunately, most of these compounds also exhibit reactive functionalities, and this deters the majority of medicinal chemists and pharmacologists from trying to use them in drug development. However, this group of compounds is experiencing a renaissance, and large numbers of them are being tested for antiprotozoal, antibacterial, antifungal, and antiviral activities. The most useful of these compounds exhibited IC50 values in the nanomolar range, which makes them promising drug candidates. In addition to these activities, their interactions with living systems were intensively explored, revealing that squaric acid analogues inhibit various enzymes and often serve as receptor antagonists and that the squaric acid moiety may be used as a non-classical isosteric replacement for other functional groups such as carboxylate. In summary, this review is focused on squaric acid and its analogues and their use in medicinal chemistry and should serve as a guide for other researchers in the field to demonstrate the potential of these compounds based on previous research.
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Affiliation(s)
- Jan Chasák
- Department of Organic Chemistry, Faculty of Science, Palacky University Olomouc, 17. listopadu 12, 771 46, Olomouc, Czech Republic
| | - Veronika Šlachtová
- Department of Organic Chemistry, Faculty of Science, Palacky University Olomouc, 17. listopadu 12, 771 46, Olomouc, Czech Republic
| | - Milan Urban
- Medicinal Chemistry, Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University in Olomouc, Hněvotínská 5, 779 00, Olomouc, Czech Republic
| | - Lucie Brulíková
- Department of Organic Chemistry, Faculty of Science, Palacky University Olomouc, 17. listopadu 12, 771 46, Olomouc, Czech Republic.
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15
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Agnew-Francis KA, Williams CM. Squaramides as Bioisosteres in Contemporary Drug Design. Chem Rev 2020; 120:11616-11650. [DOI: 10.1021/acs.chemrev.0c00416] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Kylie A. Agnew-Francis
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Craig M. Williams
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
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16
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Ivancová I, Pohl R, Hubálek M, Hocek M. Squaramate-Modified Nucleotides and DNA for Specific Cross-Linking with Lysine-Containing Peptides and Proteins. Angew Chem Int Ed Engl 2019; 58:13345-13348. [PMID: 31328344 PMCID: PMC6771961 DOI: 10.1002/anie.201906737] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 07/12/2019] [Indexed: 01/31/2023]
Abstract
Squaramate-linked 2'-deoxycytidine 5'-O-triphosphate was synthesized and found to be good substrate for KOD XL DNA polymerase in primer extension or PCR synthesis of modified DNA. The resulting squaramate-linked DNA reacts with primary amines to form a stable diamide linkage. This reaction was used for bioconjugations of DNA with Cy5 and Lys-containing peptides. Squaramate-linked DNA formed covalent cross-links with histone proteins. This reactive nucleotide has potential for other bioconjugations of nucleic acids with amines, peptides or proteins without need of any external reagent.
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Affiliation(s)
- Ivana Ivancová
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesFlemingovo nam. 216610Prague 6Czech Republic
- Department of Organic ChemistryFaculty of ScienceCharles University in PragueHlavova 8CZ-12843Prague 2Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesFlemingovo nam. 216610Prague 6Czech Republic
| | - Martin Hubálek
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesFlemingovo nam. 216610Prague 6Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesFlemingovo nam. 216610Prague 6Czech Republic
- Department of Organic ChemistryFaculty of ScienceCharles University in PragueHlavova 8CZ-12843Prague 2Czech Republic
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17
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Ivancová I, Pohl R, Hubálek M, Hocek M. Squaramate‐Modified Nucleotides and DNA for Specific Cross‐Linking with Lysine‐Containing Peptides and Proteins. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201906737] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Ivana Ivancová
- Institute of Organic Chemistry and BiochemistryCzech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
- Department of Organic ChemistryFaculty of ScienceCharles University in Prague Hlavova 8 CZ-12843 Prague 2 Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and BiochemistryCzech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Martin Hubálek
- Institute of Organic Chemistry and BiochemistryCzech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and BiochemistryCzech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
- Department of Organic ChemistryFaculty of ScienceCharles University in Prague Hlavova 8 CZ-12843 Prague 2 Czech Republic
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18
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Santos Pereira-Dutra F, Cancela M, Valandro Meneghetti B, Bunselmeyer Ferreira H, Mariante Monteiro K, Zaha A. Functional characterization of the translation initiation factor eIF4E of Echinococcus granulosus. Parasitol Res 2019; 118:2843-2855. [PMID: 31401657 DOI: 10.1007/s00436-019-06421-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 08/02/2019] [Indexed: 01/24/2023]
Abstract
The eukaryotic initiation factor 4E (eIF4E) specifically recognizes the 5' mRNA cap, a rate-limiting step in the translation initiation process. Although the 7-methylguanosine cap (MMGcap) is the most common 5' cap structure in eukaryotes, the trans-splicing process that occurs in several organism groups, including nematodes and flatworms, leads to the addition of a trimethylguanosine cap (TMGcap) to some RNA transcripts. In some helminths, eIF4E can have a dual capacity to bind both MMGcap and TMGcap. In the present work, we evaluated the distribution of eIF4E protein sequences in platyhelminths and we showed that only one gene coding for eIF4E is present in most parasitic flatworms. Based on this result, we cloned the Echinococcus granulosus cDNA sequence encoding eIF4E in Escherichia coli, expressed the recombinant eIF4E as a fusion protein to GST, and tested its ability to capture mRNAs through the 5' cap using pull-down assay and qPCR. Our results indicate that the recombinant eIF4E was able to bind preferentially 5'-capped mRNAs compared with rRNAs from total RNA preparations of E. granulosus. By qPCR, we observed an enrichment in MMG-capped mRNA compared with TMG-capped mRNAs among Eg-eIF4E-GST pull-down RNAs. Eg-eIF4E structural model using the Schistosoma mansoni eIF4E as template showed to be well preserved with only a few differences between chemically similar amino acid residues at the binding sites. These data showed that E. granulosus eIF4E can be used as a potential tool to study full-length 5'-capped mRNA, besides being a potential drug target against parasitic flatworms.
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Affiliation(s)
- Filipe Santos Pereira-Dutra
- Laboratório de Biologia Molecular de Cestodeos, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, UFRGS, Avenida Bento Gonçalves, 9500, Caixa Postal 15053, Porto Alegre, RS, CEP 91501-970, Brazil.,Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, UFRGS, Porto Alegre, Brazil
| | - Martin Cancela
- Laboratório de Biologia Molecular de Cestodeos, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, UFRGS, Avenida Bento Gonçalves, 9500, Caixa Postal 15053, Porto Alegre, RS, CEP 91501-970, Brazil.,Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, UFRGS, Porto Alegre, Brazil
| | - Bruna Valandro Meneghetti
- Laboratório de Biologia Molecular de Cestodeos, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, UFRGS, Avenida Bento Gonçalves, 9500, Caixa Postal 15053, Porto Alegre, RS, CEP 91501-970, Brazil.,Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, UFRGS, Porto Alegre, Brazil
| | - Henrique Bunselmeyer Ferreira
- Laboratório de Biologia Molecular de Cestodeos, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, UFRGS, Avenida Bento Gonçalves, 9500, Caixa Postal 15053, Porto Alegre, RS, CEP 91501-970, Brazil.,Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, UFRGS, Porto Alegre, Brazil.,Departamento de Biologia Molecular e Biotecnologia, Instituto de Biociências, UFRGS, Porto Alegre, Brazil
| | - Karina Mariante Monteiro
- Laboratório de Biologia Molecular de Cestodeos, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, UFRGS, Avenida Bento Gonçalves, 9500, Caixa Postal 15053, Porto Alegre, RS, CEP 91501-970, Brazil.,Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, UFRGS, Porto Alegre, Brazil.,Departamento de Biologia Molecular e Biotecnologia, Instituto de Biociências, UFRGS, Porto Alegre, Brazil
| | - Arnaldo Zaha
- Laboratório de Biologia Molecular de Cestodeos, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, UFRGS, Avenida Bento Gonçalves, 9500, Caixa Postal 15053, Porto Alegre, RS, CEP 91501-970, Brazil. .,Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, UFRGS, Porto Alegre, Brazil. .,Departamento de Biologia Molecular e Biotecnologia, Instituto de Biociências, UFRGS, Porto Alegre, Brazil.
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19
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Frosi Y, Usher R, Lian DTG, Lane DP, Brown CJ. Monitoring flux in signalling pathways through measurements of 4EBP1-mediated eIF4F complex assembly. BMC Biol 2019; 17:40. [PMID: 31118010 PMCID: PMC6530213 DOI: 10.1186/s12915-019-0658-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 04/29/2019] [Indexed: 01/10/2023] Open
Abstract
Background The most commonly occurring cancer mutations, including oncogenes such as MYC, Ras and PIK3C, are found in signal transductions pathways feeding into the translational machinery. A broad range of translation initiation factors are also commonly found to be either amplified or mis-regulated in tumours, including eIF4E (elongation initiation factor 4E). eIF4E is a subunit of the eIF4F protein initiation complex and required for its recruitment. Here we measure the formation of the eIF4F complex through interactions of eIF4E and eIF4G subunits, and the effect of oncogenic signalling pathways on complex formation. Results We developed a protein fragment complementation (PCA) assay that can accurately measure the status of the eIF4E-eIF4G interaction in cells and quantify the signalling flux through the RAS/ERK and PI3K/AKT pathways regulating eIF4F assembly. Complex disruption induced by inhibition of either pathway was shown to be a function of the phosphorylation status of 4EBP1, a key mediator of eIF4F assembly that interacts directly with eIF4E, confirming 4EBP1’s ability to integrate multiple signals affecting cap-dependent translation. Maximal measured disruption of the eIF4F complex occurred under combined mTORC1 and mTORC2 inhibition, whilst combined inhibition of both RAS/ERK and PI3K/AKT pathways in parallel resulted in greater inhibition of eIF4F formation than individually. v-Myc-mediated resistance to dual mTORC/PI3K inhibition was also principally demonstrated to depend on the lack of competent 4EBP1 available in the cell to bind eIF4E. Conclusions We show that 4EBP1 is a critical regulator of the mitogen responsive RAS/ERK and PI3K/AKT pathways and a key transducer of resistance mechanisms that affect small molecule inhibition of these pathways, principally by attenuating their effects on cap-dependent translation. These findings highlight the importance of highly efficacious direct inhibitors of eIF4E and eIF4F assembly, which could potentially target a wide spectrum of tumours containing differing mutations that effect these pathways and which confer chemo-resistance. Electronic supplementary material The online version of this article (10.1186/s12915-019-0658-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yuri Frosi
- p53 Laboratory, A*STAR (Agency for Science, Technology and Research), 8A Biomedical Grove, #06-04/05, Neuros/Immunos, Singapore, 138648, Singapore
| | - Rachael Usher
- p53 Laboratory, A*STAR (Agency for Science, Technology and Research), 8A Biomedical Grove, #06-04/05, Neuros/Immunos, Singapore, 138648, Singapore
| | - Dawn Thean Gek Lian
- p53 Laboratory, A*STAR (Agency for Science, Technology and Research), 8A Biomedical Grove, #06-04/05, Neuros/Immunos, Singapore, 138648, Singapore
| | - David P Lane
- p53 Laboratory, A*STAR (Agency for Science, Technology and Research), 8A Biomedical Grove, #06-04/05, Neuros/Immunos, Singapore, 138648, Singapore
| | - Christopher J Brown
- p53 Laboratory, A*STAR (Agency for Science, Technology and Research), 8A Biomedical Grove, #06-04/05, Neuros/Immunos, Singapore, 138648, Singapore.
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20
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Kaur T, Menon A, Garner AL. Synthesis of 7-benzylguanosine cap-analogue conjugates for eIF4E targeted degradation. Eur J Med Chem 2019; 166:339-350. [PMID: 30735900 DOI: 10.1016/j.ejmech.2019.01.080] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 01/29/2019] [Accepted: 01/29/2019] [Indexed: 10/27/2022]
Abstract
Eukaryotic translation initiation factor 4E (eIF4E) is a key player in the initiation of cap-dependent translation through recognition of the m7GpppX cap at the 5' terminus of coding mRNAs. As eIF4E overexpression has been observed in a number of human diseases, most notably cancer, targeting this oncogenic translation initiation factor has emerged as a promising strategy for the development of novel anti-cancer therapeutics. Toward this end, in the present study, we have rationally designed a series of Bn7GxP-based PROTACs for the targeted degradation of eIF4E. Herein we describe our synthetic efforts, in addition to biochemical and cellular characterization of these compounds.
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Affiliation(s)
- Tanpreet Kaur
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 1600 Huron Parkway, Ann Arbor, MI, 48109, USA
| | - Arya Menon
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 1600 Huron Parkway, Ann Arbor, MI, 48109, USA
| | - Amanda L Garner
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 1600 Huron Parkway, Ann Arbor, MI, 48109, USA.
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21
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Dürr E, Doherty W, Lee SY, El‐Sagheer AH, Shivalingam A, McHugh PJ, Brown T, McGouran JF. Squaramide-Based 5'-Phosphate Replacements Bind to the DNA Repair Exonuclease SNM1A. ChemistrySelect 2018; 3:12824-12829. [PMID: 31414040 PMCID: PMC6685075 DOI: 10.1002/slct.201803375] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 11/19/2018] [Indexed: 12/26/2022]
Abstract
Phosphate groups are often crucial to biological activity and interactions of oligonucleotides, but confer poor membrane permeability. In addition, the group's lability to enzymatic hydrolysis is an obstacle to its use in therapeutics and in biological tools. We present the synthesis of N-oxyamide and squaramide modifications at the 5'-end of oligonucleotides as phosphate replacements and their biological evaluation using the 5'-exonuclease SNM1A. The squaryl diamide modification showed minimal recognition as a 5'-phosphate mimic; however, modest inhibition of SNM1A, postulated to occur through metal coordination at the active site, was observed. Their facile incorporation after solid-phase synthesis and recognition by the exonuclease makes squaryl diamides attractive neutral 5'-phosphate replacements for oligonucleotides. This work is the first example of squaryl diamide modifications at the 5'-terminal position of oligonucleotides and of the potential use of modified oligonucleotides to bind to the metal center of SNM1A.
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Affiliation(s)
- Eva‐Maria Dürr
- School of ChemistryTrinity Biomedical Sciences InstituteTrinity College Dublin152-160 Pearse St.Dublin 2Ireland
| | - William Doherty
- School of ChemistryTrinity Biomedical Sciences InstituteTrinity College Dublin152-160 Pearse St.Dublin 2Ireland
| | - Sook Y. Lee
- Department of OncologyWeatherall Institute of Molecular MedicineUniversity of Oxford, John Radcliffe HospitalOxford OX3 9DSUK
- Department of ChemistryUniversity of Oxford12 Mansfield RoadOxford OX1 3TAUK
| | - Afaf H. El‐Sagheer
- Department of ChemistryUniversity of Oxford12 Mansfield RoadOxford OX1 3TAUK
- Chemistry Branch, Department of Science and MathematicsFaculty of Petroleum and Mining Engineering, Suez UniversitySuez43721Egypt
| | - Arun Shivalingam
- Department of ChemistryUniversity of Oxford12 Mansfield RoadOxford OX1 3TAUK
| | - Peter J. McHugh
- Department of OncologyWeatherall Institute of Molecular MedicineUniversity of Oxford, John Radcliffe HospitalOxford OX3 9DSUK
| | - Tom Brown
- Department of ChemistryUniversity of Oxford12 Mansfield RoadOxford OX1 3TAUK
| | - Joanna F. McGouran
- School of ChemistryTrinity Biomedical Sciences InstituteTrinity College Dublin152-160 Pearse St.Dublin 2Ireland
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22
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Boriack-Sjodin PA, Ribich S, Copeland RA. RNA-modifying proteins as anticancer drug targets. Nat Rev Drug Discov 2018; 17:435-453. [PMID: 29773918 DOI: 10.1038/nrd.2018.71] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
All major biological macromolecules (DNA, RNA, proteins and lipids) undergo enzyme-catalysed covalent modifications that impact their structure, function and stability. A variety of covalent modifications of RNA have been identified and demonstrated to affect RNA stability and translation to proteins; these mechanisms of translational control have been termed epitranscriptomics. Emerging data suggest that some epitranscriptomic mechanisms are altered in human cancers as well as other human diseases. In this Review, we examine the current understanding of RNA modifications with a focus on mRNA methylation, highlight their possible roles in specific cancer indications and discuss the emerging potential of RNA-modifying proteins as therapeutic targets.
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23
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Kozarski M, Kubacka D, Wojtczak BA, Kasprzyk R, Baranowski MR, Kowalska J. 7-Methylguanosine monophosphate analogues with 5'-(1,2,3-triazoyl) moiety: Synthesis and evaluation as the inhibitors of cNIIIB nucleotidase. Bioorg Med Chem 2017; 26:191-199. [PMID: 29195795 DOI: 10.1016/j.bmc.2017.11.032] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 11/16/2017] [Accepted: 11/20/2017] [Indexed: 12/26/2022]
Abstract
The hydrolysis of nucleoside 5'-monophosphates to the corresponding nucleosides and inorganic phosphate is catalysed by 5'-nucleotidases, thereby contributing to the control of endogenous nucleotide turnover and affecting the fate of exogenously delivered nucleotide- and nucleoside-derived therapeutics in cells. A recently identified nucleotidase cNIIIB shows preference towards 7-methylguanosine monophosphate (m7GMP) as a substrate, which suggests its potential involvement in mRNA degradation. However, the extent of biological functions and the significance of cNIIIB remains to be elucidated. Here, we synthesised a series of m7GMP analogues carrying a 1,2,3-triazole moiety at the 5' position as the potential inhibitors of human cNIIIB. The compounds were synthesised by using the copper-catalysed azide-alkyne cycloaddition (CuAAC) between 5'-azido-5'-deoxy-7-methylguanosine and different phosphate or phosphonate derivatives carrying terminal alkyne. The analogues were evaluated as cNIIIB inhibitors using HPLC and malachite green assays, demonstrating that compound 1a, carrying a 1,2,3-triazoylphosphonate moiety, inhibits cNIIIB activity at micromolar concentrations (IC50 87.8 ± 7.5 µM), while other analogues showed no activity. In addition, compound 1d was identified as an artifical substrate for HscNIIIB. Further characterization of inhibitor 1a revealed that it is poorly recognised by other m7G-binding proteins, eIF4E and DcpS, indicating its selectivity towards cNIIIB. The first inhibitor (1a) and unnatural substrate (1d) of cNIIIB, identified here, can be used as molecular probes for the elucidation of biological roles of cNIIIB, including the verification of its proposed function in mRNA metabolism.
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Affiliation(s)
- Mateusz Kozarski
- University of Warsaw, Faculty of Physics, Institute of Experimental Physics, Division of Biophysics, Pasteura 5, 02-093 Warsaw, Poland
| | - Dorota Kubacka
- University of Warsaw, Faculty of Physics, Institute of Experimental Physics, Division of Biophysics, Pasteura 5, 02-093 Warsaw, Poland
| | - Blazej A Wojtczak
- University of Warsaw, Centre of New Technologies, Banacha 2c, 02-097 Warsaw, Poland
| | - Renata Kasprzyk
- University of Warsaw, Centre of New Technologies, Banacha 2c, 02-097 Warsaw, Poland; University of Warsaw, College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, Banacha 2c, 02-097 Warsaw, Poland
| | - Marek R Baranowski
- University of Warsaw, Faculty of Physics, Institute of Experimental Physics, Division of Biophysics, Pasteura 5, 02-093 Warsaw, Poland
| | - Joanna Kowalska
- University of Warsaw, Faculty of Physics, Institute of Experimental Physics, Division of Biophysics, Pasteura 5, 02-093 Warsaw, Poland.
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