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Mendes E, Aljnadi IM, Bahls B, Victor BL, Paulo A. Major Achievements in the Design of Quadruplex-Interactive Small Molecules. Pharmaceuticals (Basel) 2022; 15:300. [PMID: 35337098 PMCID: PMC8953082 DOI: 10.3390/ph15030300] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 12/17/2022] Open
Abstract
Organic small molecules that can recognize and bind to G-quadruplex and i-Motif nucleic acids have great potential as selective drugs or as tools in drug target discovery programs, or even in the development of nanodevices for medical diagnosis. Hundreds of quadruplex-interactive small molecules have been reported, and the challenges in their design vary with the intended application. Herein, we survey the major achievements on the therapeutic potential of such quadruplex ligands, their mode of binding, effects upon interaction with quadruplexes, and consider the opportunities and challenges for their exploitation in drug discovery.
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Affiliation(s)
- Eduarda Mendes
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal; (E.M.); (I.M.A.); (B.B.)
| | - Israa M. Aljnadi
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal; (E.M.); (I.M.A.); (B.B.)
- Faculty of Sciences, BioISI, Biosystems and Integrative Sciences Institute, Universidade de Lisboa, 1749-016 Lisbon, Portugal;
| | - Bárbara Bahls
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal; (E.M.); (I.M.A.); (B.B.)
- Faculty of Sciences, BioISI, Biosystems and Integrative Sciences Institute, Universidade de Lisboa, 1749-016 Lisbon, Portugal;
| | - Bruno L. Victor
- Faculty of Sciences, BioISI, Biosystems and Integrative Sciences Institute, Universidade de Lisboa, 1749-016 Lisbon, Portugal;
| | - Alexandra Paulo
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal; (E.M.); (I.M.A.); (B.B.)
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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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Zhirov AM, Kovalev DA, Ulshina DV, Pisarenko SV, Demidov OP, Borovlev IV. Diazapyrenes: interaction with nucleic acids and biological activity. Chem Heterocycl Compd (N Y) 2020; 56:674-693. [PMID: 32836316 PMCID: PMC7366485 DOI: 10.1007/s10593-020-02717-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 11/26/2019] [Indexed: 12/22/2022]
Abstract
The review summarizes data on the practical aspects of the interaction of nucleic acids with diazapyrene derivatives. The information on biological activity is given and the probable mechanisms underlying the action of diazapyrenes are analyzed. It contains 119 references.
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Affiliation(s)
- Andrey M. Zhirov
- Stavropol Research Anti-Plague Institute, 13-15 Sovetskaya St, Stavropol, 355035 Russia
| | - Dmitry A. Kovalev
- Stavropol Research Anti-Plague Institute, 13-15 Sovetskaya St, Stavropol, 355035 Russia
| | - Diana V. Ulshina
- Stavropol Research Anti-Plague Institute, 13-15 Sovetskaya St, Stavropol, 355035 Russia
| | - Sergey V. Pisarenko
- Stavropol Research Anti-Plague Institute, 13-15 Sovetskaya St, Stavropol, 355035 Russia
| | - Oleg P. Demidov
- North Caucasus Federal University, 1a Pushkina St, Stavropol, 355017 Russia
| | - Ivan V. Borovlev
- North Caucasus Federal University, 1a Pushkina St, Stavropol, 355017 Russia
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Ravichandran S, Ahn JH, Kim KK. Unraveling the Regulatory G-Quadruplex Puzzle: Lessons From Genome and Transcriptome-Wide Studies. Front Genet 2019; 10:1002. [PMID: 31681431 PMCID: PMC6813735 DOI: 10.3389/fgene.2019.01002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 09/20/2019] [Indexed: 12/20/2022] Open
Abstract
G-quadruplexes (G4s) are among the best-characterized DNA secondary structures and are enriched in regulatory regions, especially promoters, of several prokaryote and eukaryote genomes, indicating a possible role in cis regulation of genes. Many studies have focused on evaluating the impact of specific G4-forming sequences in the promoter regions of genes. However, the lack of correlation between the presence of G4s and the functional impact on cis gene regulation, evidenced by the variable expression fold change in the presence of G4 stabilizers, shows that not all G4s affect transcription in the same manner. This indicates that the regulatory effect of the G4 is significantly influenced by its position, the surrounding DNA topology, and other environmental factors within the cell. In this review, we compare individual gene studies with high-throughput differential expression studies to highlight the importance of formulating a combined approach that can be applied in humans, bacteria, and viruses to better understand the effect of G4-mediated gene regulation.
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Affiliation(s)
- Subramaniyam Ravichandran
- Department of Molecular Cell Biology, Institute for Antimicrobial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon, South Korea
| | - Jin-Hyun Ahn
- Department of Molecular Cell Biology, Institute for Antimicrobial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon, South Korea
| | - Kyeong Kyu Kim
- Department of Molecular Cell Biology, Institute for Antimicrobial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon, South Korea.,Samsung Biomedical Research Institute, Samsung Advanced Institute for Health Sciences and Technology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
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Mori H, Evans-Yamamoto D, Ishiguro S, Tomita M, Yachie N. Fast and global detection of periodic sequence repeats in large genomic resources. Nucleic Acids Res 2019; 47:e8. [PMID: 30304510 PMCID: PMC6344855 DOI: 10.1093/nar/gky890] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 09/20/2018] [Indexed: 12/12/2022] Open
Abstract
Periodically repeating DNA and protein elements are involved in various important biological events including genomic evolution, gene regulation, protein complex formation, and immunity. Notably, the currently used genome editing tools such as ZFNs, TALENs, and CRISPRs are also all associated with periodically repeating biomolecules of natural organisms. Despite the biological importance of periodically repeating sequences and the expectation that new genome editing modules could be discovered from such periodical repeats, no software that globally detects such structured elements in large genomic resources in a high-throughput and unsupervised manner has been developed. We developed new software, SPADE (Search for Patterned DNA Elements), that exhaustively explores periodic DNA and protein repeats from large-scale genomic datasets based on k-mer periodicity evaluation. With a simple constraint, sequence periodicity, SPADE captured reported genome-editing-associated sequences and other protein families involving repeating domains such as tetratricopeptide, ankyrin and WD40 repeats with better performance than the other software designed for limited sets of repetitive biomolecular sequences, suggesting the high potential of this software to contribute to the discovery of new biological events and new genome editing modules.
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Affiliation(s)
- Hideto Mori
- Synthetic Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan.,Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0035, Japan.,Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa 252-0882, Japan
| | - Daniel Evans-Yamamoto
- Synthetic Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan.,Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0035, Japan.,Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa 252-0882, Japan
| | - Soh Ishiguro
- Synthetic Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan.,Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0035, Japan.,Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa 252-0882, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0035, Japan.,Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa 252-0882, Japan.,Department of Environment and Information Studies, Keio University, Fujisawa 252-0882, Japan
| | - Nozomu Yachie
- Synthetic Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan.,Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0035, Japan.,Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa 252-0882, Japan.,Department of Biological Sciences, School of Science, The University of Tokyo, Tokyo 113-0033, Japan.,PRESTO, Japan Science and Technology Agency (JST), Tokyo 153-8904, Japan
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Saranathan N, Vivekanandan P. G-Quadruplexes: More Than Just a Kink in Microbial Genomes. Trends Microbiol 2019; 27:148-163. [PMID: 30224157 PMCID: PMC7127049 DOI: 10.1016/j.tim.2018.08.011] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 08/17/2018] [Accepted: 08/24/2018] [Indexed: 02/06/2023]
Abstract
G-quadruplexes (G4s) are noncanonical nucleic acid secondary structures formed by guanine-rich DNA and RNA sequences. In this review we aim to provide an overview of the biological roles of G4s in microbial genomes with emphasis on recent discoveries. G4s are enriched and conserved in the regulatory regions of microbes, including bacteria, fungi, and viruses. Importantly, G4s in hepatitis B virus (HBV) and hepatitis C virus (HCV) genomes modulate genes crucial for virus replication. Recent studies on Epstein-Barr virus (EBV) shed light on the role of G4s within the microbial transcripts as cis-acting regulatory signals that modulate translation and facilitate immune evasion. Furthermore, G4s in microbial genomes have been linked to radioresistance, antigenic variation, recombination, and latency. G4s in microbial genomes represent novel therapeutic targets for antimicrobial therapy.
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Affiliation(s)
- Nandhini Saranathan
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India
| | - Perumal Vivekanandan
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India.
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Amplification-free and direct fluorometric determination of telomerase activity in cell lysates using chimeric DNA-templated silver nanoclusters. Mikrochim Acta 2019; 186:81. [DOI: 10.1007/s00604-018-3194-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 12/20/2018] [Indexed: 12/16/2022]
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Abstract
Advances in understanding mechanisms of nucleic acids have revolutionized molecular biology and medicine, but understanding of nontraditional nucleic acid conformations is less developed. The guanine quadruplex (G4) alternative DNA structure was first described in the 1960s, but the existence of G4 structures (G4-S) and their participation in myriads of biological functions are still underappreciated. Despite many tools to study G4s and many examples of roles for G4s in eukaryotic molecular processes and issues with uncontrolled G4-S formation, there is relatively little knowledge about the roles of G4-S in viral or prokaryotic systems. This review summarizes the state of the art with regard to G4-S in eukaryotes and their potential roles in human disease before discussing the evidence that G4-S have equivalent importance in affecting viral and bacterial life.
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Affiliation(s)
- H Steven Seifert
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA;
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Perrone R, Lavezzo E, Riello E, Manganelli R, Palù G, Toppo S, Provvedi R, Richter SN. Mapping and characterization of G-quadruplexes in Mycobacterium tuberculosis gene promoter regions. Sci Rep 2017; 7:5743. [PMID: 28720801 PMCID: PMC5515968 DOI: 10.1038/s41598-017-05867-z] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 06/02/2017] [Indexed: 12/04/2022] Open
Abstract
Mycobacterium tuberculosis is the causative agent of tuberculosis (TB), one of the top 10 causes of death worldwide in 2015. The recent emergence of strains resistant to all current drugs urges the development of compounds with new mechanisms of action. G-quadruplexes are nucleic acids secondary structures that may form in G-rich regions to epigenetically regulate cellular functions. Here we implemented a computational tool to scan the presence of putative G-quadruplex forming sequences in the genome of Mycobacterium tuberculosis and analyse their association to transcription start sites. We found that the most stable G-quadruplexes were in the promoter region of genes belonging to definite functional categories. Actual G-quadruplex folding of four selected sequences was assessed by biophysical and biomolecular techniques: all molecules formed stable G-quadruplexes, which were further stabilized by two G-quadruplex ligands. These compounds inhibited Mycobacterium tuberculosis growth with minimal inhibitory concentrations in the low micromolar range. These data support formation of Mycobacterium tuberculosis G-quadruplexes in vivo and their potential regulation of gene transcription, and prompt the use of G4 ligands to develop original antitubercular agents.
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Affiliation(s)
- Rosalba Perrone
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121, Padua, Italy
| | - Enrico Lavezzo
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121, Padua, Italy
| | - Erika Riello
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121, Padua, Italy
| | - Riccardo Manganelli
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121, Padua, Italy
| | - Giorgio Palù
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121, Padua, Italy
| | - Stefano Toppo
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121, Padua, Italy.
| | - Roberta Provvedi
- Department of Biology, University of Padua, via Ugo Bassi 58/b, 35121, Padua, Italy.
| | - Sara N Richter
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121, Padua, Italy.
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Waller ZAE, Pinchbeck BJ, Buguth BS, Meadows TG, Richardson DJ, Gates AJ. Control of bacterial nitrate assimilation by stabilization of G-quadruplex DNA. Chem Commun (Camb) 2016; 52:13511-13514. [PMID: 27805200 PMCID: PMC5123632 DOI: 10.1039/c6cc06057a] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Here we present a chemical-biology study in the model soil bacterium Paracoccus denitrificans, where we show ligand-specific control of nitrate assimilation. Stabilization of a G-quadruplex in the promoter region of the nas genes, encoding the assimilatory nitrate/nitrite reductase system, is achieved using known quadruplex ligands and results in attenuation of gene transcription.
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Affiliation(s)
- Zoë A E Waller
- School of Pharmacy, University of East Anglia, Norwich Research Park, NR4 7TJ, UK.
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Computational understanding and experimental characterization of twice-as-smart quadruplex ligands as chemical sensors of bacterial nucleotide second messengers. Sci Rep 2016; 6:33888. [PMID: 27667717 PMCID: PMC5036188 DOI: 10.1038/srep33888] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 09/05/2016] [Indexed: 12/20/2022] Open
Abstract
A twice-as-smart ligand is a small molecule that experiences a structural switch upon interaction with its target (i.e., smart ligand) that concomitantly triggers its fluorescence (i.e., smart probe). Prototypes of twice-as-smart ligands were recently developed to track and label G-quadruplexes: these higher-order nucleic acid structures originate in the assembly of four guanine(G)-rich DNA or RNA strands, whose stability is imparted by the formation and the self-assembly of G-quartets. The first prototypes of twice-as-smart quadruplex ligands were designed to exploit the self-association of quartets, being themselves synthetic G-quartets. While their quadruplex recognition capability has been thoroughly documented, some doubts remain about the precise photophysical mechanism that underlies their peculiar spectroscopic properties. Here, we uncovered this mechanism via complete theoretical calculations. Collected information was then used to develop a novel application of twice-as-smart ligands, as efficient chemical sensors of bacterial signaling pathways via the fluorescent detection of naturally occurring extracellular quadruplexes formed by cyclic dimeric guanosine monophosphate (c-di-GMP).
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