1
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Shukla C, Datta B. G-quadruplexes in long non-coding RNAs and their interactions with proteins. Int J Biol Macromol 2024; 278:134946. [PMID: 39187110 DOI: 10.1016/j.ijbiomac.2024.134946] [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: 06/07/2024] [Revised: 08/19/2024] [Accepted: 08/20/2024] [Indexed: 08/28/2024]
Abstract
Long non-coding RNAs (lncRNAs) have emerged as crucial regulators of cellular processes, with their dysregulation linked to various disease states. Among the structural motifs in lncRNAs, RNA G-quadruplexes (rG4s) have gained increasing attention due to their diverse roles in cellular function and disease pathogenesis. This review provides an updated and comprehensive overview of rG4s in lncRNAs, elucidating their formation, interaction with proteins, and distinctive roles in cellular processes. We discuss current methodologies for experimentally probing RNA G4s, including the use of specific small molecules, biomolecular ligands and fluorescent probes. The commonly found RNA G4-interacting protein domains are summarised along with potential strategies for disrupting lncRNA G4-protein interactions from a therapeutic perspective.
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Affiliation(s)
- Chinmayee Shukla
- Department of Biological Sciences and Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, 382355, Gujarat, India
| | - Bhaskar Datta
- Department of Biological Sciences and Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, 382355, Gujarat, India; Department of Chemistry, Indian Institute of Technology Gandhinagar, Gandhinagar, 382355, Gujarat, India.
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2
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Teng X, Hu D, Dai Y, Jing H, Hu W, Zhang Q, Zhang N, Li J. Discovery of A G-Quadruplex Unwinder That Unleashes the Translation of G-Quadruplex-Containing mRNA without Inducing DNA Damage. Angew Chem Int Ed Engl 2024; 63:e202407353. [PMID: 38953247 DOI: 10.1002/anie.202407353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 06/28/2024] [Accepted: 07/01/2024] [Indexed: 07/03/2024]
Abstract
To explore the mechanisms and therapeutic strategies for G-quadruplex (G4) mediated diseases, it is crucial to manipulate and intervene in intracellular G4 structures using small molecular tools. While hundreds of G4 stabilizers have been developed, there is a significant gap in the availability of G4 unwinding agents. Here, we propose a strategy to disrupt G-quadruplexes by forming G-C hydrogen bonds with chemically modified cytidine trimers. We validated a good G4 unwinder, the 2'-F cytidine trimer (2'-F C3). 2'-F C3 does not inhibit cell growth nor cause severe DNA damage at a concentration below 10 μM. Moreover, 2'-F C3 does not affect gene transcription nor RNA splicing, while it significantly enhances the translation of G4-containing mRNA and upregulates RNA splicing, RNA processing and cell cycle pathways. The discovery of this G4 unwinder provides a functional tool for the chemical modulation of G4s in living cells.
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Affiliation(s)
- Xucong Teng
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
- New Cornerstone Science Laboratory, Shenzhen, 518054, China
- Beijing Life Science Academy, Beijing, 102209, China
- Center for BioAnalytical Chemistry, Hefei National Laboratory of Physical Science at Microscale, University of Science and Technology of China, Hefei, 230026, China
| | - Difei Hu
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
| | - Yicong Dai
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
| | - Haitao Jing
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, China
| | - Wenxuan Hu
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, China
| | - Qiushuang Zhang
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
| | - Na Zhang
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, China
| | - Jinghong Li
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
- New Cornerstone Science Laboratory, Shenzhen, 518054, China
- Beijing Life Science Academy, Beijing, 102209, China
- Center for BioAnalytical Chemistry, Hefei National Laboratory of Physical Science at Microscale, University of Science and Technology of China, Hefei, 230026, China
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3
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Johnson K, Seidel JM, Cech TR. Small molecule telomerase inhibitors are also potent inhibitors of telomeric C-strand synthesis. RNA (NEW YORK, N.Y.) 2024; 30:1213-1226. [PMID: 38918043 PMCID: PMC11331414 DOI: 10.1261/rna.080043.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 06/10/2024] [Indexed: 06/27/2024]
Abstract
Telomere replication is essential for continued proliferation of human cells, such as stem cells and cancer cells. Telomerase lengthens the telomeric G-strand, while C-strand replication is accomplished by CST-polymerase α-primase (CST-PP). Replication of both strands is inhibited by formation of G-quadruplex (GQ) structures in the G-rich single-stranded DNA. TMPyP4 and pyridostatin (PDS), which stabilize GQ structures in both DNA and RNA, inhibit telomerase in vitro, and in human cells they cause telomere shortening that has been attributed to telomerase inhibition. Here, we show that TMPyP4 and PDS also inhibit C-strand synthesis by stabilizing DNA secondary structures and thereby preventing CST-PP from binding to telomeric DNA. We also show that these small molecules inhibit CST-PP binding to a DNA sequence containing no consecutive guanine residues, which is unlikely to form GQs. Thus, while these "telomerase inhibitors" indeed inhibit telomerase, they are also robust inhibitors of telomeric C-strand synthesis. Furthermore, given their binding to GQ RNA and their limited specificity for GQ structures, they may disrupt many other protein-nucleic acid interactions in human cells.
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Affiliation(s)
- Kaitlin Johnson
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80303, USA
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado 80303, USA
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, Colorado 80303, USA
| | - Julia M Seidel
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80303, USA
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado 80303, USA
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, Colorado 80303, USA
| | - Thomas R Cech
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80303, USA
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado 80303, USA
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, Colorado 80303, USA
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4
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Laigre E, Bonnet H, Beauvineau C, Lavergne T, Verga D, Defrancq E, Dejeu J, Teulade-Fichou MP. Systematic Evaluation of Benchmark G4 Probes and G4 Clinical Drugs using three Biophysical Methods: A Guideline to Evaluate Rapidly G4-Binding Affinity. Chembiochem 2024; 25:e202400210. [PMID: 38619969 DOI: 10.1002/cbic.202400210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 04/17/2024]
Abstract
G-quadruplex DNA structures (G4) are proven to interfere with most genetic and epigenetic processes. Small molecules binding these structures (G4 ligands) are invaluable tools to probe G4-biology and address G4-druggability in various diseases (cancer, viral infections). However, the large number of reported G4 ligands (>1000) could lead to confusion while selecting one for a given application. Herein we conducted a systematic affinity ranking of 11 popular G4 ligands vs 5 classical G4 sequences using FRET-melting, G4-FID assays and SPR. Interestingly SPR data globally align with the rankings obtained from the two semi-quantitative assays despite discrepancies due to limits and characteristics of each assay. In the whole, PhenDC3 emerges as the most potent binder irrespective of the G4 sequence. Immediately below PDS, PDC-360A, BRACO19, TMPyP4 and RHPS4 feature strong to medium binding again with poor G4 topology discrimination. More strikingly, the G4 drugs Quarfloxin, CX5461 and c-PDS exhibit weak affinity with all G4s studied. Finally, NMM and Cu-ttpy showed heterogeneous behaviors due, in part, to their physicochemical particularities poorly compatible with screening conditions. The remarkable properties of PhenDC3 led us to propose its use for benchmarking FRET-melting and G4-FID assays for rapid G4-affinity evaluation of newly developed ligands.
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Affiliation(s)
- E Laigre
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, F-91405, Orsay, France
- CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405, Orsay, France
| | - H Bonnet
- DCM, UMR 5250, Univ. Grenoble Alpes, CNRS, 570 Rue de la Chimie, 38000, Grenoble, France
| | - C Beauvineau
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, F-91405, Orsay, France
- CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405, Orsay, France
| | - T Lavergne
- DCM, UMR 5250, Univ. Grenoble Alpes, CNRS, 570 Rue de la Chimie, 38000, Grenoble, France
| | - D Verga
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, F-91405, Orsay, France
- CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405, Orsay, France
| | - E Defrancq
- DCM, UMR 5250, Univ. Grenoble Alpes, CNRS, 570 Rue de la Chimie, 38000, Grenoble, France
| | - J Dejeu
- DCM, UMR 5250, Univ. Grenoble Alpes, CNRS, 570 Rue de la Chimie, 38000, Grenoble, France
- SUPMICROTECH, Université Franche-Comté, CNRS, Institut FEMTO-ST, 25000, Besançon, France
| | - M-P Teulade-Fichou
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, F-91405, Orsay, France
- CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405, Orsay, France
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5
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Cai JH, Yang DY, Zhang JJ, Tan JH, Huang ZS, Chen SB. Constructing triazole-modified quinazoline derivatives as selective c-MYC G-quadruplex ligands and potent anticancer agents through click chemistry. Bioorg Chem 2024; 144:107173. [PMID: 38335759 DOI: 10.1016/j.bioorg.2024.107173] [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: 01/04/2024] [Revised: 01/26/2024] [Accepted: 01/31/2024] [Indexed: 02/12/2024]
Abstract
c-MYC is a hallmark of various cancers, playing a critical role in promoting tumorigenesis. The formation of G-quadruplex (G4) in the c-MYC promoter region significantly suppresses its expression. Therefore, developing small-molecule ligands to stabilize c-MYC G4 formation and subsequentially suppress c-MYC expression is an attractive topic for c-MYC-driven cancer therapy. However, achieving selective ligands for c-MYC G4 poses challenges. In this study, we developed a series of triazole-modified quinazoline (TMQ) derivatives as potential c-MYC G4 ligands and c-MYC transcription inhibitors from 4-anilinoquinazoline lead 7a using click chemistry. Importantly, the c-MYC G4 stabilizing ability and antiproliferation activity were well correlated among these new derivatives, particularly in the c-MYC highly expressed colorectal cancer cell line HCT116. Among them, compound A6 exhibited good selectivity in stabilizing c-MYC G4 and in suppressing c-MYC transcription better than 7a. This compound induced G4 formation, selectively inhibited G4-related c-MYC transcription and suppressed the progression of HCT116 cells. These findings identify a new c-MYC transcription inhibitor and provide new insights for optimizing c-MYC G4-targeting ligands.
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Affiliation(s)
- Jiong-Heng Cai
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Dan-Yan Yang
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Jun-Jie Zhang
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Jia-Heng Tan
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhi-Shu Huang
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China.
| | - Shuo-Bin Chen
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China.
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6
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Sahayasheela VJ, Sugiyama H. RNA G-quadruplex in functional regulation of noncoding RNA: Challenges and emerging opportunities. Cell Chem Biol 2024; 31:53-70. [PMID: 37909035 DOI: 10.1016/j.chembiol.2023.08.010] [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: 04/18/2023] [Revised: 07/12/2023] [Accepted: 08/22/2023] [Indexed: 11/02/2023]
Abstract
G-quadruplexes (G4s) are stable, noncanonical structures formed in guanine (G)-rich sequences of DNA/RNA. G4 structures are reported to play a regulatory role in various cellular processes and, recently, a considerable number of studies have attributed new biological functions to these structures, especially in RNA. Noncoding RNA (ncRNA), which does not translate into a functional protein, is widely expressed and has been shown to play a key role in shaping cellular activity. There has been growing evidence of G4 formation in several ncRNA classes, and it has been identified as a key part for diverse biological functions and physio-pathological contexts in neurodegenerative diseases and cancer. This review discusses RNA G4s (rG4s) in ncRNA, focusing on the molecular mechanism underlying its function. This review also aims to highlight potential and emerging opportunities to identify and target the rG4s in ncRNA to understand its function and, ultimately, treat many diseases.
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Affiliation(s)
- Vinodh J Sahayasheela
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto 606-8502, Japan; Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Ushinomaecho, Sakyo-Ku, Kyoto 606-8501, Japan.
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7
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Mou X, Kwok CK. Peptides Selected by G4-mRNA Display-Seq Enable RNA G-Quadruplex Recognition and Gene Regulation. J Am Chem Soc 2023; 145:18693-18697. [PMID: 37582058 DOI: 10.1021/jacs.3c04534] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2023]
Abstract
G-quadruplexes (G4s) are noncanonical secondary structures that play critical roles in both chemistry and biology. Although several approaches have been developed for G4 targeting, such as chemicals and antibodies, there is currently no general and efficient platform for G4-specific peptides. In this study, we developed a new platform, G4-mRNA display-Seq, for selecting peptides that specifically recognize the G4 target of interest. By using an RNA G4 (rG4) found in human telomerase RNA (hTERC) as the target, we have identified a novel short peptide, namely, peptide 11 (pep11), which displays high affinity and selectivity to hTERC rG4. Furthermore, we designed tandem and cyclic versions of pep11 and found that both modified versions exhibit stronger binding affinity with preferential rG4 selectivity. Notably, we have demonstrated that these peptides can negatively regulate gene expression by targeting rG4. Our results provide a universal platform for the discovery of G4-targeting peptides and demonstrate the ability of these peptides to regulate G4-mediated gene functions.
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Affiliation(s)
- Xi Mou
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR 999077, China
| | - Chun Kit Kwok
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR 999077, China
- Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, China
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8
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Rota Sperti F, Mitteaux J, Zell J, Pipier A, Valverde IE, Monchaud D. The multivalent G-quadruplex (G4)-ligands MultiTASQs allow for versatile click chemistry-based investigations. RSC Chem Biol 2023; 4:456-465. [PMID: 37415864 PMCID: PMC10320843 DOI: 10.1039/d3cb00009e] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 05/12/2023] [Indexed: 07/08/2023] Open
Abstract
Chemical biology hinges on multivalent molecular tools that can specifically interrogate and/or manipulate cellular circuitries from the inside. The success of many of these approaches relies on molecular tools that make it possible to visualize biological targets in cells and then isolate them for identification purposes. To this end, click chemistry has become in just a few years a vital tool in offering practically convenient solutions to address highly complicated biological questions. We report here on two clickable molecular tools, the biomimetic G-quadruplex (G4) ligands MultiTASQ and azMultiTASQ, which benefit from the versatility of two types of bioorthogonal chemistry, CuAAC and SPAAC (the discovery of which was very recently awarded the Nobel Prize of chemistry). These two MultiTASQs are used here to both visualize G4s in and identify G4s from human cells. To this end, we developed click chemo-precipitation of G-quadruplexes (G4-click-CP) and in situ G4 click imaging protocols, which provide unique insights into G4 biology in a straightforward and reliable manner.
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Affiliation(s)
- Francesco Rota Sperti
- ICMUB, CNRS UMR6302, Université de Bourgogne 9 Avenue Alain Savary 21078 Dijon France
| | - Jérémie Mitteaux
- ICMUB, CNRS UMR6302, Université de Bourgogne 9 Avenue Alain Savary 21078 Dijon France
| | - Joanna Zell
- ICMUB, CNRS UMR6302, Université de Bourgogne 9 Avenue Alain Savary 21078 Dijon France
| | - Angélique Pipier
- ICMUB, CNRS UMR6302, Université de Bourgogne 9 Avenue Alain Savary 21078 Dijon France
| | - Ibai E Valverde
- ICMUB, CNRS UMR6302, Université de Bourgogne 9 Avenue Alain Savary 21078 Dijon France
| | - David Monchaud
- ICMUB, CNRS UMR6302, Université de Bourgogne 9 Avenue Alain Savary 21078 Dijon France
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9
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Monti L, Di Antonio M. G-Quadruplexes as Key Transcriptional Regulators in Neglected Trypanosomatid Parasites. Chembiochem 2023; 24:e202300265. [PMID: 37146230 PMCID: PMC10946822 DOI: 10.1002/cbic.202300265] [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: 04/01/2023] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 05/07/2023]
Abstract
G-quadruplexes (G4s) are nucleic acid secondary structures that have been linked to the functional regulation of eukaryotic organisms. G4s have been extensively characterised in humans and emerging evidence suggests that they might also be biologically relevant for human pathogens. This indicates that G4s might represent a novel class of therapeutic targets for tackling infectious diseases. Bioinformatic studies revealed a high prevalence of putative quadruplex-forming sequences (PQSs) in the genome of protozoans, which highlights their potential roles in regulating vital processes of these parasites, including DNA transcription and replication. In this work, we focus on the neglected trypanosomatid parasites, Trypanosoma and Leishmania spp., which cause debilitating and deadly diseases across the poorest populations worldwide. We review three examples where G4-formation might be key to modulate transcriptional activity in trypanosomatids, providing an overview of experimental approaches that can be used to exploit the regulatory roles and relevance of these structures to fight parasitic infections.
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Affiliation(s)
- Ludovica Monti
- Chemistry Department, Imperial College LondonMolecular Sciences Research Hub82 Wood LaneW12 0BZLondonUK
| | - Marco Di Antonio
- Chemistry Department, Imperial College LondonMolecular Sciences Research Hub82 Wood LaneW12 0BZLondonUK
- The Francis Crick Institute1 Midland RoadNW1 1ATLondonUK
- The Institute of Chemical BiologyMolecular Sciences Research Hub82 Wood LaneW12 0BZLondonUK
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10
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Mikutis S, Rebelo M, Yankova E, Gu M, Tang C, Coelho AR, Yang M, Hazemi ME, Pires de Miranda M, Eleftheriou M, Robertson M, Vassiliou GS, Adams DJ, Simas JP, Corzana F, Schneekloth JS, Tzelepis K, Bernardes GJL. Proximity-Induced Nucleic Acid Degrader (PINAD) Approach to Targeted RNA Degradation Using Small Molecules. ACS CENTRAL SCIENCE 2023; 9:892-904. [PMID: 37252343 PMCID: PMC10214512 DOI: 10.1021/acscentsci.3c00015] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Indexed: 05/31/2023]
Abstract
Nature has evolved intricate machinery to target and degrade RNA, and some of these molecular mechanisms can be adapted for therapeutic use. Small interfering RNAs and RNase H-inducing oligonucleotides have yielded therapeutic agents against diseases that cannot be tackled using protein-centered approaches. Because these therapeutic agents are nucleic acid-based, they have several inherent drawbacks which include poor cellular uptake and stability. Here we report a new approach to target and degrade RNA using small molecules, proximity-induced nucleic acid degrader (PINAD). We have utilized this strategy to design two families of RNA degraders which target two different RNA structures within the genome of SARS-CoV-2: G-quadruplexes and the betacoronaviral pseudoknot. We demonstrate that these novel molecules degrade their targets using in vitro, in cellulo, and in vivo SARS-CoV-2 infection models. Our strategy allows any RNA binding small molecule to be converted into a degrader, empowering RNA binders that are not potent enough to exert a phenotypic effect on their own. PINAD raises the possibility of targeting and destroying any disease-related RNA species, which can greatly expand the space of druggable targets and diseases.
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Affiliation(s)
- Sigitas Mikutis
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Maria Rebelo
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028, Lisboa, Portugal
| | - Eliza Yankova
- Wellcome-MRC
Cambridge Stem Cell Institute, University
of Cambridge, Cambridge CB2 0AW, U.K.
- Milner
Therapeutics Institute, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, U.K.
| | - Muxin Gu
- Wellcome-MRC
Cambridge Stem Cell Institute, University
of Cambridge, Cambridge CB2 0AW, U.K.
| | - Cong Tang
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028, Lisboa, Portugal
| | - Ana R. Coelho
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028, Lisboa, Portugal
| | - Mo Yang
- Chemical
Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Madoka E. Hazemi
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Marta Pires de Miranda
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028, Lisboa, Portugal
| | - Maria Eleftheriou
- Wellcome-MRC
Cambridge Stem Cell Institute, University
of Cambridge, Cambridge CB2 0AW, U.K.
- Milner
Therapeutics Institute, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, U.K.
| | - Max Robertson
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - George S. Vassiliou
- Wellcome-MRC
Cambridge Stem Cell Institute, University
of Cambridge, Cambridge CB2 0AW, U.K.
| | - David J. Adams
- Experimental
Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, U.K.
| | - J. Pedro Simas
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028, Lisboa, Portugal
- Católica
Biomedical Research and Católica Medical School, Universidade Católica Portuguesa, 1649-023 Lisboa, Portugal
| | - Francisco Corzana
- Departamento
de Química, Centro de Investigación en Síntesis
Química, Universidad de La Rioja, 26006 Logroño, Spain
| | - John S. Schneekloth
- Chemical
Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Konstantinos Tzelepis
- Wellcome-MRC
Cambridge Stem Cell Institute, University
of Cambridge, Cambridge CB2 0AW, U.K.
- Milner
Therapeutics Institute, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, U.K.
| | - Gonçalo J. L. Bernardes
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028, Lisboa, Portugal
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11
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G-Quadruplexes Regulate miRNA Biogenesis in Live Zebrafish Embryos. Int J Mol Sci 2023; 24:ijms24054828. [PMID: 36902262 PMCID: PMC10002522 DOI: 10.3390/ijms24054828] [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: 01/27/2023] [Revised: 02/16/2023] [Accepted: 02/20/2023] [Indexed: 03/06/2023] Open
Abstract
RNA guanine quadruplexes (G4s) regulate RNA functions, metabolism, and processing. G4s formed within precursors of microRNAs (pre-miRNAs) may impair pre-miRNAs maturation by Dicer, thus repressing mature miRNA biogenesis. As miRNAs are essential for proper embryonic development, we studied the role of G4s on miRNA biogenesis in vivo during zebrafish embryogenesis. We performed a computational analysis on zebrafish pre-miRNAs to find putative G4 forming sequences (PQSs). The precursor of the miRNA 150 (pre-miR-150) was found to contain an evolutionarily conserved PQS formed by three G-tetrads and able to fold in vitro as G4. MiR-150 controls the expression of myb, which shows a well-defined knock-down phenotype in zebrafish developing embryos. We microinjected zebrafish embryos with in vitro transcribed pre-miR-150 synthesized using either GTP (G-pre-miR-150) or 7-Deaza-GTP, a GTP analogue unable to form G4s (7DG-pre-miR-150). Compared to embryos injected with G-pre-miR-150, embryos injected with 7DG-pre-miR-150 showed higher levels of miRNA 150 (miR-150) and lower levels of myb mRNA and stronger phenotypes associated with myb knock-down. The incubation of pre-miR-150 prior to the injection with the G4 stabilizing ligand pyridostatin (PDS) reverted gene expression variations and rescued the phenotypes related to myb knock-down. Overall, results suggest that the G4 formed in pre-miR-150 functions in vivo as a conserved regulatory structure competing with the stem-loop structure necessary for miRNA biogenesis.
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12
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Chaudhuri R, Prasanth T, Dash J. Expanding the Toolbox of Target Directed Bio-Orthogonal Synthesis: In Situ Direct Macrocyclization by DNA Templates. Angew Chem Int Ed Engl 2023; 62:e202215245. [PMID: 36437509 DOI: 10.1002/anie.202215245] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/11/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022]
Abstract
Herein, we demonstrate for the first time that noncanonical DNA can direct macrocyclization-like challenging reactions to synthesize gene modulators. The planar G-quartets present in DNA G-quadruplexes (G4s) provide a size complementary reaction platform for the bio-orthogonal macrocyclization of bifunctional azide and alkyne fragments over oligo- and polymerization. G4s immobilized on gold-coated magnetic nanoparticles have been used as target templates to enable easy identification of a selective peptidomimetic macrocycle. Structurally similar macrocycles have been synthesized to understand their functional role in the modulation of gene function. The innate fluorescence of the in situ formed macrocycle has been utilized to monitor its cellular localization using a G4 antibody and its in cell formation from the corresponding azide and alkyne fragments. The successful execution of in situ macrocyclization in vitro and in cells would open up a new dimension for target-directed therapeutic applications.
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Affiliation(s)
- Ritapa Chaudhuri
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A and 2B Raja S.C. Mullick Road, Jadavpur, Kolkata, 700099, India
| | - Thumpati Prasanth
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A and 2B Raja S.C. Mullick Road, Jadavpur, Kolkata, 700099, India.,Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research Kolkata, Chunilal Bhawan,168, Maniktala Main Road, P.O. Bengal Chemicals, P.S. Phoolbagan, Kolkata, 700054, India
| | - Jyotirmayee Dash
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A and 2B Raja S.C. Mullick Road, Jadavpur, Kolkata, 700099, India
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13
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Kharel P, Fay M, Manasova EV, Anderson PJ, Kurkin AV, Guo JU, Ivanov P. Stress promotes RNA G-quadruplex folding in human cells. Nat Commun 2023; 14:205. [PMID: 36639366 PMCID: PMC9839774 DOI: 10.1038/s41467-023-35811-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 01/03/2023] [Indexed: 01/15/2023] Open
Abstract
Guanine (G)-rich nucleic acids can fold into G-quadruplex (G4) structures under permissive conditions. Although many RNAs contain sequences that fold into RNA G4s (rG4s) in vitro, their folding and functions in vivo are not well understood. In this report, we showed that the folding of putative rG4s in human cells into rG4 structures is dynamically regulated under stress. By using high-throughput dimethylsulfate (DMS) probing, we identified hundreds of endogenous stress-induced rG4s, and validated them by using an rG4 pull-down approach. Our results demonstrate that stress-induced rG4s are enriched in mRNA 3'-untranslated regions and enhance mRNA stability. Furthermore, stress-induced rG4 folding is readily reversible upon stress removal. In summary, our study revealed the dynamic regulation of rG4 folding in human cells and suggested that widespread rG4 motifs may have a global regulatory impact on mRNA stability and cellular stress response.
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Affiliation(s)
- Prakash Kharel
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Marta Fay
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Ekaterina V Manasova
- Chemistry Department of Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Paul J Anderson
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Harvard Medical School Initiative for RNA Medicine, Boston, MA, 02115, USA
| | - Alexander V Kurkin
- Chemistry Department of Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Junjie U Guo
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, 06520, USA.
| | - Pavel Ivanov
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
- Harvard Medical School Initiative for RNA Medicine, Boston, MA, 02115, USA.
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14
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Laskova J, Serdyukov A, Kosenko I, Ananyev I, Titova E, Druzina A, Sivaev I, Antonets AA, Nazarov AA, Bregadze VI. New Azido Coumarins as Potential Agents for Fluorescent Labeling and Their "Click" Chemistry Reactions for the Conjugation with closo-Dodecaborate Anion. Molecules 2022; 27:molecules27238575. [PMID: 36500667 PMCID: PMC9738631 DOI: 10.3390/molecules27238575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
Novel fluorescent 7-methoxy- and 7-(diethylamino)-coumarins modified with azido-group on the side chain have been synthesized. Their photophysical properties and single crystals structure characteristics have been studied. In order to demonstrate the possibilities of fluorescent labeling, obtained coumarins have been tested with closo-dodecaborate derivative bearing terminal alkynyl group. CuI catalyzed Huisgen 1,3-dipolar cycloaddition reaction has led to fluorescent conjugates formation. The absorption-emission spectra of the formed conjugates have been presented. The antiproliferative activity and uptake of compounds against several human cell lines were evaluated.
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Affiliation(s)
- Julia Laskova
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, 28 Vavilov Str., 119334 Moscow, Russia
- Correspondence: ; Tel.: +41-78-243-1408
| | - Alexander Serdyukov
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, 28 Vavilov Str., 119334 Moscow, Russia
- M.V. Lomonosov Institute of Fine Chemical Technology, MIREA—Technological University, 86 Vernadsky Avenue, 119571 Moscow, Russia
| | - Irina Kosenko
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, 28 Vavilov Str., 119334 Moscow, Russia
| | - Ivan Ananyev
- N.S. Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, 31 Leninsky Avenue, 119991 Moscow, Russia
| | - Ekaterina Titova
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, 28 Vavilov Str., 119334 Moscow, Russia
| | - Anna Druzina
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, 28 Vavilov Str., 119334 Moscow, Russia
| | - Igor Sivaev
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, 28 Vavilov Str., 119334 Moscow, Russia
- Basic Department of Chemistry of Innovative Materials and Technologies, G.V. Plekhanov Russian University of Economics, 36 Stremyannyi Line, 117997 Moscow, Russia
| | - Anastasia A. Antonets
- Department of Chemistry, M.V. Lomonosov Moscow State University, Leninskie Gory 1/3, 119991 Moscow, Russia
| | - Alexey A. Nazarov
- Department of Chemistry, M.V. Lomonosov Moscow State University, Leninskie Gory 1/3, 119991 Moscow, Russia
| | - Vladimir I. Bregadze
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, 28 Vavilov Str., 119334 Moscow, Russia
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15
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Bedwell E, McCarthy WJ, Coyne AG, Abell C. Development of potent inhibitors by fragment-linking strategies. Chem Biol Drug Des 2022; 100:469-486. [PMID: 35854428 DOI: 10.1111/cbdd.14120] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/12/2022] [Accepted: 07/17/2022] [Indexed: 11/29/2022]
Abstract
Fragment-based drug discovery (FBDD) is a method of identifying small molecule hits that can be elaborated rationally through fragment growing, merging, and linking, to afford high affinity ligands for biological targets. Despite the promised theoretical potential of fragment linking, examples are still surprisingly sparse and remain overshadowed by the successes of fragment growing. The aim of this review is to outline a number of key examples of fragment linking strategies and discuss their strengths and limitations. Structure-based approaches including X-ray crystallography and in silico methods fragment optimisation are discussed, as well as fragment linking guided by NMR experiments. Target-guided approaches, exploiting the biological target to assemble its own inhibitors through dynamic combinatorial chemistry (DCC) and kinetic target-guided synthesis (KTGS), are identified as alternative efficient methods for fragment linking.
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Affiliation(s)
- Elizabeth Bedwell
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambrdige, United Kingdom
| | - William J McCarthy
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambrdige, United Kingdom
| | - Anthony G Coyne
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambrdige, United Kingdom
| | - Chris Abell
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambrdige, United Kingdom
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16
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Zhao H, Wong HY, Ji D, Lyu K, Kwok CK. Novel L-RNA Aptamer Controls APP Gene Expression in Cells by Targeting RNA G-Quadruplex Structure. ACS APPLIED MATERIALS & INTERFACES 2022; 14:30582-30594. [PMID: 35762921 DOI: 10.1021/acsami.2c06390] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Guanine quadruplex (G4) structure is a four-stranded nucleic acid secondary structure motif with unique chemical properties and important biological roles. Amyloid precursor protein (APP) is an Alzheimer's disease (AD)-related gene, and recently, we reported the formation of RNA G4 (rG4) at the 3'UTR of APP mRNA and demonstrated its repressive role in translation. Herein, we apply rG4-SELEX to develop a novel L-RNA aptamer, L-Apt.8f, which binds to APP 3'UTR D-rG4 strongly with subnanomolar affinity. We structurally characterize the aptamer and find that it contains a thermostable and parallel G4 motif, and mutagenesis analysis identifies the key nucleotides that are involved in the target recognition. We also reveal that the L-Apt.8f-APP D-rG4 interaction is enantiomeric-, magnesium ion-, and potassium ion-dependent. Notably, L-Apt.8f preferentially recognizes APP rG4 over other structural motifs, and it can control the APP reporter gene and native transcript translation in cells. Our work introduces a novel strategy and reports a new L-aptamer candidate to target APP 3'UTR rG4 structure, which laid the foundation for further applying L-RNA as an important class of biomolecule for practical L-aptamer-based targeting and controlling of gene expression in cells.
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Affiliation(s)
- Haizhou Zhao
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR 999077, China
| | - Hei Yuen Wong
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR 999077, China
| | - Danyang Ji
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR 999077, China
| | - Kaixin Lyu
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR 999077, China
| | - Chun Kit Kwok
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR 999077, China
- Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, China
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17
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Katsuda Y, Sato SI, Inoue M, Tsugawa H, Kamura T, Kida T, Matsumoto R, Asamitsu S, Shioda N, Shiroto S, Oosawatsu Y, Yatsuzuka K, Kitamura Y, Hagihara M, Ihara T, Uesugi M. Small molecule-based detection of non-canonical RNA G-quadruplex structures that modulate protein translation. Nucleic Acids Res 2022; 50:8143-8153. [PMID: 35801908 PMCID: PMC9371906 DOI: 10.1093/nar/gkac580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 05/24/2022] [Accepted: 06/23/2022] [Indexed: 11/29/2022] Open
Abstract
Tandem repeats of guanine-rich sequences in RNA often form thermodynamically stable four-stranded RNA structures. Such RNA G-quadruplexes have long been considered to be linked to essential biological processes, yet their physiological significance in cells remains unclear. Here, we report a approach that permits the detection of RNA G-quadruplex structures that modulate protein translation in mammalian cells. The approach combines antibody arrays and RGB-1, a small molecule that selectively stabilizes RNA G-quadruplex structures. Analysis of the protein and mRNA products of 84 cancer-related human genes identified Nectin-4 and CapG as G-quadruplex-controlled genes whose mRNAs harbor non-canonical G-quadruplex structures on their 5′UTR region. Further investigations revealed that the RNA G-quadruplex of CapG exhibits a structural polymorphism, suggesting a possible mechanism that ensures the translation repression in a KCl concentration range of 25–100 mM. The approach described in the present study sets the stage for further discoveries of RNA G-quadruplexes.
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Affiliation(s)
- Yousuke Katsuda
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Shin-Ichi Sato
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Maimi Inoue
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Hisashi Tsugawa
- Graduate School of Science and Technology, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori 036-8561, Japan
| | - Takuto Kamura
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Tomoki Kida
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Rio Matsumoto
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Sefan Asamitsu
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto 860-0811, Japan
| | - Norifumi Shioda
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto 860-0811, Japan.,Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe, Chuo-ku, Kumamoto 862-0973, Japan
| | - Shuhei Shiroto
- Graduate School of Science and Technology, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori 036-8561, Japan
| | - Yoshiki Oosawatsu
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Kenji Yatsuzuka
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Yusuke Kitamura
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Masaki Hagihara
- Graduate School of Science and Technology, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori 036-8561, Japan
| | - Toshihiro Ihara
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Motonari Uesugi
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.,School of Pharmacy, Fudan University, Shanghai 201203, China
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18
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Santos T, Miranda A, Imbert L, Monchaud D, Salgado GF, Cabrita EJ, Cruz C. Targeting a G-quadruplex from let-7e pre-miRNA with small molecules and nucleolin. J Pharm Biomed Anal 2022; 215:114757. [PMID: 35462282 DOI: 10.1016/j.jpba.2022.114757] [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: 12/12/2021] [Revised: 02/28/2022] [Accepted: 04/03/2022] [Indexed: 10/18/2022]
Abstract
Let-7e precursor microRNA has the potential to adopt a G-quadruplex (rG4) structure and recently, its roles in oncology have been the focus of much attention, as it is now known that let-7e pre-miRNA is frequently dysregulated in cancers. Therefore, it is crucial to unveil and fully characterize its ability to adopt a rG4 structure, which could be stabilized or destabilized by small molecules and proteins such as nucleolin, a protein that is deeply associated with miRNA biogenesis. Herein, by combining a set of different methods such as circular dichroism (CD), nuclear magnetic resonance (NMR), UV spectroscopy (thermal difference spectra (TDS) and isothermal difference spectra (IDS)) and polyacrylamide gel electrophoresis (PAGE), we demonstrate the formation of the rG4 structure found in let-7e pre-miRNA sequence in the presence of K+ (5'-GGGCUGAGGUAGGAGG-3'). The ability of eight small molecules (or ligands) to bind to and stabilize this rG4 structure was also fully assessed. The dissociation constants for each RNA G-quadruplex/ligand complex, determined by surface plasmon resonance (SPR), ranged in the 10-6 to 10-9 M range. Lastly, the binding of the rG4 structure to nucleolin in the presence and absence of ligands was evaluated via CD, SPR, PAGE and confocal microscopy. The small molecules 360 A and PDS demonstrated attractive properties to targetthe rG4 structure of let-7e pre-miRNA and control its biology. Our findings also highlighted that the interaction of TMPyP4 with the G-quadruplex of let-7e precursor miRNA could block the formation of the complex between the rG4 and nucleolin. Overall, this study introduces an approach to target the rG4 found in let-7e pre-miRNA which opens up a new opportunity to control the microRNA biogenesis.
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Affiliation(s)
- Tiago Santos
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, Covilhã 6200-506, Portugal
| | - André Miranda
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, Covilhã 6200-506, Portugal
| | - Lionel Imbert
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), Grenoble, France; Univ. Grenoble Alpes, CNRS, CEA, EMBL Integrated Structural Biology Grenoble (ISBG), Grenoble, France
| | - David Monchaud
- Institut de Chimie Moléculaire de l'Université de Bourgogne (ICMUB), CNRS UMR 6302, UBFC Dijon, Dijon 21078, France
| | - Gilmar F Salgado
- ARNA Laboratory, Université de Bordeaux, Inserm U1212, CNRS UMR 5320, IECB, Pessac 33607, France
| | - Eurico J Cabrita
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica 2829-516, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, Caparica 2819-516, Portugal
| | - Carla Cruz
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, Covilhã 6200-506, Portugal.
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19
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Georgakopoulos-Soares I, Parada GE, Hemberg M. Secondary structures in RNA synthesis, splicing and translation. Comput Struct Biotechnol J 2022; 20:2871-2884. [PMID: 35765654 PMCID: PMC9198270 DOI: 10.1016/j.csbj.2022.05.041] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/19/2022] [Accepted: 05/21/2022] [Indexed: 11/30/2022] Open
Abstract
Even though the functional role of mRNA molecules is primarily decided by the nucleotide sequence, several properties are determined by secondary structure conformations. Examples of secondary structures include long range interactions, hairpins, R-loops and G-quadruplexes and they are formed through interactions of non-adjacent nucleotides. Here, we discuss advances in our understanding of how secondary structures can impact RNA synthesis, splicing, translation and mRNA half-life. During RNA synthesis, secondary structures determine RNA polymerase II (RNAPII) speed, thereby influencing splicing. Splicing is also determined by RNA binding proteins and their binding rates are modulated by secondary structures. For the initiation of translation, secondary structures can control the choice of translation start site. Here, we highlight the mechanisms by which secondary structures modulate these processes, discuss advances in technologies to detect and study them systematically, and consider the roles of RNA secondary structures in disease.
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Affiliation(s)
- Ilias Georgakopoulos-Soares
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Guillermo E. Parada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5A 1A8, Canada
| | - Martin Hemberg
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA, USA
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20
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Gratal P, Arias-Pérez MS, Gude L. 1H-imidazo[4,5-f][1,10]phenanthroline carbohydrate conjugates: synthesis, DNA interactions and cytotoxic activity. Bioorg Chem 2022; 125:105851. [DOI: 10.1016/j.bioorg.2022.105851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 04/05/2022] [Accepted: 04/29/2022] [Indexed: 11/02/2022]
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21
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Rocca R, Scionti F, Nadai M, Moraca F, Maruca A, Costa G, Catalano R, Juli G, Di Martino MT, Ortuso F, Alcaro S, Tagliaferri P, Tassone P, Richter SN, Artese A. Chromene Derivatives as Selective TERRA G-Quadruplex RNA Binders with Antiproliferative Properties. Pharmaceuticals (Basel) 2022; 15:ph15050548. [PMID: 35631373 PMCID: PMC9147070 DOI: 10.3390/ph15050548] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 04/20/2022] [Accepted: 04/22/2022] [Indexed: 11/30/2022] Open
Abstract
In mammalian cells, telomerase transcribes telomeres in large G-rich non-coding RNA, known as telomeric repeat-containing RNA (TERRA), which folds into noncanonical nucleic acid secondary structures called G-quadruplexes (G4s). Since TERRA G4 has been shown to be involved in telomere length and translation regulation, it could provide valuable insight into fundamental biological processes, such as cancer growth, and TERRA G4 binders could represent an innovative strategy for cancer treatment. In this work, the three best candidates identified in our previous virtual screening campaign on bimolecular DNA/RNA G4s were investigated on the monomolecular Tel DNA and TERRA G4s by means of molecular modelling simulations and in vitro and in cell analysis. The results obtained in this work highlighted the stabilizing power of all the three candidates on TERRA G4. In particular, the two compounds characterized by a chromene scaffold were selective TERRA G4 binders, while the compound with a naphthyridine core acted as a dual Tel/TERRA G4-binder. A biophysical investigation by circular dichroism confirmed the relative stabilization efficiency of the compounds towards TERRA and Tel G4s. The TERRA G4 stabilizing hits showed good antiproliferative activity against colorectal and lung adenocarcinoma cell lines. Lead optimization to increase TERRA G4 stabilization may provide new powerful tools against cancer.
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Affiliation(s)
- Roberta Rocca
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, Campus “Salvatore Venuta”, Viale Europa, 88100 Catanzaro, Italy; (R.R.); (G.J.); (M.T.D.M.); (P.T.); (P.T.)
- Net4science Srl, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy; (F.M.); (A.M.); (G.C.); (R.C.); (F.O.); (S.A.)
| | - Francesca Scionti
- Institute for Biomedical Research and Innovation (IRIB), National Research Council of Italy (CNR), 98164 Messina, Italy;
| | - Matteo Nadai
- Department of Molecular Medicine, University of Padua, Via A. Gabelli 63, 35121 Padua, Italy;
| | - Federica Moraca
- Net4science Srl, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy; (F.M.); (A.M.); (G.C.); (R.C.); (F.O.); (S.A.)
- Department of Pharmacy, University of Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
| | - Annalisa Maruca
- Net4science Srl, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy; (F.M.); (A.M.); (G.C.); (R.C.); (F.O.); (S.A.)
- Department of Health Sciences, Magna Graecia University of Catanzaro, Campus “Salvatore Venuta”, Viale Europa, 88100 Catanzaro, Italy
| | - Giosuè Costa
- Net4science Srl, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy; (F.M.); (A.M.); (G.C.); (R.C.); (F.O.); (S.A.)
- Department of Health Sciences, Magna Graecia University of Catanzaro, Campus “Salvatore Venuta”, Viale Europa, 88100 Catanzaro, Italy
| | - Raffaella Catalano
- Net4science Srl, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy; (F.M.); (A.M.); (G.C.); (R.C.); (F.O.); (S.A.)
- Department of Health Sciences, Magna Graecia University of Catanzaro, Campus “Salvatore Venuta”, Viale Europa, 88100 Catanzaro, Italy
| | - Giada Juli
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, Campus “Salvatore Venuta”, Viale Europa, 88100 Catanzaro, Italy; (R.R.); (G.J.); (M.T.D.M.); (P.T.); (P.T.)
| | - Maria Teresa Di Martino
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, Campus “Salvatore Venuta”, Viale Europa, 88100 Catanzaro, Italy; (R.R.); (G.J.); (M.T.D.M.); (P.T.); (P.T.)
| | - Francesco Ortuso
- Net4science Srl, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy; (F.M.); (A.M.); (G.C.); (R.C.); (F.O.); (S.A.)
- Department of Health Sciences, Magna Graecia University of Catanzaro, Campus “Salvatore Venuta”, Viale Europa, 88100 Catanzaro, Italy
| | - Stefano Alcaro
- Net4science Srl, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy; (F.M.); (A.M.); (G.C.); (R.C.); (F.O.); (S.A.)
- Department of Health Sciences, Magna Graecia University of Catanzaro, Campus “Salvatore Venuta”, Viale Europa, 88100 Catanzaro, Italy
| | - Pierosandro Tagliaferri
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, Campus “Salvatore Venuta”, Viale Europa, 88100 Catanzaro, Italy; (R.R.); (G.J.); (M.T.D.M.); (P.T.); (P.T.)
| | - Pierfrancesco Tassone
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, Campus “Salvatore Venuta”, Viale Europa, 88100 Catanzaro, Italy; (R.R.); (G.J.); (M.T.D.M.); (P.T.); (P.T.)
| | - Sara N. Richter
- Department of Molecular Medicine, University of Padua, Via A. Gabelli 63, 35121 Padua, Italy;
- Correspondence: (S.N.R.); (A.A.)
| | - Anna Artese
- Net4science Srl, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy; (F.M.); (A.M.); (G.C.); (R.C.); (F.O.); (S.A.)
- Department of Health Sciences, Magna Graecia University of Catanzaro, Campus “Salvatore Venuta”, Viale Europa, 88100 Catanzaro, Italy
- Correspondence: (S.N.R.); (A.A.)
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22
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Holoubek J, Bednářová K, Haviernik J, Huvarová I, Dvořáková Z, Černý J, Outlá M, Salát J, Konkol'ová E, Boura E, Růžek D, Vorlíčková M, Eyer L, Renčiuk D. Guanine quadruplexes in the RNA genome of the tick-borne encephalitis virus: their role as a new antiviral target and in virus biology. Nucleic Acids Res 2022; 50:4574-4600. [PMID: 35420134 PMCID: PMC9071444 DOI: 10.1093/nar/gkac225] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 03/21/2022] [Accepted: 03/25/2022] [Indexed: 12/11/2022] Open
Abstract
We have identified seven putative guanine quadruplexes (G4) in the RNA genome of tick-borne encephalitis virus (TBEV), a flavivirus causing thousands of human infections and numerous deaths every year. The formation of G4s was confirmed by biophysical methods on synthetic oligonucleotides derived from the predicted TBEV sequences. TBEV-5, located at the NS4b/NS5 boundary and conserved among all known flaviviruses, was tested along with its mutated variants for interactions with a panel of known G4 ligands, for the ability to affect RNA synthesis by the flaviviral RNA-dependent RNA polymerase (RdRp) and for effects on TBEV replication fitness in cells. G4-stabilizing TBEV-5 mutations strongly inhibited RdRp RNA synthesis and exhibited substantially reduced replication fitness, different plaque morphology and increased sensitivity to G4-binding ligands in cell-based systems. In contrast, strongly destabilizing TBEV-5 G4 mutations caused rapid reversion to the wild-type genotype. Our results suggest that there is a threshold of stability for G4 sequences in the TBEV genome, with any deviation resulting in either dramatic changes in viral phenotype or a rapid return to this optimal level of G4 stability. The data indicate that G4s are critical elements for efficient TBEV replication and are suitable targets to tackle TBEV infection.
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Affiliation(s)
- Jiří Holoubek
- Veterinary Research Institute, Emerging Viral Diseases, Brno CZ-62100, Czech Republic.,Department of Experimental Biology, Faculty of Science, Masaryk University, CZ-62500 Brno, Czech Republic.,Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, CZ-37005 Ceske Budejovice, Czech Republic
| | - Klára Bednářová
- Department of Biophysics of Nucleic Acids, Institute of Biophysics of the Czech Academy of Sciences, Brno CZ-61200, Czech Republic
| | - Jan Haviernik
- Veterinary Research Institute, Emerging Viral Diseases, Brno CZ-62100, Czech Republic.,Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, CZ-37005 Ceske Budejovice, Czech Republic
| | - Ivana Huvarová
- Veterinary Research Institute, Emerging Viral Diseases, Brno CZ-62100, Czech Republic
| | - Zuzana Dvořáková
- Department of Biophysics of Nucleic Acids, Institute of Biophysics of the Czech Academy of Sciences, Brno CZ-61200, Czech Republic
| | - Jiří Černý
- Faculty of Tropical Agrisciences, Czech University of Life Sciences Prague, CZ-16500 Prague, Czech Republic
| | - Martina Outlá
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics of the Czech Academy of Sciences, Brno CZ-61200, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, CZ-62500 Brno, Czech Republic
| | - Jiří Salát
- Veterinary Research Institute, Emerging Viral Diseases, Brno CZ-62100, Czech Republic.,Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, CZ-37005 Ceske Budejovice, Czech Republic
| | - Eva Konkol'ová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy ofSciences, CZ-16000 Prague, Czech Republic
| | - Evzen Boura
- Institute of Organic Chemistry and Biochemistry of the Czech Academy ofSciences, CZ-16000 Prague, Czech Republic
| | - Daniel Růžek
- Veterinary Research Institute, Emerging Viral Diseases, Brno CZ-62100, Czech Republic.,Department of Experimental Biology, Faculty of Science, Masaryk University, CZ-62500 Brno, Czech Republic.,Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, CZ-37005 Ceske Budejovice, Czech Republic
| | - Michaela Vorlíčková
- Department of Biophysics of Nucleic Acids, Institute of Biophysics of the Czech Academy of Sciences, Brno CZ-61200, Czech Republic
| | - Luděk Eyer
- Veterinary Research Institute, Emerging Viral Diseases, Brno CZ-62100, Czech Republic.,Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, CZ-37005 Ceske Budejovice, Czech Republic
| | - Daniel Renčiuk
- Department of Biophysics of Nucleic Acids, Institute of Biophysics of the Czech Academy of Sciences, Brno CZ-61200, Czech Republic
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23
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Teng X, Dai Y, Li J. Methodological advances of bioanalysis and biochemical targeting of intracellular G-quadruplexes. EXPLORATION (BEIJING, CHINA) 2022; 2:20210214. [PMID: 37323879 PMCID: PMC10191030 DOI: 10.1002/exp.20210214] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 01/11/2022] [Indexed: 06/17/2023]
Abstract
G-quadruplexes (G4s) are a kind of non-canonical nucleic acid secondary structures, which involve in various biological processes in living cells. The relationships between G4s and human diseases, such as tumors, neurodegenerative diseases, and viral infections, have attracted great attention in the last decade. G4s are considered as a promising new target for disease treatment. For instance, G4 ligands are reported to be potentially effective in SARS-COV-2 treatment. However, because of the lack of analytical methods with high performance for the identification of intracellular G4s, the detailed mechanisms of the biofunctions of G4s remain elusive. Meanwhile, through demonstrating the principles of how the G4s systematically modulate the cellular processes with advanced detection methods, biochemical targeting of G4s in living cells can be realized by chemical and biological tools and becomes useful in biomedicine. This review highlights recent methodological advances about intracellular G4s and provides an outlook on the improvement of the bioanalysis and biochemical targeting tools of G4s.
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Affiliation(s)
- Xucong Teng
- Department of Chemistry, Center for BioAnalytical Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical BiologyTsinghua UniversityBeijingChina
| | - Yicong Dai
- Department of Chemistry, Center for BioAnalytical Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical BiologyTsinghua UniversityBeijingChina
| | - Jinghong Li
- Department of Chemistry, Center for BioAnalytical Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical BiologyTsinghua UniversityBeijingChina
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24
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Dai Y, Teng X, Li J. Single‐Cell Visualization of Monogenic RNA G‐quadruplex and Occupied G‐quadruplex Ratio through a Module‐Assembled Multifunctional Probes Assay (MAMPA). Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202111132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Yicong Dai
- Department of Chemistry Center for BioAnalytical Chemistry Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology Tsinghua University Beijing 100084 China
| | - Xucong Teng
- Department of Chemistry Center for BioAnalytical Chemistry Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology Tsinghua University Beijing 100084 China
| | - Jinghong Li
- Department of Chemistry Center for BioAnalytical Chemistry Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology Tsinghua University Beijing 100084 China
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25
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Masson T, Landras Guetta C, Laigre E, Cucchiarini A, Duchambon P, Teulade-Fichou MP, Verga D. BrdU immuno-tagged G-quadruplex ligands: a new ligand-guided immunofluorescence approach for tracking G-quadruplexes in cells. Nucleic Acids Res 2021; 49:12644-12660. [PMID: 34875077 PMCID: PMC8682774 DOI: 10.1093/nar/gkab1166] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 10/14/2021] [Accepted: 11/10/2021] [Indexed: 11/13/2022] Open
Abstract
G-quadruplexes (G4s) are secondary structures forming in G-rich nucleic acids. G4s are assumed to play critical roles in biology, nonetheless their detection in cells is still challenging. For tracking G4s, synthetic molecules (G4 ligands) can be used as reporters and have found wide application for this purpose through chemical functionalization with a fluorescent tag. However, this approach is limited by a low-labeling degree impeding precise visualization in specific subcellular regions. Herein, we present a new visualization strategy based on the immuno-recognition of 5-bromo-2′-deoxyuridine (5-BrdU) modified G4 ligands, functionalized prior- or post-G4-target binding by CuAAC. Remarkably, recognition of the tag by antibodies leads to the detection of the modified ligands exclusively when bound to a G4 target both in vitro, as shown by ELISA, and in cells, thereby providing a highly efficient G4-ligand Guided Immunofluorescence Staining (G4-GIS) approach. The obtained signal amplification revealed well-defined fluorescent foci located in the perinuclear space and RNase treatment revealed the preferential binding to G4-RNA. Furthermore, ligand treatment affected significantly BG4 foci formation in cells. Our work headed to the development of a new imaging approach combining the advantages of immunostaining and G4-recognition by G4 ligands leading to visualization of G4/ligands species in cells with unrivaled precision and sensitivity.
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Affiliation(s)
- Thibaut Masson
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, F-91405 Orsay, France.,CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405 Orsay, France
| | - Corinne Landras Guetta
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, F-91405 Orsay, France.,CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405 Orsay, France
| | - Eugénie Laigre
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, F-91405 Orsay, France.,CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405 Orsay, France
| | - Anne Cucchiarini
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, F-91405 Orsay, France.,CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405 Orsay, France
| | - Patricia Duchambon
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, F-91405 Orsay, France.,CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405 Orsay, France
| | - Marie-Paule Teulade-Fichou
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, F-91405 Orsay, France.,CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405 Orsay, France
| | - Daniela Verga
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, F-91405 Orsay, France.,CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405 Orsay, France
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26
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Miron CE, Chen M, Mergny JL, Petitjean A. Portrait of a Family of Highly Stabilizing and Selective Guanine Quadruplex Platinum(II)-Based Binders. Chemistry 2021; 28:e202103839. [PMID: 34862673 DOI: 10.1002/chem.202103839] [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: 10/25/2021] [Indexed: 11/12/2022]
Abstract
The long-standing history of platinum coordination complexes in nucleic acid recognition attests to the unique suitability of such species for therapeutic applications. Here, we report the synthetic exploration and development of a family of di-imine ligands, and their platinum(II) complexes, elaborated on a 3-(2-pyridyl)-[1,2,4]triazolo[4,3-a]pyridine platform which, in its unsubstituted form, has recently been shown to display exceptional capabilities for guanine quadruplex (G4) targeting. The identification of facile, high-yielding synthetic methods for the derivatization of this platform for the incorporation of additional sites of interactions with guanine quadruplex loops and grooves, along with the optimization of platinum(II) complexation methods, are discussed. Gratifyingly, preliminary biophysical screening of this novel family of binders validates all but one family members as robust G4 binders and highlights enhanced selectivity for quadruplex versus duplex DNA compared to the parent compound. These results bear promise for practical developments based on this platform.
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Affiliation(s)
- Caitlin E Miron
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, ON K7L3N6, Canada.,Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC H3A0B8, Canada
| | - Mickey Chen
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, ON K7L3N6, Canada
| | - Jean-Louis Mergny
- Institut Européen de Chimie et Biologie, 2 rue Escarpit, F-33607, Pessac, France.,Laboratoire d'Optique et Biosciences, École Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128, Palaiseau cedex, France
| | - Anne Petitjean
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, ON K7L3N6, Canada
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27
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Dai Y, Teng X, Li J. Single-cell Visualization of Monogenic RNA G-quadruplex and Occupied G-quadruplex Ratio through Module Assembled Multifunctional Probes Assay (MAMPA). Angew Chem Int Ed Engl 2021; 61:e202111132. [PMID: 34773681 DOI: 10.1002/anie.202111132] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/24/2021] [Indexed: 11/12/2022]
Abstract
G-quadruplexes (G4s), non-canonical nucleic acid secondary structure, regulate many biological functions and are considered as potential molecular targets for therapeutics of cancers. However, due to the lack of analytical methods, the regulating mechanism of monogenic G4s is still unclear. Here, we developed a Module Assembled Multifunctional Probes Assay (MAMPA) for visualizing endogenous G4s in individual genes in single cells. Two modular probes separately recognize G4 structures and the adjacent RNA sequences, and the module assembly enables imaging of G4s in an individual RNA with high specificity. Through imaging G4s in several individual genes, we found that G4s were steadily occupied by G4 Binding Proteins (G4BPs) in various mRNAs in every cell line and defined "Occupied G4 Ratio". In all, we demonstrated MAMPA was suitable for most experiment situations and found that Occupied G4 Ratios had the potential to become a new parameter for the study of G4s in living cells.
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Affiliation(s)
- Yicong Dai
- Tsinghua University, Department of Chemistry, 100084, CHINA
| | - Xucong Teng
- Tsinghua University, Department of Chemistry, CHINA
| | - Jinghong Li
- Tsinghua University, Department of Chemistry, Haidian Street, Beijing, CHINA
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28
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Chen H, Guo X, Li X, Tang Y, Sun H. An increase in DNA G-quadruplex formation in acute myelocytic leukemia is detected by a supramolecular probe. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 260:119968. [PMID: 34049005 DOI: 10.1016/j.saa.2021.119968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 05/14/2021] [Accepted: 05/16/2021] [Indexed: 06/12/2023]
Abstract
Acute myeloid leukemia (AML) is a common acute leukemia in both adults and children, with poor early detection and diagnosis. Therefore, identifying new indicators for AML detection is significant for effective treatment. Here, we developed a supramolecular probe that exhibits high specificity and sensitivity to G-quadruplex structures in physiological buffer solution, chromosomes, and cells. Using this probe, we tested the DNA extracted from different types of cells and found that the DNA extracted from human acute myeloid leukemia cells HL-60 and KG-1 enhanced the probe fluorescence more significantly than the DNA extracted from other cells. This phenomenon may be related to a large number of G-quadruplexes in acute myeloid leukemia cells, implicating that G-quadruplex levels may be a potential indicator for the detection of acute myeloid leukemia.
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Affiliation(s)
- Hongbo Chen
- Beijing National Laboratory for Molecular Sciences (BNLMS), State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, PR China; Shenzhou Space Biology Science and Technology Corporation, Ltd, China Academy of Space Technology, Beijing 100190, PR China
| | - Xiaomeng Guo
- Beijing National Laboratory for Molecular Sciences (BNLMS), State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Xinquan Li
- Department of Hematology, Tsinghua University Affiliated Beijing Tsinghua Changgung Hospital, Beijing 102218, PR China
| | - Yalin Tang
- Beijing National Laboratory for Molecular Sciences (BNLMS), State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China.
| | - Hongxia Sun
- Beijing National Laboratory for Molecular Sciences (BNLMS), State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, PR China.
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29
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Zou M, Li JY, Zhang MJ, Li JH, Huang JT, You PD, Liu SW, Zhou CQ. G-quadruplex binder pyridostatin as an effective multi-target ZIKV inhibitor. Int J Biol Macromol 2021; 190:178-188. [PMID: 34461156 DOI: 10.1016/j.ijbiomac.2021.08.121] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 08/15/2021] [Accepted: 08/16/2021] [Indexed: 12/13/2022]
Abstract
At present, there are still no anti-Zika virus (ZIKV) drugs or vaccines approved by FDA with accurate targets and antiviral mechanisms. Considering the RNA G-quadruplex sequences in ZIKV genome, it is very meaningful to develop G-quadruplex binders as potential anti-ZIKV drugs with novel and accurate targets. In this paper, five classical G-quadruplex binders including Ber, Braco 19, NiL, 360A and PDS have been chosen to discuss their interaction with ZIKV RNA G-quadruplexes. PDS shows higher binding affinity and thermal stability than the other G-quadruplex binders. This property is further evidenced in cells by immunofluorescence microscopy. And PDS shows higher anti-ZIKV activity (EC50 = 4.2 ± 0.4 μM) than the other G-quadruplex binders as well as the positive control ribavirin, with a low cytotoxicity. By time-of-addition assay, PDS exerts antiviral activity at the post-entry process of ZIKV replication cycle, thus inhibiting ZIKV mRNA replication and protein expression. Furthermore, PDS combines with ZIKV NS2B-NS3 protease and reduces its catalytic activity. This study suggests that G-quadruplex binder PDS is an effective multi-target ZIKV inhibitor, which provides more guidance to design some novel anti-ZIKV drugs targeting ZIKV RNA G-quadruplexes.
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Affiliation(s)
- Min Zou
- Guangdong Provincial Key Laboratory of New Drug Screening, Guangzhou Key Laboratory of Drug Research for Emerging Virus Prevention and Treatment, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China
| | - Jing-Yan Li
- Guangdong Provincial Key Laboratory of New Drug Screening, Guangzhou Key Laboratory of Drug Research for Emerging Virus Prevention and Treatment, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China
| | - Meng-Jia Zhang
- Guangdong Provincial Key Laboratory of New Drug Screening, Guangzhou Key Laboratory of Drug Research for Emerging Virus Prevention and Treatment, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China
| | - Jun-Hui Li
- Guangdong Provincial Key Laboratory of New Drug Screening, Guangzhou Key Laboratory of Drug Research for Emerging Virus Prevention and Treatment, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China
| | - Jun-Tao Huang
- Guangdong Provincial Key Laboratory of New Drug Screening, Guangzhou Key Laboratory of Drug Research for Emerging Virus Prevention and Treatment, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China
| | - Pei-Dan You
- Guangdong Provincial Key Laboratory of New Drug Screening, Guangzhou Key Laboratory of Drug Research for Emerging Virus Prevention and Treatment, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China
| | - Shu-Wen Liu
- Guangdong Provincial Key Laboratory of New Drug Screening, Guangzhou Key Laboratory of Drug Research for Emerging Virus Prevention and Treatment, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China.
| | - Chun-Qiong Zhou
- Guangdong Provincial Key Laboratory of New Drug Screening, Guangzhou Key Laboratory of Drug Research for Emerging Virus Prevention and Treatment, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China.
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30
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Takahashi S, Kotar A, Tateishi-Karimata H, Bhowmik S, Wang ZF, Chang TC, Sato S, Takenaka S, Plavec J, Sugimoto N. Chemical Modulation of DNA Replication along G-Quadruplex Based on Topology-Dependent Ligand Binding. J Am Chem Soc 2021; 143:16458-16469. [PMID: 34554731 DOI: 10.1021/jacs.1c05468] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Ligands that bind to and stabilize guanine-quadruplex (G4) structures to regulate DNA replication have therapeutic potential for cancer and neurodegenerative diseases. Because there are several G4 topologies, ligands that bind to their specific types may have the ability to preferentially regulate the replication of only certain genes. Here, we demonstrated that binding ligands stalled the replication of template DNA at G4, depending on different topologies. For example, naphthalene diimide derivatives bound to the G-quartet of G4 with an additional interaction between the ligand and the loop region of a hybrid G4 type from human telomeres, which efficiently repressed the replication of the G4. Thus, these inhibitory effects were not only stability-dependent but also topology-selective based on the manner in which G4 structures interacted with G4 ligands. Our original method, referred to as a quantitative study of topology-dependent replication (QSTR), was developed to evaluate correlations between replication rate and G4 stability. QSTR enabled the systematic categorization of ligands based on topology-dependent binding. It also demonstrated accuracy in determining quantitatively how G4 ligands control the intermediate state of replication and the kinetics of G4 unwinding. Hence, the QSTR index would facilitate the design of new drugs capable of controlling the topology-dependent regulation of gene expression.
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Affiliation(s)
- Shuntaro Takahashi
- FIBER (Frontier Institute for Biomolecular Engineering Research), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Anita Kotar
- Slovenian NMR Center, National Institute of Chemistry, SI-1000 Ljubljana, Slovenia
| | - Hisae Tateishi-Karimata
- FIBER (Frontier Institute for Biomolecular Engineering Research), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Sudipta Bhowmik
- Department of Biophysics, Molecular Biology and Bioinformatics, University College of Science, University of Calcutta, 92, A.P.C. Road, Kolkata 700009, India
| | - Zi-Fu Wang
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106, Taiwan
| | - Ta-Chau Chang
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106, Taiwan
| | - Shinobu Sato
- Department of Applied Chemistry, Kyushu Institute of Technology, Fukuoka 804-8550, Japan
| | - Shigeori Takenaka
- Department of Applied Chemistry, Kyushu Institute of Technology, Fukuoka 804-8550, Japan
| | - Janez Plavec
- Slovenian NMR Center, National Institute of Chemistry, SI-1000 Ljubljana, Slovenia
| | - Naoki Sugimoto
- FIBER (Frontier Institute for Biomolecular Engineering Research), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
- FIRST (Graduate School of Frontiers of Innovative Research in Science and Technology), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
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Targeting of Telomeric Repeat-Containing RNA G-Quadruplexes: From Screening to Biophysical and Biological Characterization of a New Hit Compound. Int J Mol Sci 2021; 22:ijms221910315. [PMID: 34638655 PMCID: PMC8508872 DOI: 10.3390/ijms221910315] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/10/2021] [Accepted: 09/22/2021] [Indexed: 12/19/2022] Open
Abstract
DNA G-quadruplex (G4) structures, either within gene promoter sequences or at telomeres, have been extensively investigated as potential small-molecule therapeutic targets. However, although G4s forming at the telomeric DNA have been extensively investigated as anticancer targets, few studies focus on the telomeric repeat-containing RNA (TERRA), transcribed from telomeres, as potential pharmacological targets. Here, a virtual screening approach to identify a library of drug-like putative TERRA G4 binders, in tandem with circular dichroism melting assay to study their TERRA G4-stabilizing properties, led to the identification of a new hit compound. The affinity of this compound for TERRA RNA and some DNA G4s was analyzed through several biophysical techniques and its biological activity investigated in terms of antiproliferative effect, DNA damage response (DDR) activation, and TERRA RNA expression in high vs. low TERRA-expressing human cancer cells. The selected hit showed good affinity for TERRA G4 and no binding to double-stranded DNA. In addition, biological assays showed that this compound is endowed with a preferential cytotoxic effect on high TERRA-expressing cells, where it induces a DDR at telomeres, probably by displacing TERRA from telomeres. Our studies demonstrate that the identification of TERRA G4-targeting drugs with potential pharmacological effects is achievable, shedding light on new perspectives aimed at discovering new anticancer agents targeting these G4 structures.
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Caterino M, Paeschke K. Action and function of helicases on RNA G-quadruplexes. Methods 2021; 204:110-125. [PMID: 34509630 PMCID: PMC9236196 DOI: 10.1016/j.ymeth.2021.09.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/02/2021] [Accepted: 09/07/2021] [Indexed: 12/12/2022] Open
Abstract
Methodological progresses and piling evidence prove the rG4 biology in vivo. rG4s step in virtually every aspect of RNA biology. Helicases unwinding of rG4s is a fine regulatory layer to the downstream processes and general cell homeostasis. The current knowledge is however limited to a few cell lines. The regulation of helicases themselves is delineating as a important question. Non-helicase rG4-processing proteins likely play a role.
The nucleic acid structure called G-quadruplex (G4) is currently discussed to function in nucleic acid-based mechanisms that influence several cellular processes. They can modulate the cellular machinery either positively or negatively, both at the DNA and RNA level. The majority of what we know about G4 biology comes from DNA G4 (dG4) research. RNA G4s (rG4), on the other hand, are gaining interest as researchers become more aware of their role in several aspects of cellular homeostasis. In either case, the correct regulation of G4 structures within cells is essential and demands specialized proteins able to resolve them. Small changes in the formation and unfolding of G4 structures can have severe consequences for the cells that could even stimulate genome instability, apoptosis or proliferation. Helicases are the most relevant negative G4 regulators, which prevent and unfold G4 formation within cells during different pathways. Yet, and despite their importance only a handful of rG4 unwinding helicases have been identified and characterized thus far. This review addresses the current knowledge on rG4s-processing helicases with a focus on methodological approaches. An example of a non-helicase rG4s-unwinding protein is also briefly described.
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Affiliation(s)
- Marco Caterino
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, 53127 Bonn, Germany
| | - Katrin Paeschke
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, 53127 Bonn, Germany.
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Translational control by DHX36 binding to 5'UTR G-quadruplex is essential for muscle stem-cell regenerative functions. Nat Commun 2021; 12:5043. [PMID: 34413292 PMCID: PMC8377060 DOI: 10.1038/s41467-021-25170-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 06/06/2021] [Indexed: 12/30/2022] Open
Abstract
Skeletal muscle has a remarkable ability to regenerate owing to its resident stem cells (also called satellite cells, SCs). SCs are normally quiescent; when stimulated by damage, they activate and expand to form new fibers. The mechanisms underlying SC proliferative progression remain poorly understood. Here we show that DHX36, a helicase that unwinds RNA G-quadruplex (rG4) structures, is essential for muscle regeneration by regulating SC expansion. DHX36 (initially named RHAU) is barely expressed at quiescence but is highly induced during SC activation and proliferation. Inducible deletion of Dhx36 in adult SCs causes defective proliferation and muscle regeneration after damage. System-wide mapping in proliferating SCs reveals DHX36 binding predominantly to rG4 structures at various regions of mRNAs, while integrated polysome profiling shows that DHX36 promotes mRNA translation via 5′-untranslated region (UTR) rG4 binding. Furthermore, we demonstrate that DHX36 specifically regulates the translation of Gnai2 mRNA by unwinding its 5′ UTR rG4 structures and identify GNAI2 as a downstream effector of DHX36 for SC expansion. Altogether, our findings uncover DHX36 as an indispensable post-transcriptional regulator of SC function and muscle regeneration acting through binding and unwinding rG4 structures at 5′ UTR of target mRNAs. Skeletal muscle stem cells (or satellite cells, SCs) are normally quiescent but activate and expand in response to injury. Here the authors show that induction of DHX36 helicase during SC activation promotes mRNA translation by binding to 5′UTR mRNA G-quadruplexes (rG4) in targets including Gnai2 and unwinding them.
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Santos T, Salgado GF, Cabrita EJ, Cruz C. G-Quadruplexes and Their Ligands: Biophysical Methods to Unravel G-Quadruplex/Ligand Interactions. Pharmaceuticals (Basel) 2021; 14:769. [PMID: 34451866 PMCID: PMC8401999 DOI: 10.3390/ph14080769] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 07/31/2021] [Accepted: 08/03/2021] [Indexed: 12/12/2022] Open
Abstract
Progress in the design of G-quadruplex (G4) binding ligands relies on the availability of approaches that assess the binding mode and nature of the interactions between G4 forming sequences and their putative ligands. The experimental approaches used to characterize G4/ligand interactions can be categorized into structure-based methods (circular dichroism (CD), nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography), affinity and apparent affinity-based methods (surface plasmon resonance (SPR), isothermal titration calorimetry (ITC) and mass spectrometry (MS)), and high-throughput methods (fluorescence resonance energy transfer (FRET)-melting, G4-fluorescent intercalator displacement assay (G4-FID), affinity chromatography and microarrays. Each method has unique advantages and drawbacks, which makes it essential to select the ideal strategies for the biological question being addressed. The structural- and affinity and apparent affinity-based methods are in several cases complex and/or time-consuming and can be combined with fast and cheap high-throughput approaches to improve the design and development of new potential G4 ligands. In recent years, the joint use of these techniques permitted the discovery of a huge number of G4 ligands investigated for diagnostic and therapeutic purposes. Overall, this review article highlights in detail the most commonly used approaches to characterize the G4/ligand interactions, as well as the applications and types of information that can be obtained from the use of each technique.
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Affiliation(s)
- Tiago Santos
- CICS-UBI—Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal;
| | - Gilmar F. Salgado
- ARNA Laboratory, Université de Bordeaux, Inserm U1212, CNRS UMR 5320, IECB, 33607 Pessac, France;
| | - Eurico J. Cabrita
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal;
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
| | - Carla Cruz
- CICS-UBI—Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal;
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Transcription/Replication Conflicts in Tumorigenesis and Their Potential Role as Novel Therapeutic Targets in Multiple Myeloma. Cancers (Basel) 2021; 13:cancers13153755. [PMID: 34359660 PMCID: PMC8345052 DOI: 10.3390/cancers13153755] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/13/2021] [Accepted: 07/22/2021] [Indexed: 12/24/2022] Open
Abstract
Simple Summary Multiple myeloma is a hematologic cancer characterized by the accumulation of malignant plasma cells in the bone marrow. It remains a mostly incurable disease due to the inability to overcome refractory disease and drug-resistant relapse. Oncogenic transformation of PC in multiple myeloma is thought to occur within the secondary lymphoid organs. However, the precise molecular events leading to myelomagenesis remain obscure. Here, we identified genes involved in the prevention and the resolution of conflicts between the replication and transcription significantly overexpressed during the plasma cell differentiation process and in multiple myeloma cells. We discussed the potential role of these factors in myelomagenesis and myeloma biology. The specific targeting of these factors might constitute a new therapeutic strategy in multiple myeloma. Abstract Plasma cells (PCs) have an essential role in humoral immune response by secretion of antibodies, and represent the final stage of B lymphocytes differentiation. During this differentiation, the pre-plasmablastic stage is characterized by highly proliferative cells that start to secrete immunoglobulins (Igs). Thus, replication and transcription must be tightly regulated in these cells to avoid transcription/replication conflicts (TRCs), which could increase replication stress and lead to genomic instability. In this review, we analyzed expression of genes involved in TRCs resolution during B to PC differentiation and identified 41 genes significantly overexpressed in the pre-plasmablastic stage. This illustrates the importance of mechanisms required for adequate processing of TRCs during PCs differentiation. Furthermore, we identified that several of these factors were also found overexpressed in purified PCs from patients with multiple myeloma (MM) compared to normal PCs. Malignant PCs produce high levels of Igs concomitantly with cell cycle deregulation. Therefore, increasing the TRCs occurring in MM cells could represent a potent therapeutic strategy for MM patients. Here, we describe the potential roles of TRCs resolution factors in myelomagenesis and discuss the therapeutic interest of targeting the TRCs resolution machinery in MM.
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Lyu K, Chow EYC, Mou X, Chan TF, Kwok CK. RNA G-quadruplexes (rG4s): genomics and biological functions. Nucleic Acids Res 2021; 49:5426-5450. [PMID: 33772593 PMCID: PMC8191793 DOI: 10.1093/nar/gkab187] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 03/02/2021] [Accepted: 03/24/2021] [Indexed: 02/07/2023] Open
Abstract
G-quadruplexes (G4s) are non-classical DNA or RNA secondary structures that have been first observed decades ago. Over the years, these four-stranded structural motifs have been demonstrated to have significant regulatory roles in diverse biological processes, but challenges remain in detecting them globally and reliably. Compared to DNA G4s (dG4s), the study of RNA G4s (rG4s) has received less attention until recently. In this review, we will summarize the innovative high-throughput methods recently developed to detect rG4s on a transcriptome-wide scale, highlight the many novel and important functions of rG4 being discovered in vivo across the tree of life, and discuss the key biological questions to be addressed in the near future.
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Affiliation(s)
- Kaixin Lyu
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Eugene Yui-Ching Chow
- School of Life Sciences, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Xi Mou
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Ting-Fung Chan
- School of Life Sciences, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Chun Kit Kwok
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China.,Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China
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Zhang X, Spiegel J, Martínez Cuesta S, Adhikari S, Balasubramanian S. Chemical profiling of DNA G-quadruplex-interacting proteins in live cells. Nat Chem 2021; 13:626-633. [PMID: 34183817 PMCID: PMC8245323 DOI: 10.1038/s41557-021-00736-9] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 05/18/2021] [Indexed: 12/17/2022]
Abstract
DNA-protein interactions regulate critical biological processes. Identifying proteins that bind to specific, functional genomic loci is essential to understand the underlying regulatory mechanisms on a molecular level. Here we describe a co-binding-mediated protein profiling (CMPP) strategy to investigate the interactome of DNA G-quadruplexes (G4s) in native chromatin. CMPP involves cell-permeable, functionalized G4-ligand probes that bind endogenous G4s and subsequently crosslink to co-binding G4-interacting proteins in situ. We first showed the robustness of CMPP by proximity labelling of a G4 binding protein in vitro. Employing this approach in live cells, we then identified hundreds of putative G4-interacting proteins from various functional classes. Next, we confirmed a high G4-binding affinity and selectivity for several newly discovered G4 interactors in vitro, and we validated direct G4 interactions for a functionally important candidate in cellular chromatin using an independent approach. Our studies provide a chemical strategy to map protein interactions of specific nucleic acid features in living cells.
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Affiliation(s)
- Xiaoyun Zhang
- Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Jochen Spiegel
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | - Sergio Martínez Cuesta
- Department of Chemistry, University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
- Data Sciences and Quantitative Biology, Discovery Sciences, AstraZeneca, Cambridge, UK
| | | | - Shankar Balasubramanian
- Department of Chemistry, University of Cambridge, Cambridge, UK.
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK.
- School of Clinical Medicine, University of Cambridge, Cambridge, UK.
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38
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Palma E, Carvalho J, Cruz C, Paulo A. Metal-Based G-Quadruplex Binders for Cancer Theranostics. Pharmaceuticals (Basel) 2021; 14:605. [PMID: 34201682 PMCID: PMC8308583 DOI: 10.3390/ph14070605] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/21/2021] [Accepted: 06/21/2021] [Indexed: 12/11/2022] Open
Abstract
The ability of fluorescent small molecules, such as metal complexes, to selectively recognize G-quadruplex (G4) structures has opened a route to develop new probes for the visualization of these DNA structures in cells. The main goal of this review is to update the most recent research efforts towards the development of novel cancer theranostic agents using this type of metal-based probes that specifically recognize G4 structures. This encompassed a comprehensive overview of the most significant progress in the field, namely based on complexes with Cu, Pt, and Ru that are among the most studied metals to obtain this class of molecules. It is also discussed the potential interest of obtaining G4-binders with medical radiometals (e.g., 99mTc, 111In, 64Cu, 195mPt) suitable for diagnostic and/or therapeutic applications within nuclear medicine modalities, in order to enable their theranostic potential.
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Affiliation(s)
- Elisa Palma
- C2TN-Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10, 2695-066 Bobadela LRS, Portugal;
| | - Josué Carvalho
- CICS-UBI-Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal; (J.C.); (C.C.)
| | - Carla Cruz
- CICS-UBI-Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal; (J.C.); (C.C.)
| | - António Paulo
- C2TN-Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10, 2695-066 Bobadela LRS, Portugal;
- DECN-Departamento de Engenharia e Ciências Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10, 2695-066 Bobadela LRS, Portugal
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Roy S, Ali A, Bhattacharya S. Theoretical Insight into the Library Screening Approach for Binding of Intermolecular G-Quadruplex RNA and Small Molecules through Docking and Molecular Dynamics Simulation Studies. J Phys Chem B 2021; 125:5489-5501. [PMID: 34029082 DOI: 10.1021/acs.jpcb.0c10991] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The interactions of intermolecular G-quadruplex RNA and small molecules have been investigated by computational studies. Various anthraquinone, bisbenzimidazole, and carbazole-benzimidazole based ligands have shown a distinct preference to G-quadruplex structures as opposed to the corresponding duplex forms of DNA that were docked with telomeric G-quadruplex RNA. The comparative binding study of such ligands with G-quadruplex (G4) RNA showed higher binding affinities toward carbazole-benzimidazole ligands than those of the anthraquinone and bisbenzimidazole based ligands. A molecular dynamics simulation study was used to examine quadruplex-ligand interactions. Analysis of the binding free energy indicated the formation of the thermodynamically favorable RNA-ligand complex. The formation of several H-bonding interactions and the change of the solvent accessible surface area (SASA) also support the effective binding of the carbazole-benzimidazole ligands with G4 RNA structures. Thus, the library screening approach has assisted in getting a structure-activity relationship for the selected small molecules toward the G-quadruplex RNA binding, which can be applied in the targeting of G-quadruplex RNA medicated anticancer therapeutics.
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Affiliation(s)
- Soma Roy
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Asfa Ali
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Santanu Bhattacharya
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, Karnataka 560012, India.,School of Applied & Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata, West Bengal 700032, India
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40
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Ye S, Chen Z, Zhang X, Li F, Guo L, Hou XM, Wu WQ, Wang J, Liu C, Zheng K, Sun B. Proximal Single-Stranded RNA Destabilizes Human Telomerase RNA G-Quadruplex and Induces Its Distinct Conformers. J Phys Chem Lett 2021; 12:3361-3366. [PMID: 33783224 DOI: 10.1021/acs.jpclett.1c00250] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Single-stranded guanine-rich RNA sequences have a propensity to fold into compact G-quadruplexes (RG4s). The conformational transitions of these molecules provide an important way to regulate their biological functions. Here, we examined the stability and conformation of an RG4-forming sequence identified near the end of human telomerase RNA. We found that a proximal single-stranded (ss) RNA significantly impairs RG4 stability at physiological K+ concentrations, resulting in a reduced RG4 rupture force of ∼ 24.4 pN and easier accessibility of the G-rich sequence. The destabilizing effect requires a minimum of six nucleotides of ssRNA and is effective at either end of RG4. Remarkably, this RG4-forming sequence, under the influence of such a proximal ssRNA, exhibits interconversions between at least three less stable RG4 conformers that might represent potential intermediates along its folding/unfolding pathway. This work provides insights into the stability and folding dynamics of RG4 that are essential for understanding its biological functions.
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Affiliation(s)
- Shasha Ye
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ziting Chen
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xia Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Fangfang Li
- State Key Laboratory of Reproductive Medicine, Center for Global Health, Nanjing Medical University, Nanjing, 211166, China
| | - Lijuan Guo
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xi-Miao Hou
- College of Life Sciences, Northwest A&F University, Yangling, 712100, China
| | - Wen-Qiang Wu
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, 475001, China
| | - Jian Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Cong Liu
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Ke Zheng
- State Key Laboratory of Reproductive Medicine, Center for Global Health, Nanjing Medical University, Nanjing, 211166, China
| | - Bo Sun
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
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Lejault P, Mitteaux J, Sperti FR, Monchaud D. How to untie G-quadruplex knots and why? Cell Chem Biol 2021; 28:436-455. [PMID: 33596431 DOI: 10.1016/j.chembiol.2021.01.015] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 12/08/2020] [Accepted: 01/20/2021] [Indexed: 12/12/2022]
Abstract
For over two decades, the prime objective of the chemical biology community studying G-quadruplexes (G4s) has been to use chemicals to interact with and stabilize G4s in cells to obtain mechanistic interpretations. This strategy has been undoubtedly successful, as demonstrated by recent advances. However, these insights have also led to a fundamental rethinking of G4-targeting strategies: due to the prevalence of G4s in the human genome, transcriptome, and ncRNAome (collectively referred to as the G4ome), and their involvement in human diseases, should we continue developing G4-stabilizing ligands or should we invest in designing molecular tools to unfold G4s? Here, we first focus on how, when, and where G4s fold in cells; then, we describe the enzymatic systems that have evolved to counteract G4 folding and how they have been used as tools to manipulate G4s in cells; finally, we present strategies currently being implemented to devise new molecular G4 unwinding agents.
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Affiliation(s)
- Pauline Lejault
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon, France
| | - Jérémie Mitteaux
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon, France
| | - Francesco Rota Sperti
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon, France
| | - David Monchaud
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon, France.
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Reznichenko O, Cucchiarini A, Gabelica V, Granzhan A. Quadruplex DNA-guided ligand selection from dynamic combinatorial libraries of acylhydrazones. Org Biomol Chem 2021; 19:379-386. [PMID: 33325973 DOI: 10.1039/d0ob01908a] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Dynamic combinatorial libraries of acylhydrazones were prepared from diacylhydrazides and several cationic or neutral aldehydes in the presence of 5-methoxyanthranilic acid catalyst. Pull-down experiments with magnetic beads functionalized with a G-quadruplex (G4)-forming oligonucleotide led to the identification of putative ligands, which were resynthesized or emulated by close structural analogues. G4-binding properties of novel derivatives were assessed by fluorimetric titrations, mass spectrometry and thermal denaturation experiments, giving evidence of strong binding (Kd < 10 nM) for two compounds.
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Affiliation(s)
- Oksana Reznichenko
- CNRS UMR9187, Inserm U1196, Institut Curie, PSL Research University, 91405 Orsay, France. and CNRS UMR9187, Inserm U1196, Université Paris Saclay, 91405 Orsay, France
| | - Anne Cucchiarini
- CNRS UMR9187, Inserm U1196, Institut Curie, PSL Research University, 91405 Orsay, France. and CNRS UMR9187, Inserm U1196, Université Paris Saclay, 91405 Orsay, France
| | - Valérie Gabelica
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, 33600 Pessac, France
| | - Anton Granzhan
- CNRS UMR9187, Inserm U1196, Institut Curie, PSL Research University, 91405 Orsay, France. and CNRS UMR9187, Inserm U1196, Université Paris Saclay, 91405 Orsay, France
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Pomeislová A, Vrzal L, Kozák J, Dobiaš J, Hubálek M, Dvořáková H, Reyes‐Gutiérrez PE, Teplý F, Veverka V. Kinetic Target-Guided Synthesis of Small-Molecule G-Quadruplex Stabilizers. ChemistryOpen 2020; 9:1236-1250. [PMID: 33304739 PMCID: PMC7713561 DOI: 10.1002/open.202000261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 11/02/2020] [Indexed: 12/25/2022] Open
Abstract
The formation of a G-quadruplex motif in the promoter region of the c-MYC protooncogene prevents its expression. Accordingly, G-quadruplex stabilization by a suitable ligand may be a viable approach for anticancer therapy. In our study, we used the 4-(4-methylpiperazin-1-yl)aniline molecule, previously identified as a fragment library screen hit, as a template for the SAR-guided design of a new small library of clickable fragments and subjected them to click reactions, including kinetic target-guided synthesis in the presence of a G-quadruplex forming oligonucleotide Pu24. We tested the clickable fragments and products of click reactions for their G-quadruplex stabilizing activity and determined their mode of binding to the c-MYC G-quadruplex by NMR spectroscopy. The enhanced stabilizing potency of click products in biology assays (FRET, Polymerase extension assay) matched the increased yields of in situ click reactions. In conclusion, we identified the newly synthesized click products of bis-amino derivatives of 4-(4-methylpiperazin-1-yl)aniline as potent stabilizers of c-MYC G-quadruplex, and their further evolution may lead to the development of an efficient tool for cancer treatment.
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Affiliation(s)
- Alice Pomeislová
- Institute of Organic Chemistry and BiochemistryThe Czech Academy of Sciences Flemingovo nam. 2PragueCzech Republic
- Department of Organic ChemistryCharles UniversityPragueCzech Republic
| | - Lukáš Vrzal
- Institute of Organic Chemistry and BiochemistryThe Czech Academy of Sciences Flemingovo nam. 2PragueCzech Republic
- NMR laboratoryUniversity of Chemistry and TechnologyPragueCzech Republic
| | - Jaroslav Kozák
- Institute of Organic Chemistry and BiochemistryThe Czech Academy of Sciences Flemingovo nam. 2PragueCzech Republic
| | - Juraj Dobiaš
- Institute of Organic Chemistry and BiochemistryThe Czech Academy of Sciences Flemingovo nam. 2PragueCzech Republic
| | - Martin Hubálek
- Institute of Organic Chemistry and BiochemistryThe Czech Academy of Sciences Flemingovo nam. 2PragueCzech Republic
| | - Hana Dvořáková
- NMR laboratoryUniversity of Chemistry and TechnologyPragueCzech Republic
| | - Paul E. Reyes‐Gutiérrez
- Institute of Organic Chemistry and BiochemistryThe Czech Academy of Sciences Flemingovo nam. 2PragueCzech Republic
| | - Filip Teplý
- Institute of Organic Chemistry and BiochemistryThe Czech Academy of Sciences Flemingovo nam. 2PragueCzech Republic
| | - Václav Veverka
- Institute of Organic Chemistry and BiochemistryThe Czech Academy of Sciences Flemingovo nam. 2PragueCzech Republic
- Department of Cell BiologyCharles UniversityPragueCzech Republic
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44
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Gagliardi D, Costamagna G, Taiana M, Andreoli L, Biella F, Bersani M, Bresolin N, Comi GP, Corti S. Insights into disease mechanisms and potential therapeutics for C9orf72-related amyotrophic lateral sclerosis/frontotemporal dementia. Ageing Res Rev 2020; 64:101172. [PMID: 32971256 DOI: 10.1016/j.arr.2020.101172] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 08/31/2020] [Indexed: 12/12/2022]
Abstract
In 2011, a hexanucleotide repeat expansion (HRE) in the noncoding region of C9orf72 was associated with the most frequent genetic cause of frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS). The main pathogenic mechanisms in C9-ALS/FTD are haploinsufficiency of the C9orf72 protein and gain of function toxicity from bidirectionally-transcribed repeat-containing RNAs and dipeptide repeat proteins (DPRs) resulting from non-canonical RNA translation. Additionally, abnormalities in different downstream cellular mechanisms, such as nucleocytoplasmic transport and autophagy, play a role in pathogenesis. Substantial research efforts using in vitro and in vivo models have provided valuable insights into the contribution of each mechanism in disease pathogenesis. However, conflicting evidence exists, and a unifying theory still lacks. Here, we provide an overview of the recently published literature on clinical, neuropathological and molecular features of C9-ALS/FTD. We highlight the supposed neuronal role of C9orf72 and the HRE pathogenic cascade, mainly focusing on the contribution of RNA foci and DPRs to neurodegeneration and discussing the several downstream mechanisms. We summarize the emerging biochemical and neuroimaging biomarkers, as well as the potential therapeutic approaches. Despite promising results, a specific disease-modifying treatment is still not available to date and greater insights into disease mechanisms may help in this direction.
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Affiliation(s)
- Delia Gagliardi
- Dino Ferrari Centre, Neuroscience Section, Department of Pathophysiology and Transplantation (DEPT), University of Milan, Via Francesco Sforza 35, 20122 Milan, Italy
| | - Gianluca Costamagna
- Dino Ferrari Centre, Neuroscience Section, Department of Pathophysiology and Transplantation (DEPT), University of Milan, Via Francesco Sforza 35, 20122 Milan, Italy
| | - Michela Taiana
- Dino Ferrari Centre, Neuroscience Section, Department of Pathophysiology and Transplantation (DEPT), University of Milan, Via Francesco Sforza 35, 20122 Milan, Italy
| | - Luca Andreoli
- Dino Ferrari Centre, Neuroscience Section, Department of Pathophysiology and Transplantation (DEPT), University of Milan, Via Francesco Sforza 35, 20122 Milan, Italy
| | - Fabio Biella
- Dino Ferrari Centre, Neuroscience Section, Department of Pathophysiology and Transplantation (DEPT), University of Milan, Via Francesco Sforza 35, 20122 Milan, Italy
| | - Margherita Bersani
- Dino Ferrari Centre, Neuroscience Section, Department of Pathophysiology and Transplantation (DEPT), University of Milan, Via Francesco Sforza 35, 20122 Milan, Italy
| | - Nereo Bresolin
- Dino Ferrari Centre, Neuroscience Section, Department of Pathophysiology and Transplantation (DEPT), University of Milan, Via Francesco Sforza 35, 20122 Milan, Italy; Neurology Unit, IRCCS Foundation Ca' Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122, Milan, Italy
| | - Giacomo Pietro Comi
- Dino Ferrari Centre, Neuroscience Section, Department of Pathophysiology and Transplantation (DEPT), University of Milan, Via Francesco Sforza 35, 20122 Milan, Italy; Neurology Unit, IRCCS Foundation Ca' Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122, Milan, Italy
| | - Stefania Corti
- Dino Ferrari Centre, Neuroscience Section, Department of Pathophysiology and Transplantation (DEPT), University of Milan, Via Francesco Sforza 35, 20122 Milan, Italy; Neurology Unit, IRCCS Foundation Ca' Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122, Milan, Italy.
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45
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Ciszewski L, Lu-Nguyen N, Slater A, Brennan A, Williams HEL, Dickson G, Searle MS, Popplewell L. G-quadruplex ligands mediate downregulation of DUX4 expression. Nucleic Acids Res 2020; 48:4179-4194. [PMID: 32182342 PMCID: PMC7192601 DOI: 10.1093/nar/gkaa146] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 01/29/2020] [Accepted: 03/03/2020] [Indexed: 12/26/2022] Open
Abstract
Abnormal DUX4 expression in skeletal muscles plays a key role in facioscapulohumeral muscular dystrophy (FSHD) pathogenesis, although the molecular mechanisms regulating DUX4 expression are not fully defined. Using bioinformatic analysis of the genomic DUX4 locus, we have identified a number of putative G-quadruplexes (GQs) forming sequences. Their presence was confirmed in synthetic oligonucleotiode sequences derived from the enhancer, promoter and transcript of DUX4 through circular dichroism and nuclear magnetic resonance analysis. We further examined the binding affinity of a naturally occurring GQ stabilizing compound, berberine, to these non-canonical genetic structures using UV–Vis and fluorescence spectroscopy. Subsequent in vitro study in FSHD patient myoblasts indicated that berberine treatment reduced DUX4 expression and also expression of genes normally switched on by DUX4. Further investigation in a mouse model overexpressing exogenous DUX4 confirmed the therapeutic effects of berberine in downregulating DUX4 protein expression, inhibiting muscle fibrosis, and consequently rescuing muscle function. Our data demonstrate for the first time that GQs are present in the DUX4 locus and that the GQ interactive ligand reduces DUX4 expression suggesting potential role of GQs in FSHD pathogenesis. Our work provides the basis of a novel therapeutic strategy for the treatment of FSHD.
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Affiliation(s)
- Lukasz Ciszewski
- Department of Biological Sciences, Royal Holloway-University of London, Egham, Surrey TW20 0EX, UK
| | - Ngoc Lu-Nguyen
- Department of Biological Sciences, Royal Holloway-University of London, Egham, Surrey TW20 0EX, UK
| | - Alex Slater
- Centre for Biomolecular Sciences, School of Chemistry, University Park, University of Nottingham, Nottingham NG7 2RD, UK
| | - Andrew Brennan
- Centre for Biomolecular Sciences, School of Chemistry, University Park, University of Nottingham, Nottingham NG7 2RD, UK
| | - Huw E L Williams
- Centre for Biomolecular Sciences, School of Chemistry, University Park, University of Nottingham, Nottingham NG7 2RD, UK
| | - George Dickson
- Department of Biological Sciences, Royal Holloway-University of London, Egham, Surrey TW20 0EX, UK
| | - Mark S Searle
- Centre for Biomolecular Sciences, School of Chemistry, University Park, University of Nottingham, Nottingham NG7 2RD, UK
| | - Linda Popplewell
- Department of Biological Sciences, Royal Holloway-University of London, Egham, Surrey TW20 0EX, UK
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46
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Paul R, Dutta D, Paul R, Dash J. Target-Directed Azide-Alkyne Cycloaddition for Assembling HIV-1 TAR RNA Binding Ligands. Angew Chem Int Ed Engl 2020; 59:12407-12411. [PMID: 32329147 PMCID: PMC7687225 DOI: 10.1002/anie.202003461] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Indexed: 01/05/2023]
Abstract
The highly conserved HIV-1 transactivation response element (TAR) binds to the trans-activator protein Tat and facilitates viral replication in its latent state. The inhibition of Tat-TAR interactions by selectively targeting TAR RNA has been used as a strategy to develop potent antiviral agents. Therefore, HIV-1 TAR RNA represents a paradigmatic system for therapeutic intervention. Herein, we have employed biotin-tagged TAR RNA to assemble its own ligands from a pool of reactive azide and alkyne building blocks. To identify the binding sites and selectivity of the ligands, the in situ cycloaddition has been further performed using control nucleotide (TAR DNA and TAR RNA without bulge) templates. The hit triazole-linked thiazole peptidomimetic products have been isolated from the biotin-tagged target templates using streptavidin beads. The major triazole lead generated by the TAR RNA presumably binds in the bulge region, shows specificity for TAR RNA over TAR DNA, and inhibits Tat-TAR interactions.
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Affiliation(s)
- Rakesh Paul
- School of Chemical SciencesIndian Association for the Cultivation of ScienceJadavpurKolkata700 032India
| | - Debasish Dutta
- School of Chemical SciencesIndian Association for the Cultivation of ScienceJadavpurKolkata700 032India
| | - Raj Paul
- School of Chemical SciencesIndian Association for the Cultivation of ScienceJadavpurKolkata700 032India
| | - Jyotirmayee Dash
- School of Chemical SciencesIndian Association for the Cultivation of ScienceJadavpurKolkata700 032India
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47
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Paul R, Dutta D, Paul R, Dash J. Target‐Directed Azide‐Alkyne Cycloaddition for Assembling HIV‐1 TAR RNA Binding Ligands. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202003461] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Rakesh Paul
- School of Chemical Sciences Indian Association for the Cultivation of Science Jadavpur Kolkata 700 032 India
| | - Debasish Dutta
- School of Chemical Sciences Indian Association for the Cultivation of Science Jadavpur Kolkata 700 032 India
| | - Raj Paul
- School of Chemical Sciences Indian Association for the Cultivation of Science Jadavpur Kolkata 700 032 India
| | - Jyotirmayee Dash
- School of Chemical Sciences Indian Association for the Cultivation of Science Jadavpur Kolkata 700 032 India
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48
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Goldberg DC, Fones L, Vivinetto AL, Caufield JT, Ratan RR, Cave JW. Manipulating Adult Neural Stem and Progenitor Cells with G-Quadruplex Ligands. ACS Chem Neurosci 2020; 11:1504-1518. [PMID: 32315155 DOI: 10.1021/acschemneuro.0c00194] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
G-quadruplexes are pervasive nucleic acid secondary structures in mammalian genomes and transcriptomes that regulate gene expression and genome duplication. Small molecule ligands that modify the stability of G-quadruplexes are widely studied in cancer, but whether G-quadruplex ligands can also be used to manipulate cell function under normal development and homeostatic conditions is largely unexplored. Here we show that two related G-quadruplex ligands (pyridostatin and carboxypyridostatin) can reduce proliferation of adult neural stem cell and progenitor cells derived from the adult mouse subventricular zone both in vitro and in vivo. Studies with neurosphere cultures show that pyridostatin reduces proliferation by a mechanism associated with DNA damage and cell death. By contrast, selectively targeting RNA G-quadruplex stability with carboxypyridostatin diminishes proliferation through a mechanism that promotes cell cycle exit and the production of oligodendrocyte progenitors. The ability to generate oligodendrocyte progenitors by targeting RNA G-quadruplex stability, however, is dependent on the cellular environment. Together, these findings show that ligands that can selectively stabilize RNA G-quadruplexes are an important, new class of molecular tool for neural stem and progenitor cell engineering, whereas ligands that target DNA G-quadruplexes have limited utility due to their toxicity.
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Affiliation(s)
- David C. Goldberg
- Burke Neurological Institute, White Plains, New York 10605, United States
| | - Lilah Fones
- Burke Neurological Institute, White Plains, New York 10605, United States
| | - Ana L. Vivinetto
- Burke Neurological Institute, White Plains, New York 10605, United States
| | - Joseph T. Caufield
- Burke Neurological Institute, White Plains, New York 10605, United States
| | - Rajiv R. Ratan
- Burke Neurological Institute, White Plains, New York 10605, United States
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, New York 10065, United States
| | - John W. Cave
- Burke Neurological Institute, White Plains, New York 10605, United States
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, New York 10065, United States
- Department of Chemistry and Life Science, United States Military Academy, West Point, New York 10996, United States
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49
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Liao TC, Ma TZ, Chen SB, Cilibrizzi A, Zhang MJ, Li JH, Zhou CQ. Human telomere double G-quadruplex recognition by berberine-bisquinolinium imaging conjugates in vitro and cells. Int J Biol Macromol 2020; 158:S0141-8130(20)33034-8. [PMID: 32339571 DOI: 10.1016/j.ijbiomac.2020.04.171] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 04/21/2020] [Accepted: 04/21/2020] [Indexed: 10/24/2022]
Abstract
Molecular tools of double or multimeric G-quadruplexes have been given higher requirements on detection sensitivity, thermal stabilization and cell imaging to establish functions of these G-quadruplex aggregates and biological mechanisms as anticancer reagents. Here, two smart berberine-bisquinolinium conjugates (Ber-360A and Ber-PDS) by linking the berberine fluorophore ligand and an established G-quadruplex binder (i.e. bisquinolinium scaffold), have been designed and evaluated their activities and mechanisms for G-quadruplex aggregation. Two conjugates, especially Ber-PDS, are two highly selective, sensitive and fluorescent sensors which can distinguish human telomere double G-quadruplexes from other type G-quadruplexes and ds DNA. These two ligands could be the first example to stack two adjacent G-quadruplex units and fluorescently recognize human telomere double G-quadruplexes. Furthermore, conjugate Ber-PDS could enter the nucleoli and target G-quadruplex DNA through microscopy experiments, and also display strong telomerase inhibition and antitumor activities.
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Affiliation(s)
- Ting-Cong Liao
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China
| | - Tian-Zhu Ma
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China
| | - Suo-Bin Chen
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 51006, PR China
| | - Agostino Cilibrizzi
- Institute of Pharmaceutical Science, King's College London, London SE1 9NH, United Kingdom
| | - Meng-Jia Zhang
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China
| | - Jun-Hui Li
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China
| | - Chun-Qiong Zhou
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China.
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50
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Kamura T, Katsuda Y, Kitamura Y, Ihara T. G-quadruplexes in mRNA: A key structure for biological function. Biochem Biophys Res Commun 2020; 526:261-266. [PMID: 32209257 DOI: 10.1016/j.bbrc.2020.02.168] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 02/16/2020] [Accepted: 02/29/2020] [Indexed: 10/24/2022]
Abstract
The last several years have seen exciting advances in the understanding of the structure and function of higher-order structures of RNA. Expression levels of some specific genes were shown to be directly regulated by environmentally-responsive formation of certain secondary structures such as stem-loops and pseudoknots. Even among these noncanonical structures, RNA G-quadruplexes, which form on the regions of guanine-rich sequences in mRNA, are highly stable structures that are involved in a variety of biological processes. However, many questions regarding the biological significance of RNA G-quadruplexes remain unsettled, mainly because it is difficult to locate the structures in mRNA. This review focuses on emerging methods that locate RNA G-quadruplexes in mRNA by computational and biochemical techniques. In addition, recent reports on the biological functions of RNA G-quadruplexes are also covered to highlight their various roles in cells, such as in regulating mRNA processing and translation.
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Affiliation(s)
- Takuto Kamura
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto, 860-8555, Japan
| | - Yousuke Katsuda
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto, 860-8555, Japan.
| | - Yusuke Kitamura
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto, 860-8555, Japan
| | - Toshihiro Ihara
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto, 860-8555, Japan
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