1
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Subroyen S, Pillay L, Bux F, Kumari S. Evaluating storage conditions and enhancement strategies on viral biomarker recovery for WBE applications. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2024; 90:213-224. [PMID: 39007315 DOI: 10.2166/wst.2024.203] [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: 03/04/2024] [Accepted: 05/31/2024] [Indexed: 07/16/2024]
Abstract
Wastewater-based epidemiology (WBE) is a valuable disease surveillance tool. However, little is known on how factors such as transportation, storage, and wastewater characteristics influence the accuracy of the quantification methods. Hence, this study investigated the impact of storage temperatures and physicochemical characteristics of wastewater on SARS-CoV-2 and influenza A stability using droplet digital PCR. Additionally, strategies to enhance viral recovery were explored. Municipal influent wastewater stored between ±25 and -80 °C was assessed for a period of 84 days to determine viral degradation. Degradation up to 94.1% of influenza A and SARS-CoV-2 was observed in all samples with the highest at ±25 °C. Viral degradation was correlated to the changes in wastewater physicochemical characteristics. The low degradation observed of SARS-CoV-2 in the spiked pellets were indicative of viral adhesion to wastewater solids, which correlated with changes in pH. Ultrasonication frequencies ranging from 4 to 16 kHz, increased SARS-CoV-2 concentrations in the supernatant between 3.30 and 35.65%, indicating viral RNA attachment to wastewater solids. These results highlight the importance of additional pretreatment methods for maximizing RNA recovery from wastewater samples. Based on these findings, it was deduced that wastewater preservation studies are essential, and pretreatment should be included in the WBE methodology.
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Affiliation(s)
- Sueyanka Subroyen
- Institute for Water and Wastewater Technology, Durban University of Technology, P.O. Box 1334, Durban 4000, South Africa
| | - Leanne Pillay
- Institute for Water and Wastewater Technology, Durban University of Technology, P.O. Box 1334, Durban 4000, South Africa
| | - Faizal Bux
- Institute for Water and Wastewater Technology, Durban University of Technology, P.O. Box 1334, Durban 4000, South Africa
| | - Sheena Kumari
- Institute for Water and Wastewater Technology, Durban University of Technology, P.O. Box 1334, Durban 4000, South Africa E-mail:
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2
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Brázda V, Valková N, Dobrovolná M, Mergny JL. Abundance of G-Quadruplex Forming Sequences in the Hepatitis Delta Virus Genomes. ACS OMEGA 2024; 9:4096-4101. [PMID: 38284014 PMCID: PMC10809645 DOI: 10.1021/acsomega.3c09288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 12/15/2023] [Accepted: 12/19/2023] [Indexed: 01/30/2024]
Abstract
Hepatitis delta virus (HDV) is a highly unusual RNA satellite virus that depends on the presence of hepatitis B virus (HBV) to be infectious. Its compact and variable single-stranded RNA genome consists of eight major genotypes distributed unevenly across different continents. The significance of noncanonical secondary structures such as G-quadruplexes (G4s) is increasingly recognized at the DNA and RNA levels, particularly for transcription, replication, and translation. G4s are formed from guanine-rich sequences and have been identified in the vast majority of viral, eukaryotic, and prokaryotic genomes. In this study, we analyzed the G4 propensity of HDV genomes by using G4Hunter. Unlike HBV, which has a G4 density similar to that of the human genome, HDV displays a significantly higher number of potential quadruplex-forming sequences (PQS), with a density more than four times greater than that of the human genome. This finding suggests a critical role for G4s in HDV, especially given that the PQS regions are conserved across HDV genotypes. Furthermore, the prevalence of G4-forming sequences may represent a promising target for therapeutic interventions to control HDV replication.
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Affiliation(s)
- Václav Brázda
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno 621 00, Czech Republic
- Faculty
of Chemistry, Brno University of Technology, Purkyňova 118, Brno 61200, Czech Republic
| | - Natália Valková
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno 621 00, Czech Republic
| | - Michaela Dobrovolná
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno 621 00, Czech Republic
- Faculty
of Chemistry, Brno University of Technology, Purkyňova 118, Brno 61200, Czech Republic
| | - Jean-Louis Mergny
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno 621 00, Czech Republic
- Laboratoire
d’Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, Palaiseau 91120, France
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3
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Pathak R. G-Quadruplexes in the Viral Genome: Unlocking Targets for Therapeutic Interventions and Antiviral Strategies. Viruses 2023; 15:2216. [PMID: 38005893 PMCID: PMC10674748 DOI: 10.3390/v15112216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/01/2023] [Accepted: 11/03/2023] [Indexed: 11/26/2023] Open
Abstract
G-quadruplexes (G4s) are unique non-canonical four-stranded nucleic acid secondary structures formed by guanine-rich DNA or RNA sequences. Sequences with the potential to form quadruplex motifs (pG4s) are prevalent throughout the genomes of all organisms, spanning from prokaryotes to eukaryotes, and are enriched within regions of biological significance. In the past few years, the identification of pG4s within most of the Baltimore group viruses has attracted increasing attention due to their occurrence in regulatory regions of the genome and the subsequent implications for regulating critical stages of viral life cycles. In this context, the employment of specific G4 ligands has aided in comprehending the intricate G4-mediated regulatory mechanisms in the viral life cycle, showcasing the potential of targeting viral G4s as a novel antiviral strategy. This review offers a thorough update on the literature concerning G4s in viruses, including their identification and functional significance across most of the human-infecting viruses. Furthermore, it delves into potential therapeutic avenues targeting G4s, encompassing various G4-binding ligands, G4-interacting proteins, and oligonucleotide-based strategies. Finally, the article highlights both progress and challenges in the field, providing valuable insights into leveraging this unusual nucleic acid structure for therapeutic purposes.
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Affiliation(s)
- Rajiv Pathak
- Department of Genetics, Albert Einstein College of Medicine, New York, NY 10461, USA
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4
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Yan MP, Wee CE, Yen KP, Stevens A, Wai LK. G-quadruplex ligands as therapeutic agents against cancer, neurological disorders and viral infections. Future Med Chem 2023; 15:1987-2009. [PMID: 37933551 DOI: 10.4155/fmc-2023-0202] [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] [Indexed: 11/08/2023] Open
Abstract
G-quadruplexes (G4s) within the human genome have undergone extensive molecular investigation, with a strong focus on telomeres, gene promoters and repetitive regulatory sequences. G4s play central roles in regulating essential biological processes, including telomere maintenance, replication, transcription and translation. Targeting these molecular processes with G4-binding ligands holds substantial therapeutic potential in anticancer treatments and has also shown promise in treating neurological, skeletal and muscular disorders. The presence of G4s in bacterial and viral genomes also suggests that G4-binding ligands could be a critical tool in fighting infections. This review provides an overview of the progress and applications of G4-binding ligands, their proposed mechanisms of action, challenges faced and prospects for their utilization in anticancer treatments, neurological disorders and antiviral activities.
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Affiliation(s)
- Mock Phooi Yan
- Centre for Drug & Herbal Development, Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Jalan Raja Muda Abdul Aziz, Kuala Lumpur, 50300, Malaysia
| | - Chua Eng Wee
- Centre for Drug & Herbal Development, Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Jalan Raja Muda Abdul Aziz, Kuala Lumpur, 50300, Malaysia
| | - Khor Poh Yen
- Faculty Pharmacy & Health Sciences, Universiti Kuala Lumpur, Royal College of Medicine Perak, 3, Jalan Greentown, Ipoh, Perak, 30450, Malaysia
| | - Aaron Stevens
- Department of Pathology & Molecular Medicine, University of Otago, Wellington, 6021, New Zealand
| | - Lam Kok Wai
- Centre for Drug & Herbal Development, Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Jalan Raja Muda Abdul Aziz, Kuala Lumpur, 50300, Malaysia
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5
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Nicoletto G, Richter SN, Frasson I. Presence, Location and Conservation of Putative G-Quadruplex Forming Sequences in Arboviruses Infecting Humans. Int J Mol Sci 2023; 24:ijms24119523. [PMID: 37298474 DOI: 10.3390/ijms24119523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/12/2023] [Accepted: 05/12/2023] [Indexed: 06/12/2023] Open
Abstract
Guanine quadruplexes (G4s) are non-canonical nucleic acid structures formed by guanine (G)-rich tracts that assemble into a core of stacked planar tetrads. G4s are found in the human genome and in the genomes of human pathogens, where they are involved in the regulation of gene expression and genome replication. G4s have been proposed as novel pharmacological targets in humans and their exploitation for antiviral therapy is an emerging research topic. Here, we report on the presence, conservation and localization of putative G4-forming sequences (PQSs) in human arboviruses. The prediction of PQSs was performed on more than twelve thousand viral genomes, belonging to forty different arboviruses that infect humans, and revealed that the abundance of PQSs in arboviruses is not related to the genomic GC content, but depends on the type of nucleic acid that constitutes the viral genome. Positive-strand ssRNA arboviruses, especially Flaviviruses, are significantly enriched in highly conserved PQSs, located in coding sequences (CDSs) or untranslated regions (UTRs). In contrast, negative-strand ssRNA and dsRNA arboviruses contain few conserved PQSs. Our analyses also revealed the presence of bulged PQSs, accounting for 17-26% of the total predicted PQSs. The data presented highlight the presence of highly conserved PQS in human arboviruses and present non-canonical nucleic acid-structures as promising therapeutic targets in arbovirus infections.
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Affiliation(s)
- Giulia Nicoletto
- Department of Molecular Medicine, University of Padua, Via A. Gabelli 63, 35121 Padua, Italy
| | - Sara N Richter
- Department of Molecular Medicine, University of Padua, Via A. Gabelli 63, 35121 Padua, Italy
| | - Ilaria Frasson
- Department of Molecular Medicine, University of Padua, Via A. Gabelli 63, 35121 Padua, Italy
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6
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Real-Hohn A, Groznica M, Kontaxis G, Zhu R, Chaves OA, Vazquez L, Hinterdorfer P, Kowalski H, Blaas D. Stabilization of the Quadruplex-Forming G-Rich Sequences in the Rhinovirus Genome Inhibits Uncoating-Role of Na + and K . Viruses 2023; 15:1003. [PMID: 37112983 PMCID: PMC10141139 DOI: 10.3390/v15041003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/14/2023] [Accepted: 04/17/2023] [Indexed: 04/29/2023] Open
Abstract
Rhinoviruses (RVs) are the major cause of common cold, a respiratory disease that generally takes a mild course. However, occasionally, RV infection can lead to serious complications in patients debilitated by other ailments, e.g., asthma. Colds are a huge socioeconomic burden as neither vaccines nor other treatments are available. The many existing drug candidates either stabilize the capsid or inhibit the viral RNA polymerase, the viral proteinases, or the functions of other non-structural viral proteins; however, none has been approved by the FDA. Focusing on the genomic RNA as a possible target for antivirals, we asked whether stabilizing RNA secondary structures might inhibit the viral replication cycle. These secondary structures include G-quadruplexes (GQs), which are guanine-rich sequence stretches forming planar guanine tetrads via Hoogsteen base pairing with two or more of them stacking on top of each other; a number of small molecular drug candidates increase the energy required for their unfolding. The propensity of G-quadruplex formation can be predicted with bioinformatics tools and is expressed as a GQ score. Synthetic RNA oligonucleotides derived from the RV-A2 genome with sequences corresponding to the highest and lowest GQ scores indeed exhibited characteristics of GQs. In vivo, the GQ-stabilizing compounds, pyridostatin and PhenDC3, interfered with viral uncoating in Na+ but not in K+-containing phosphate buffers. The thermostability studies and ultrastructural imaging of protein-free viral RNA cores suggest that Na+ keeps the encapsulated genome more open, allowing PDS and PhenDC3 to diffuse into the quasi-crystalline RNA and promote the formation and/or stabilization of GQs; the resulting conformational changes impair RNA unraveling and release from the virion. Preliminary reports have been published.
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Affiliation(s)
- Antonio Real-Hohn
- Center of Medical Biochemistry, Vienna Biocenter, Max Perutz Laboratories, Medical University of Vienna, Dr. Bohr Gasse 9/3, 1030 Vienna, Austria; (M.G.)
| | - Martin Groznica
- Center of Medical Biochemistry, Vienna Biocenter, Max Perutz Laboratories, Medical University of Vienna, Dr. Bohr Gasse 9/3, 1030 Vienna, Austria; (M.G.)
- Institut Pasteur, CEDEX 15, 75724 Paris, France
| | - Georg Kontaxis
- Vienna Biocenter, Max Perutz Laboratories, Department of Structural and Computational Biology, University of Vienna, Campus Vienna BioCenter 5, 1030 Vienna, Austria;
| | - Rong Zhu
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstr. 40, 4020 Linz, Austria; (R.Z.)
| | - Otávio Augusto Chaves
- Immunopharmacology Laboratory, Oswaldo Cruz Institute (IOC/Fiocruz), Av. Brasil, 4365, Rio de Janeiro 21040-360, Brazil
| | - Leonardo Vazquez
- Immunopharmacology Laboratory, Oswaldo Cruz Institute (IOC/Fiocruz), Av. Brasil, 4365, Rio de Janeiro 21040-360, Brazil
| | - Peter Hinterdorfer
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstr. 40, 4020 Linz, Austria; (R.Z.)
| | - Heinrich Kowalski
- Center of Medical Biochemistry, Vienna Biocenter, Max Perutz Laboratories, Medical University of Vienna, Dr. Bohr Gasse 9/3, 1030 Vienna, Austria; (M.G.)
| | - Dieter Blaas
- Center of Medical Biochemistry, Vienna Biocenter, Max Perutz Laboratories, Medical University of Vienna, Dr. Bohr Gasse 9/3, 1030 Vienna, Austria; (M.G.)
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7
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Ruggiero E, Richter SN. Targeting G-quadruplexes to achieve antiviral activity. Bioorg Med Chem Lett 2023; 79:129085. [PMID: 36423824 PMCID: PMC9760570 DOI: 10.1016/j.bmcl.2022.129085] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/09/2022] [Accepted: 11/16/2022] [Indexed: 11/22/2022]
Abstract
With the emergence of new viruses in the human population and the fast mutation rates of existing viruses, new antiviral targets and compounds are needed. Most existing antiviral drugs are active against proteins of a handful of viruses. Most of these proteins in the end affect viral nucleic acid processing, but direct nucleic acid targeting is less represented due to the difficulty of selectively acting at the nucleic acid of interest. Recently, nucleic acids have been shown to fold in structures alternative to the classic double helix and Watson and Crick base-pairing. Among these non-canonical structures, G-quadruplexes (G4s) have attracted interest because of their key biological roles that are being discovered. Molecules able to selectively target G4s have been developed and since G4s have been investigated as targets in several human pathologies, including viral infections. Here, after briefly introducing viruses, G4s and the G4-binding molecules with antiviral properties, we comment on the mechanisms at the base of the antiviral activity reported for G4-binding molecules. Understanding how G4-ligands act in infected cells will possibly help designing and developing next-generation antiviral drugs.
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Affiliation(s)
| | - Sara N Richter
- Department of Molecular Medicine, University of Padua, Italy; Microbiology and Virology Unit, Padua University Hospital, Padua, Italy.
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8
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Zhai LY, Liu JF, Zhao JJ, Su AM, Xi XG, Hou XM. Targeting the RNA G-Quadruplex and Protein Interactome for Antiviral Therapy. J Med Chem 2022; 65:10161-10182. [PMID: 35862260 DOI: 10.1021/acs.jmedchem.2c00649] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In recent years, G-quadruplexes (G4s), types of noncanonical four-stranded nucleic acid structures, have been identified in many viruses that threaten human health, such as HIV and Epstein-Barr virus. In this context, G4 ligands were designed to target the G4 structures, among which some have shown promising antiviral effects. In this Perspective, we first summarize the diversified roles of RNA G4s in different viruses. Next, we introduce small-molecule ligands developed as G4 modulators and highlight their applications in antiviral studies. In addition to G4s, we comprehensively review the medical intervention of G4-interacting proteins from both the virus (N protein, viral-encoded helicases, severe acute respiratory syndrome-unique domain, and Epstein-Barr nuclear antigen 1) and the host (heterogeneous nuclear ribonucleoproteins, RNA helicases, zinc-finger cellular nucelic acid-binding protein, and nucleolin) by inhibitors as an alternative way to disturb the normal functions of G4s. Finally, we discuss the challenges and opportunities in G4-based antiviral therapy.
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Affiliation(s)
- Li-Yan Zhai
- College of Life Sciences, Northwest A&F University, Xianyang, Shaanxi 712100, China
| | - Jing-Fan Liu
- College of Life Sciences, Northwest A&F University, Xianyang, Shaanxi 712100, China
| | - Jian-Jin Zhao
- College of Life Sciences, Northwest A&F University, Xianyang, Shaanxi 712100, China
| | - Ai-Min Su
- College of Life Sciences, Northwest A&F University, Xianyang, Shaanxi 712100, China
| | - Xu-Guang Xi
- College of Life Sciences, Northwest A&F University, Xianyang, Shaanxi 712100, China.,Laboratory of Biology and Applied Pharmacology, CNRS UMR 8113, IDA FR3242, ENS Paris-Saclay, Université Paris-Saclay, Gif-sur-Yvette 91190, France
| | - Xi-Miao Hou
- College of Life Sciences, Northwest A&F University, Xianyang, Shaanxi 712100, China
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9
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Shankar U, Mishra SK, Jain N, Tawani A, Yadav P, Kumar A. Ni +2 permease system of Helicobacter pylori contains highly conserved G-quadruplex motifs. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 101:105298. [PMID: 35526824 DOI: 10.1016/j.meegid.2022.105298] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 03/30/2022] [Accepted: 05/02/2022] [Indexed: 06/14/2023]
Abstract
The genome of a micro-organism contains all the information required for its survival inside its host cells. The guanine rich regions of the genome can form stable G-quadruplex structures that act as the regulators of gene expression. Herein, the completely sequenced genomes of Helicobacter pylori were explored for the identification and characterization of the conserved G-quadruplex motifs in this gastrointestinal pathogen. Initial in silico analysis revealed the presence of ~8241 GQ motifs in the H. pylori genome. Metal binding proteins of H. pylori are significantly enriched in the GQ motifs. Our study emphasizes the identification and characterization of four highly conserved G-quadruplex forming motifs (HPGQs) in the nickel transporter genes (nixA, niuB1, niuB2, and niuD) of the H. pylori. Nickel is a virulence determinant in H. pylori and is required as a co-factor for the urease and [NiFe] hydrogenase enzymes that are crucial for its survival in the stomach lining of humans. The presence of GQ motifs in these nickel transporter genes can affect their expression and may alter the functioning of Urease and [NiFe] hydrogenase. Similar to human and virus G-quadruplexes, targeting these conserved PGQs with bioactive molecules may represent a novel therapeutic avenue for combating infection of H. pylori. The identified HPGQs were characterized in-vitro by using CD spectroscopy, electrophoresis technique, and NMR spectroscopy at both acidic (4.5) and neutral pH (7.0). ITC revealed the specific interaction of these HPGQs with high affinity to the known G-quadruplex binding ligand, TMPyP4. The mTFP based reporter assay showed decrease in the gene expression of mTFP in the TMPyP4 treated cells as compared to the untreated and further affirmed the formation of stable G-quadruplex structures in the HPGQ motifs in vivo. This is the first report for characterizing G-quadruplex motifs in nickel transport-associated genes in the H. pylori bacterium.
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Affiliation(s)
- Uma Shankar
- Department of Biosciences and Biomedical Engineering Indore, Simrol, Indore, Madhya Pradesh 455235, India
| | - Subodh Kumar Mishra
- Department of Biosciences and Biomedical Engineering Indore, Simrol, Indore, Madhya Pradesh 455235, India
| | - Neha Jain
- Department of Biosciences and Biomedical Engineering Indore, Simrol, Indore, Madhya Pradesh 455235, India
| | - Arpita Tawani
- Department of Biosciences and Biomedical Engineering Indore, Simrol, Indore, Madhya Pradesh 455235, India
| | - Puja Yadav
- Department of Microbiology, Central University of Haryana, Mahendergarh, Haryana, India
| | - Amit Kumar
- Department of Biosciences and Biomedical Engineering Indore, Simrol, Indore, Madhya Pradesh 455235, India.
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10
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Luo Y, Verga D, Mergny JL. Iso-FRET: an isothermal competition assay to analyze quadruplex formation in vitro. Nucleic Acids Res 2022; 50:e93. [PMID: 35670668 PMCID: PMC9458428 DOI: 10.1093/nar/gkac465] [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: 10/26/2021] [Revised: 04/26/2022] [Accepted: 05/16/2022] [Indexed: 11/23/2022] Open
Abstract
Algorithms have been widely used to predict G-quadruplexes (G4s)-prone sequences. However, an experimental validation of these predictions is generally required. We previously reported a high-throughput technique to evidence G4 formation in vitro called FRET-MC. This method, while convenient and reproducible, has one known weakness: its inability to pin point G4 motifs of low thermal stability. As such quadruplexes may still be biologically relevant if formed at physiological temperature, we wanted to develop an independent assay to overcome this limitation. To this aim, we introduced an isothermal version of the competition assay, called iso-FRET, based on a duplex-quadruplex competition and a well-characterized bis-quinolinium G4 ligand, PhenDC3. G4-forming competitors act as decoys for PhenDC3, lowering its ability to stabilize the G4-forming motif reporter oligonucleotide conjugated to a fluorescence quencher (37Q). The decrease in available G4 ligand concentration restores the ability of 37Q to hybridize to its FAM-labeled short complementary C-rich strand (F22), leading to a decrease in fluorescence signal. In contrast, when no G4-forming competitor is present, PhenDC3 remains available to stabilize the 37Q quadruplex, preventing the formation of the F22 + 37Q complex. Iso-FRET was first applied to a reference panel of 70 sequences, and then used to investigate 23 different viral sequences.
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Affiliation(s)
- Yu Luo
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, Inserm, Institut Polytechnique de Paris, 91128 Palaiseau, France.,CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405 Orsay, France
| | - Daniela Verga
- CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405 Orsay, France.,CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, F-91405 Orsay, France
| | - Jean-Louis Mergny
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, Inserm, Institut Polytechnique de Paris, 91128 Palaiseau, France
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11
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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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12
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Xu J, Huang H, Zhou X. G-Quadruplexes in Neurobiology and Virology: Functional Roles and Potential Therapeutic Approaches. JACS AU 2021; 1:2146-2161. [PMID: 34977886 PMCID: PMC8715485 DOI: 10.1021/jacsau.1c00451] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Indexed: 05/11/2023]
Abstract
A G-quadruplex (G4) is a four-stranded nucleic acid secondary structure maintained by Hoogsteen hydrogen bonds established between four guanines. Experimental studies and bioinformatics predictions support the hypothesis that these structures are involved in different cellular functions associated with both DNA and RNA processes. An increasing number of diseases have been shown to be associated with abnormal G4 regulation. Here, we describe the existence of G4 and then discuss G4-related pathogenic mechanisms in neurodegenerative diseases and the viral life cycle. Furthermore, we focus on the role of G4s in the design of antiviral therapy and neuropharmacology, including G4 ligands, G4-based aptamers, G4-related proteins, and CRISPR-based sequence editing, along with a discussion of limitations and insights into the prospects of this unusual nucleic acid secondary structure in therapeutics. Finally, we highlight progress and challenges in this field and the potential G4-related research fields.
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Affiliation(s)
- Jinglei Xu
- The
Institute of Advanced Studies, Key Laboratory of Biomedical Polymers-Ministry
of Education, Wuhan University, Wuhan 430072, China
| | - Haiyan Huang
- Key
Laboratory of Biomedical Polymers-Ministry of Education, College of
Chemistry and Molecular Sciences, Wuhan
University, Wuhan 430072, China
| | - Xiang Zhou
- The
Institute of Advanced Studies, Key Laboratory of Biomedical Polymers-Ministry
of Education, Wuhan University, Wuhan 430072, China
- Key
Laboratory of Biomedical Polymers-Ministry of Education, College of
Chemistry and Molecular Sciences, Wuhan
University, Wuhan 430072, China
- Email to X.Z.:
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13
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Tomaszewska M, Szabat M, Zielińska K, Kierzek R. Identification and Structural Aspects of G-Quadruplex-Forming Sequences from the Influenza A Virus Genome. Int J Mol Sci 2021; 22:6031. [PMID: 34199658 PMCID: PMC8199785 DOI: 10.3390/ijms22116031] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/26/2021] [Accepted: 05/31/2021] [Indexed: 12/19/2022] Open
Abstract
Influenza A virus (IAV) causes seasonal epidemics and sporadic pandemics, therefore is an important research subject for scientists around the world. Despite the high variability of its genome, the structure of viral RNA (vRNA) possesses features that remain constant between strains and are biologically important for virus replication. Therefore, conserved structural motifs of vRNA can represent a novel therapeutic target. Here, we focused on the presence of G-rich sequences within the influenza A/California/07/2009(H1N1) genome and their ability to form RNA G-quadruplex structures (G4s). We identified 12 potential quadruplex-forming sequences (PQS) and determined their conservation among the IAV strains using bioinformatics tools. Then we examined the propensity of PQS to fold into G4s by various biophysical methods. Our results revealed that six PQS oligomers could form RNA G-quadruplexes. However, three of them were confirmed to adopt G4 structures by all utilized methods. Moreover, we showed that these PQS motifs are present within segments encoding polymerase complex proteins indicating their possible role in the virus biology.
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Affiliation(s)
- Maria Tomaszewska
- Department of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland;
| | - Marta Szabat
- Department of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland;
| | - Karolina Zielińska
- Department of Biomolecular NMR, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland;
| | - Ryszard Kierzek
- Department of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland;
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14
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Bohálová N, Cantara A, Bartas M, Kaura P, Šťastný J, Pečinka P, Fojta M, Mergny JL, Brázda V. Analyses of viral genomes for G-quadruplex forming sequences reveal their correlation with the type of infection. Biochimie 2021; 186:13-27. [PMID: 33839192 DOI: 10.1016/j.biochi.2021.03.017] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/30/2021] [Accepted: 03/31/2021] [Indexed: 12/12/2022]
Abstract
G-quadruplexes contribute to the regulation of key molecular processes. Their utilization for antiviral therapy is an emerging field of contemporary research. Here we present comprehensive analyses of the presence and localization of putative G-quadruplex forming sequences (PQS) in all viral genomes currently available in the NCBI database (including subviral agents). The G4Hunter algorithm was applied to a pool of 11,000 accessible viral genomes representing 350 Mbp in total. PQS frequencies differ across evolutionary groups of viruses, and are enriched in repeats, replication origins, 5'UTRs and 3'UTRs. Importantly, PQS presence and localization is connected to viral lifecycles and corresponds to the type of viral infection rather than to nucleic acid type; while viruses routinely causing persistent infections in Metazoa hosts are enriched for PQS, viruses causing acute infections are significantly depleted for PQS. The unique localization of PQS identifies the importance of G-quadruplex-based regulation of viral replication and life cycle, providing a tool for potential therapeutic targeting.
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Affiliation(s)
- Natália Bohálová
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno, 612 65, Czech Republic; Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Alessio Cantara
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno, 612 65, Czech Republic; Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Martin Bartas
- Department of Biology and Ecology/Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Ostrava, 710 00, Czech Republic
| | - Patrik Kaura
- Brno University of Technology, Faculty of Mechanical Engineering, Technická 2896/2, 616 69, Brno, Czech Republic
| | - Jiří Šťastný
- Brno University of Technology, Faculty of Mechanical Engineering, Technická 2896/2, 616 69, Brno, Czech Republic; Department of Informatics, Mendel University in Brno, Zemědělská 1, Brno, 613 00, Czech Republic
| | - Petr Pečinka
- Department of Biology and Ecology/Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Ostrava, 710 00, Czech Republic
| | - Miroslav Fojta
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno, 612 65, Czech Republic
| | - Jean-Louis Mergny
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno, 612 65, Czech Republic; Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128, Palaiseau, France
| | - Václav Brázda
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno, 612 65, Czech Republic.
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