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Liu X, Qi Q, Xiong W, Shen W, Zhang K, Fan R, Zhang Y, Zhao Y, Xu X, Li M, Zhou E, Tian T, Zhou X. Unveiling a Potent Small Molecule Disruptor for RNA G-Quadruplexes Tougher Than DNA G-Quadruplex Disruption. ACS Chem Biol 2024; 19:2032-2040. [PMID: 39225324 DOI: 10.1021/acschembio.4c00357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
This research presents a unique small molecule characterized by its ability to effectively disrupt RNA G-quadruplexes (G4s), which are notably more stable than their DNA counterparts. We conducted a comprehensive series of in vitro experiments to thoroughly assess the disruptive capabilities of this molecule on RNA G4s. These experiments included comparisons with established G4 stabilizers and DNA G4 disruptors, providing a multifaceted evaluation of the molecule's efficacy. Our extensive in vitro analyses demonstrated that this molecule effectively alters G4 structures and interactions with the BG4 protein, a well-recognized G4-specific antibody. These findings underscore the molecule's potential to modulate G4-protein interactions, indicating promising applications for manipulating cellular functions associated with G4 dynamics in future research.
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Affiliation(s)
- Xingyu Liu
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, The Institute of Molecular Medicine, Wuhan University People's Hospital, Wuhan University, Wuhan 430072, Hubei, China
| | - Qianqian Qi
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, The Institute of Molecular Medicine, Wuhan University People's Hospital, Wuhan University, Wuhan 430072, Hubei, China
| | - Wei Xiong
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, The Institute of Molecular Medicine, Wuhan University People's Hospital, Wuhan University, Wuhan 430072, Hubei, China
| | - Wei Shen
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, The Institute of Molecular Medicine, Wuhan University People's Hospital, Wuhan University, Wuhan 430072, Hubei, China
| | - Kaisong Zhang
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, The Institute of Molecular Medicine, Wuhan University People's Hospital, Wuhan University, Wuhan 430072, Hubei, China
| | - Ruochen Fan
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, The Institute of Molecular Medicine, Wuhan University People's Hospital, Wuhan University, Wuhan 430072, Hubei, China
| | - Yuanyuan Zhang
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, The Institute of Molecular Medicine, Wuhan University People's Hospital, Wuhan University, Wuhan 430072, Hubei, China
| | - Yunting Zhao
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, The Institute of Molecular Medicine, Wuhan University People's Hospital, Wuhan University, Wuhan 430072, Hubei, China
| | - Xinyan Xu
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, The Institute of Molecular Medicine, Wuhan University People's Hospital, Wuhan University, Wuhan 430072, Hubei, China
| | - Ming Li
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, The Institute of Molecular Medicine, Wuhan University People's Hospital, Wuhan University, Wuhan 430072, Hubei, China
| | - Enyi Zhou
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, The Institute of Molecular Medicine, Wuhan University People's Hospital, Wuhan University, Wuhan 430072, Hubei, China
| | - Tian Tian
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, The Institute of Molecular Medicine, Wuhan University People's Hospital, Wuhan University, Wuhan 430072, Hubei, China
| | - Xiang Zhou
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, The Institute of Molecular Medicine, Wuhan University People's Hospital, Wuhan University, Wuhan 430072, Hubei, China
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2
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Cui X, Zhang C, Fu C, Hu J, Li T, Li L. YY1 is involved in homologous recombination inhibition at guanine quadruplex sites in human cells. Nucleic Acids Res 2024; 52:7401-7413. [PMID: 38869071 PMCID: PMC11260479 DOI: 10.1093/nar/gkae502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 05/24/2024] [Accepted: 05/30/2024] [Indexed: 06/14/2024] Open
Abstract
Homologous recombination (HR) is a key process for repairing DNA double strand breaks and for promoting genetic diversity. However, HR occurs unevenly across the genome, and certain genomic features can influence its activity. One such feature is the presence of guanine quadruplexes (G4s), stable secondary structures widely distributed throughout the genome. These G4s play essential roles in gene transcription and genome stability regulation. Especially, elevated G4 levels in cells deficient in the Bloom syndrome helicase (BLM) significantly enhance HR at G4 sites, potentially threatening genome stability. Here, we investigated the role of G4-binding protein Yin Yang-1 (YY1) in modulating HR at G4 sites in human cells. Our results show that YY1's binding to G4 structures suppresses sister chromatid exchange after BLM knockdown, and YY1's chromatin occupancy negatively correlates with the overall HR rate observed across the genome. By limiting RAD51 homolog 1 (RAD51) access, YY1 preferentially binds to essential genomic regions, shielding them from excessive HR. Our findings unveil a novel role of YY1-G4 interaction, revealing novel insights into cellular mechanisms involved in HR regulation.
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Affiliation(s)
- Xinyu Cui
- Shanghai Frontiers Science Center of Drug Target Identification and Delivery, School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
- National Key Laboratory of Innovative Immunotherapy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chengwen Zhang
- Shanghai Frontiers Science Center of Drug Target Identification and Delivery, School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
- National Key Laboratory of Innovative Immunotherapy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chunqing Fu
- Shanghai Frontiers Science Center of Drug Target Identification and Delivery, School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
- National Key Laboratory of Innovative Immunotherapy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jinglei Hu
- Shanghai Frontiers Science Center of Drug Target Identification and Delivery, School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
- National Key Laboratory of Innovative Immunotherapy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Tengjiao Li
- Shanghai Frontiers Science Center of Drug Target Identification and Delivery, School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
- National Key Laboratory of Innovative Immunotherapy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lin Li
- Shanghai Frontiers Science Center of Drug Target Identification and Delivery, School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
- National Key Laboratory of Innovative Immunotherapy, Shanghai Jiao Tong University, Shanghai 200240, China
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3
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Turcotte MA, Perreault JP. Pathogenic SNPs Affect Both RNA and DNA G-Quadruplexes' Responses to Ligands. ACS Chem Biol 2024; 19:1045-1050. [PMID: 38688038 PMCID: PMC11106744 DOI: 10.1021/acschembio.4c00104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 04/12/2024] [Accepted: 04/26/2024] [Indexed: 05/02/2024]
Abstract
Single nucleotide polymorphisms (SNPs) are common genetic variations that are present in over 1% of the population and can significantly modify the structures of both DNA and RNA. G-quadruplex structures (G4) are formed by the superposition of tetrads of guanines. To date, the impact of SNPs on both G4 ligands' binding efficacies and specificities has not been investigated. Here, using a bioinformatically predicted G4 and SNPs found in the α-synuclein gene as a proof-of-concept, it was demonstrated that SNPs can modulate both DNA and RNA G4s' responses to ligands. Specifically, six widely recognized ligands (Phen-DC3, PDS, 360A, RHPS4, BRACO19, and TMPyP4) were shown to differentially affect both the structure and the polymerase stalling of the different SNPs. This work highlights the importance of choosing the appropriate G4 ligand when dealing with an SNP identified in a G-rich gene.
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Affiliation(s)
- Marc-Antoine Turcotte
- Department
of Biochemistry and Functional Genomics, Pavillon de Recherche Appliquée
sur le Cancer, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Jean-Pierre Perreault
- Department
of Biochemistry and Functional Genomics, Pavillon de Recherche Appliquée
sur le Cancer, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
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4
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Falanga AP, D'Urso A, Travagliante G, Gangemi CMA, Marzano M, D'Errico S, Terracciano M, Greco F, De Stefano L, Dardano P, Rea I, Piccialli G, Oliviero G, Borbone N. Higher-order G-quadruplex structures and porphyrin ligands: Towards a non-ambiguous relationship. Int J Biol Macromol 2024; 268:131801. [PMID: 38670185 DOI: 10.1016/j.ijbiomac.2024.131801] [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: 11/01/2023] [Revised: 01/29/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024]
Abstract
Herein, we evaluated the interaction of the tetracationic porphyrin H2TCPPSpm4 with three distinct DNA G-quadruplex (G4) models, i.e., the tetramolecular G4 d(TGGGGT)4 (Q1), the 5'-5' stacked G4-dimer [d(CGGAGGT)4]2 (Q2), and a mixture of 5'-5' stacked G-wires [d(5'-CGGT-3'-3'-GGC-5')4]n (Qn). The combined data obtained from UV-Vis, CD, fluorescence, PAGE, RLS, AFM, NMR, and HPLC-SEC experiments allowed us to shed light on the binding mode of H2TCPPSpm4 with the three G4 models differing for the type and the number of available G4 ending faces, the length of the G4 units, and the number of stacked G4 building blocks. Specifically, we found that H2TCPPSpm4 interacted with the shortest Q1 as an end-stacking ligand, whereas the groove binding mode was ascertained in the case of the Q2 and Qn G4 models. In the case of the interaction with Q1 and Qn, we found that H2TCPPSpm4 induces the formation of supramolecular aggregates at porphyrin/G4 ratios higher than 2:1, whereas no significant aggregation was observed for the interaction with Q2 up to the 5:1 ratio. These results unambiguously demonstrated the suitability of porphyrins for the development of specific G4 ligands or G4-targeting diagnostic probes, being H2TCPPSpm4 capable to distinguish between different G4s.
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Affiliation(s)
- Andrea Patrizia Falanga
- Department of Pharmacy, University of Naples Federico II, via Domenico Montesano 49, 80131 Naples, Italy
| | - Alessandro D'Urso
- Department of Chemical Sciences, University of Catania, viale Andrea Doria 6, 95125 Catania, Italy
| | - Gabriele Travagliante
- Department of Chemical Sciences, University of Catania, viale Andrea Doria 6, 95125 Catania, Italy
| | | | - Maria Marzano
- CESTEV, University of Naples Federico II, via Tommaso De Amicis 95, 80145 Naples, Italy
| | - Stefano D'Errico
- Department of Pharmacy, University of Naples Federico II, via Domenico Montesano 49, 80131 Naples, Italy
| | - Monica Terracciano
- Department of Pharmacy, University of Naples Federico II, via Domenico Montesano 49, 80131 Naples, Italy
| | - Francesca Greco
- Department of Pharmacy, University of Naples Federico II, via Domenico Montesano 49, 80131 Naples, Italy
| | - Luca De Stefano
- Institute of Applied Sciences and Intelligent Systems, Unit of Naples, National Research Council, via Pietro Castellino 111, 80131 Naples, Italy
| | - Principia Dardano
- Institute of Applied Sciences and Intelligent Systems, Unit of Naples, National Research Council, via Pietro Castellino 111, 80131 Naples, Italy
| | - Ilaria Rea
- Institute of Applied Sciences and Intelligent Systems, Unit of Naples, National Research Council, via Pietro Castellino 111, 80131 Naples, Italy
| | - Gennaro Piccialli
- Department of Pharmacy, University of Naples Federico II, via Domenico Montesano 49, 80131 Naples, Italy
| | - Giorgia Oliviero
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, via Sergio Pansini 5, 80131 Naples, Italy
| | - Nicola Borbone
- Department of Pharmacy, University of Naples Federico II, via Domenico Montesano 49, 80131 Naples, Italy.
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5
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Tevonyan LL, Beniaminov AD, Kaluzhny DN. Quenching of G4-DNA intrinsic fluorescence by ligands. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2024; 53:47-56. [PMID: 38217705 DOI: 10.1007/s00249-023-01696-3] [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: 06/30/2023] [Revised: 11/10/2023] [Accepted: 12/11/2023] [Indexed: 01/15/2024]
Abstract
G-quadruplex (G4) structures formed by the guanine-rich DNA regions exhibit several distinctive optical properties, including UV absorption and circular dichroism spectra. Some G4 DNA possess intrinsic UV fluorescence whose origin is not completely clear to date. In this work, we study the effect of TMPyP4 and Methylene Blue on the intrinsic fluorescence of the dimeric G4 DNA structure formed by two d(G3T)4 sequences. We demonstrate that binding of the ligands results in quenching of the intrinsic fluorescence, although the conformation of the G4 DNA and its dimeric structure remain preserved. The binding sites of the ligands were suggested by the photoinduced oxidation of guanines and analysis of binding isoterms. We discuss how DNA-ligand complexes can affect the intrinsic fluorescence of G4 DNA.
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Affiliation(s)
- Liana L Tevonyan
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991, Moscow, Russia
| | - Artemy D Beniaminov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991, Moscow, Russia
| | - Dmitry N Kaluzhny
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991, Moscow, Russia.
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6
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Zareie AR, Dabral P, Verma SC. G-Quadruplexes in the Regulation of Viral Gene Expressions and Their Impacts on Controlling Infection. Pathogens 2024; 13:60. [PMID: 38251367 PMCID: PMC10819198 DOI: 10.3390/pathogens13010060] [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: 11/15/2023] [Revised: 01/05/2024] [Accepted: 01/05/2024] [Indexed: 01/23/2024] Open
Abstract
G-quadruplexes (G4s) are noncanonical nucleic acid structures that play significant roles in regulating various biological processes, including replication, transcription, translation, and recombination. Recent studies have identified G4s in the genomes of several viruses, such as herpes viruses, hepatitis viruses, and human coronaviruses. These structures are implicated in regulating viral transcription, replication, and virion production, influencing viral infectivity and pathogenesis. G4-stabilizing ligands, like TMPyP4, PhenDC3, and BRACO19, show potential antiviral properties by targeting and stabilizing G4 structures, inhibiting essential viral life-cycle processes. This review delves into the existing literature on G4's involvement in viral regulation, emphasizing specific G4-stabilizing ligands. While progress has been made in understanding how these ligands regulate viruses, further research is needed to elucidate the mechanisms through which G4s impact viral processes. More research is necessary to develop G4-stabilizing ligands as novel antiviral agents. The increasing body of literature underscores the importance of G4s in viral biology and the development of innovative therapeutic strategies against viral infections. Despite some ligands' known regulatory effects on viruses, a deeper comprehension of the multifaceted impact of G4s on viral processes is essential. This review advocates for intensified research to unravel the intricate relationship between G4s and viral processes, paving the way for novel antiviral treatments.
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Affiliation(s)
| | | | - Subhash C. Verma
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, 1664 N Virginia Street, Reno, NV 89557, USA; (A.R.Z.); (P.D.)
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7
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Yang H, Xu P, Pan F, Gao J, Yuan L, Lu K. Recent Advances in Fluorescent Probes for G-quadruplex DNAs / RNAs. Mini Rev Med Chem 2024; 24:1940-1952. [PMID: 38798221 DOI: 10.2174/0113895575301818240510151309] [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: 01/28/2024] [Revised: 04/23/2024] [Accepted: 04/27/2024] [Indexed: 05/29/2024]
Abstract
Guanine-quadruplexes (G4s) are high-level structures formed by the folding of guaninerich nucleic acid sequences. G4s play important roles in various physiological processes, such as gene transcription, replication, recombination, and maintenance of chromosomal stability. Specific and sensitive monitoring of G4s lays the foundation for further understanding the structure, content, distribution, and function of G4s in organisms, which is important for the treatment and diagnosis of diseases. Moreover, visualization of G4s will provide new ideas for developing antitumor strategies targeting G4s. The design and development of G4-specific ligands are challenging due to the subtle differences in the structure of G4s. This review focuses on the progress of research on G4 fluorescent probes and their binding mechanisms to G4s. Finally, the challenges and future prospects for better detection and targeting of G4s in different organisms are discussed. This paper provides ideas for the development of novel G4 fluorescent probes.
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Affiliation(s)
- Hongyan Yang
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou, 450001, China
- School of Chemical Engineering and Food Science, Zhengzhou University of Technology, Zhengzhou, 450044, China
| | - Ping Xu
- College of Chemistry, Zhengzhou University, Zhengzhou, 450001, China
| | - Fei Pan
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, 100093, China
| | - Jinhong Gao
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou, 450001, China
| | - Libo Yuan
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou, 450001, China
| | - Kui Lu
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou, 450001, China
- School of Chemical Engineering and Food Science, Zhengzhou University of Technology, Zhengzhou, 450044, China
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8
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Shiekh S, Kodikara SG, Balci H. Structure, Topology, and Stability of Multiple G-quadruplexes in Long Telomeric Overhangs. J Mol Biol 2024; 436:168205. [PMID: 37481156 PMCID: PMC10799177 DOI: 10.1016/j.jmb.2023.168205] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/05/2023] [Accepted: 07/12/2023] [Indexed: 07/24/2023]
Abstract
Telomeres and their single stranded overhangs gradually shorten with successive cell divisions, as part of the natural aging process, but can be elongated by telomerase, a nucleoprotein complex which is activated in the majority of cancers. This prominent implication in cancer and aging has made the repetitive telomeric sequences (TTAGGG repeats) and the G-quadruplex structures that form in their overhangs the focus of intense research in the past several decades. However, until recently most in vitro efforts to understand the structure, stability, dynamics, and interactions of telomeric overhangs had been focused on short sequences that are not representative of longer sequences encountered in a physiological setting. In this review, we will provide a broad perspective about telomeres and associated factors, and introduce the agents and structural characteristics involved in organizing, maintaining, and protecting telomeric DNA. We will also present a summary of recent research performed on long telomeric sequences, nominally defined as those that can form two or more tandem G-quadruplexes, i.e., which contain eight or more TTAGGG repeats. Results of experimental studies using a broad array of experimental tools, in addition to recent computational efforts will be discussed, particularly in terms of their implications for the stability, folding topology, and compactness of the tandem G-quadruplexes that form in long telomeric overhangs.
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Affiliation(s)
- Sajad Shiekh
- Department of Physics, Kent State University, Kent, OH 44242, USA
| | | | - Hamza Balci
- Department of Physics, Kent State University, Kent, OH 44242, USA.
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9
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Polêto MD, Lemkul JA. Differences in Conformational Sampling and Intrinsic Electric Fields Drive Ion Binding in Telomeric and TERRA G-Quadruplexes. J Chem Inf Model 2023; 63:6851-6862. [PMID: 37847037 PMCID: PMC10841373 DOI: 10.1021/acs.jcim.3c01305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
The formation of G-quadruplexes (GQs) occurs in guanine-rich sequences of DNA and RNA, producing highly stable and structurally diverse noncanonical nucleic acid structures. GQs play crucial roles in regulating transcription, translation, and replication and maintaining the genome, among others; thus, changes to their structures can lead to diseases such as cancer. Previous studies using polarizable molecular dynamics simulations have shown differences in ion binding properties between telomeric and telomeric repeat-containing RNA GQs despite architectural similarities. Here, we used volume-based metadynamics and repulsive potential simulations in conjunction with polarizable force fields to quantify the impact of ion binding on the GQ dynamics and ion binding free energies. Furthermore, we describe how GQs exert electric fields on their surroundings to link dynamics with variations in the electronic structure. Our findings provide new insights into the energetic, physical, and conformational properties of GQs and expose subtle but important differences between DNA and RNA GQs with the same fold.
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Affiliation(s)
- Marcelo D Polêto
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Justin A Lemkul
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
- Center for Drug Discovery, Virginia Tech, Blacksburg, Virginia 24061, United States
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10
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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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11
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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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12
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Garnique A, Rezende-Teixeira P, Machado‐Santelli G. Telomerase inhibitors TMPyP4 and thymoquinone decreased cell proliferation and induced cell death in the non-small cell lung cancer cell line LC-HK2, modifying the pattern of focal adhesion. Braz J Med Biol Res 2023; 56:e12897. [PMID: 37909496 PMCID: PMC10609552 DOI: 10.1590/1414-431x2023e12897] [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: 06/20/2023] [Accepted: 09/13/2023] [Indexed: 11/03/2023] Open
Abstract
G-quadruplexes (G4) are structures formed at the ends of telomeres rich in guanines and stabilized by molecules that bind to specific sites. TMPyP4 and thymoquinone (TQ) are small molecules that bind to G4 and have drawn attention because of their role as telomerase inhibitors. The aim of this study was to evaluate the effects of telomerase inhibitors on cellular proliferation, senescence, and death. Two cell lines, LC-HK2 (non-small cell lung cancer - NSCLC) and RPE-1 (hTERT-immortalized), were treated with TMPyP4 (5 μM) and TQ (10 μM). Both inhibitors decreased telomerase activity. TMPyP4 increased the percentage of cells with membrane damage associated with cell death and decreased the frequency of cells in the S-phase. TMPyP4 reduced cell adhesion ability and modified the pattern of focal adhesion. TQ acted in a concentration-dependent manner, increasing the frequency of senescent cells and inducing cell cycle arrest in G1 phase. Thus, the present results showed that TMPyP4 and TQ, although acting as telomerase inhibitors, had a broader effect on other signaling pathways and processes in cells, differing from each other. However, they act both on malignant and immortalized cells, and further studies are needed before their anti-cancer potential can be considered.
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Affiliation(s)
- A.M.B. Garnique
- Departamento de Biologia Celular e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, Brasil
| | - P. Rezende-Teixeira
- Departamento de Farmacologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, Brasil
| | - G.M. Machado‐Santelli
- Departamento de Biologia Celular e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, Brasil
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13
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Roy L, Roy A, Bose D, Banerjee N, Chatterjee S. Unraveling the structural aspects of the G-quadruplex in SMO promoter and elucidating its contribution in transcriptional regulation. J Biomol Struct Dyn 2023:1-16. [PMID: 37878583 DOI: 10.1080/07391102.2023.2268200] [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: 07/24/2023] [Accepted: 10/03/2023] [Indexed: 10/27/2023]
Abstract
We located a 25 nt G-rich sequence in the promoter region of SMO oncogene. We performed an array of biophysical and biochemical assays and confirmed the formation of a parallel G quadruplex (SMO1-GQ) by the identified sequence. SMO1-GQ is highly conserved in primates. For a comprehensive characterization of the SMO quadruplex structure, we have performed spectroscopic and in silico analysis with established GQ binder small molecules TMPyP4 and BRACO-19. We observed comparatively higher stable interaction of BRACO-19 with SMO1-GQ. Structure-based, rational drug design against SMO1-GQ to target SMO oncogene requires a detailed molecular anatomy of the G-quadruplex. We structurally characterised the SMO1-GQ using DMS footprinting assay and molecular modelling, docking, and MD simulation to identify the probable atomic regions that interact with either of the small molecules. We further investigated SMO1-GQ in vivo by performing chromatin immunoprecipitation (ChIP) assay. ChIP data revealed that this gene element functions as a scaffold for a number of transcription factors: specificity protein (Sp1), nucleolin (NCL), non-metastatic cell 2 (NM23-H2), cellular nucleic acid binding protein (CNBP), and heterogeneous nuclear ribonucleoprotein K (hnRNPK) which reflects the SMO1-P1 G-quadruplex to be the master regulator of SMO1 transcriptional activity. The strong binding interaction detected between SMO1-GQ and BRACO-19 contemplates the potential of the G quadruplex as a promising anti-cancer druggable target to downregulate SMO1 oncogene driven cancers.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Laboni Roy
- Department of Biological Science, Bose Institute, Kolkata, West Bengal, India
| | - Ananya Roy
- Department of Biological Science, Bose Institute, Kolkata, West Bengal, India
| | - Debopriya Bose
- Department of Biological Science, Bose Institute, Kolkata, West Bengal, India
| | - Nilanjan Banerjee
- Department of Biological Science, Bose Institute, Kolkata, West Bengal, India
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14
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Polêto MD, Lemkul JA. Differences in Conformational Sampling and Intrinsic Electric Fields Drive Ion Binding in Telomeric and TERRA G-Quadruplexes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.10.552810. [PMID: 37645825 PMCID: PMC10461924 DOI: 10.1101/2023.08.10.552810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
The formation of G-quadruplexes (GQs) occurs in guanine-rich sequences of DNA and RNA, producing highly stable and structurally diverse noncanonical nucleic acid structures. GQs play crucial roles in regulating transcription, translation, and replication; and maintaining the genome, among others, thus changes to their structures can lead to diseases such as cancer. Previous studies using polarizable molecular dynamics simulations have shown differences in ion binding properties between telomeric and TERRA GQs despite architectural similarities. Here, we used volume-based metadynamics and repulsive potential simulations in conjunction with polarizable force fields to quantify the impact of ion binding on GQ dynamics and ion binding free energies. Furthermore, we describe how GQs exert electric fields on their surroundings to link dynamics with variations in electronic structure. Our findings provide new insights into the energetic, physical, and conformational properties of GQs and expose subtle, but important, differences between DNA and RNA GQs with the same fold.
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Affiliation(s)
- Marcelo D Polêto
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, United States
| | - Justin A Lemkul
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, United States
- Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24061, United States
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15
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Xiao CD, Jia MH, Zhong MQ, Xu Y, Yu ZT, He ZY, Lu X, Zhang Y, Zhou X, Fu LY, Shen XC. Unveiling the role of G-quadruplex structure in promoter region: Regulation of ABCA1 expression in macrophages possibly via NONO protein recruitment. Int J Biol Macromol 2023:125443. [PMID: 37353131 DOI: 10.1016/j.ijbiomac.2023.125443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 06/25/2023]
Abstract
ABCA1 has been found to be critical for cholesterol efflux in macrophages. Understanding the mechanism regulating ABCA1 expression is important for the prevention and treatment of atherosclerosis. In the present study, a G-quadruplex (G4) structure was identified in the ABCA1 promoter region. This G4 was shown to be essential for ABCA1 transcription. Stabilizing the G4 by ligands surprisingly upregulated ABCA1 expression in macrophages. Knocking out the G4 remarkably reduced ABCA1 expression, and abolished the increase of ABCA1 expression induced by the G4 ligand. By pull-down assays, the protein NONO was identified as an ABCA1 G4 binder. Overexpression or repression of NONO significantly induced upregulation and downregulation of ABCA1 expression, respectively. ChIP and EMSA experiments showed that the G4 ligand promoted the binding between the ABCA1 G4 and NONO, which led to more recruitment of NONO to the promoter region and enhanced ABCA1 transcription. Finally, the G4 ligand was shown to significantly reduce the accumulation of cholesterol in macrophages. This study showed a new insight into the regulation of gene expression by G4, and provided a new molecular mechanism regulating ABCA1 expression in macrophages. Furthermore, the study showed a possible novel application of the G4 ligand: preventing and treating atherosclerosis.
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Affiliation(s)
- Chao-Da Xiao
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, University Town, Guian New District, Guiyang 550025, China; The Key Laboratory of Optimal Utilization of Natural Medicine Resources, School of Pharmaceutical Sciences, Guizhou Medical University, University Town, Guian New District, Guiyang 550025, China.
| | - Meng-Hao Jia
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, University Town, Guian New District, Guiyang 550025, China.
| | - Ming-Qing Zhong
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, University Town, Guian New District, Guiyang 550025, China
| | - Yan Xu
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Zu-Tao Yu
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Zhi-Yong He
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, University Town, Guian New District, Guiyang 550025, China
| | - Xu Lu
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, University Town, Guian New District, Guiyang 550025, China
| | - Yan Zhang
- Department of Radiology, Affiliated Hospital of Guizhou Medical University, Guiyang 550001, China
| | - Xue Zhou
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, University Town, Guian New District, Guiyang 550025, China
| | - Lin-Yun Fu
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, University Town, Guian New District, Guiyang 550025, China
| | - Xiang-Chun Shen
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, University Town, Guian New District, Guiyang 550025, China; The Key Laboratory of Optimal Utilization of Natural Medicine Resources, School of Pharmaceutical Sciences, Guizhou Medical University, University Town, Guian New District, Guiyang 550025, China.
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16
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Bahls B, Aljnadi IM, Emídio R, Mendes E, Paulo A. G-Quadruplexes in c-MYC Promoter as Targets for Cancer Therapy. Biomedicines 2023; 11:biomedicines11030969. [PMID: 36979947 PMCID: PMC10046398 DOI: 10.3390/biomedicines11030969] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/09/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
Cancer is a societal burden demanding innovative approaches. A major problem with the conventional chemotherapeutic agents is their strong toxicity and other side effects due to their poor selectivity. Uncontrolled proliferation of cancer cells is due to mutations, deletions, or amplifications in genes (oncogenes) encoding for proteins that regulate cell growth and division, such as transcription factors, for example, c-MYC. The direct targeting of the c-MYC protein has been attempted but so far unsuccessfully, as it lacks a definite binding site for the modulators. Meanwhile, another approach has been explored since the discovery that G-quadruplex secondary DNA structures formed in the guanine-rich sequences of the c-MYC promoter region can downregulate the transcription of this oncogene. Here, we will overview the major achievements made in the last decades towards the discovery of a new class of anticancer drugs targeting G-quadruplexes in the c-MYC promoter of cancer cells.
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Affiliation(s)
- Bárbara Bahls
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal
| | - Israa M Aljnadi
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal
| | - Rita Emídio
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal
| | - Eduarda Mendes
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal
| | - Alexandra Paulo
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal
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17
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Pavlova I, Barinov N, Novikov R, Severov V, Iudin M, Vedekhina T, Larin A, Babenko V, Aralov A, Gnuchikh E, Sardushkin M, Klinov D, Tsvetkov V, Varizhuk A. Modeling G4s in chromatin context confirms partial nucleosome exclusion and reveals nucleosome-disrupting effects of the least selective G4 ligands. Biochimie 2023; 204:8-21. [PMID: 36063975 DOI: 10.1016/j.biochi.2022.08.016] [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: 11/05/2021] [Revised: 07/22/2022] [Accepted: 08/23/2022] [Indexed: 01/12/2023]
Abstract
G-quadruplexes (G4s) are gaining increasing attention as possible regulators of chromatin packaging, and robust approaches to their studies in pseudo-native context are much needed. Here, we designed a simple in vitro model of G4-prone genomic DNA and employed it to elucidate the impact of G4s and G4-stabilizing ligands on nucleosome occupancy. We obtained two 226-bp dsDNA constructs composed of the strong nucleosome positioning sequence and an internucleosomal DNA-imitating tail. The tail was G4-free in the control construct and harbored a "strong" (stable) G4 motif in the construct of interest. An additional "weak" (semi-stable) G4 motif was found within the canonical nucleosome positioning sequence. Both G4s were confirmed by optical methods and 1H NMR spectroscopy. Electrophoretic mobility assays showed that the weak G4 motif did not obstruct nucleosome assembly, while the strong G4 motif in the tail sequence diminished nucleosome yield. Atomic force microscopy data and molecular modeling confirmed that the strong G4 was maintained in the tail of the correctly assembled nucleosome structure. Using both in vitro and in silico models, we probed three known G4 ligands and detected nucleosome-disrupting effects of the least selective ligand. Our results are in line with the negative correlation between stable G4s and nucleosome density, support G4 tolerance between regularly positioned nucleosomes, and highlight the importance of considering chromatin context when targeting genomic G4s.
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Affiliation(s)
- Iuliia Pavlova
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, 119435, Russia; Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia
| | - Nikolay Barinov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, 119435, Russia
| | - Roman Novikov
- Engenlhardt Institute of Molecular Biology, Moscow, 119991, Russia; N.D. Zelinsky Institute of Organic Chemistry, Moscow, 19991, Russia
| | - Vjacheslav Severov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, 119435, Russia
| | - Mikhail Iudin
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, 119435, Russia; Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia
| | - Tatiana Vedekhina
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, 119435, Russia
| | - Andrey Larin
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, 119435, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia
| | - Vladislav Babenko
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, 119435, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia
| | - Andrey Aralov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia
| | - Evgeny Gnuchikh
- National Research Center Kurchatov Institute, Kurchatov Genomic Center, Moscow, 123182, Russia
| | - Makar Sardushkin
- Mendeleev University of Chemical Technology of Russia, 125047, Moscow, Russia
| | - Dmitry Klinov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, 119435, Russia; Peoples' Friendship University of Russia (RUDN University), 117198, Moscow, Russia
| | - Vladimir Tsvetkov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, 119435, Russia; Institute of Biodesign and Complex System Modeling, I.M. Sechenov First Moscow State Medical University, Moscow, 119991, Russia; A.V. Topchiev Institute of Petrochemical Synthesis, Leninsky Prospect Str. 29, Moscow, 119991, Russia.
| | - Anna Varizhuk
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, 119435, Russia; Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia.
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18
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Alexander A, Sumohan Pillai A, Sri Varalakshmi G, Ananthi N, Pal H, V. M. V. Enoch I, Sayed M. G-Quadruplex binding affinity variation on molecular encapsulation of ligands by porphyrin-tethered cyclodextrin. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2023.121233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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19
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To probe the binding of TMPyP4 to c-MYC G-quadruplex with in water and in imidazolium-based ionic liquids using spectroscopy coupled with molecular dynamics simulations. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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20
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Selective light-up of dimeric G-quadruplex forming aptamers for efficient VEGF165 detection. Int J Biol Macromol 2022; 224:344-357. [DOI: 10.1016/j.ijbiomac.2022.10.128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/08/2022] [Accepted: 10/13/2022] [Indexed: 11/05/2022]
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21
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Chen L, Dickerhoff J, Sakai S, Yang D. DNA G-Quadruplex in Human Telomeres and Oncogene Promoters: Structures, Functions, and Small Molecule Targeting. Acc Chem Res 2022; 55:2628-2646. [PMID: 36054116 PMCID: PMC9937053 DOI: 10.1021/acs.accounts.2c00337] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
DNA G-quadruplex secondary structures formed in guanine-rich human telomeres and oncogene promoters are functionally important and have emerged as a promising new class of cancer-specific drug targets. These globular intramolecular structures are stabilized by K+ or Na+ and form readily under physiological solution conditions. Moreover, G-quadruplexes are epigenetic features and can alter chromatin structure and function together with interactive proteins. Here, we discuss our efforts over the last two decades to understand the structures and functions of DNA G-quadruplexes formed in key oncogene promoters and human telomeres and their interactions with small molecules. Using high-field NMR spectroscopy, we determined the high-resolution structures of physiologically relevant telomeric G-quadruplexes in K+ solution with a major form (hybrid-2) and a minor form (hybrid-1), as well as a two-tetrad intermediate. The intrinsic structural polymorphism of telomeric DNA may be important for the biology of human telomeres, and we proposed a model for the interconversion. More recently, we have worked on G-quadruplexes of MYC, BCL2, PDGFR-β, VEGF, and k-RAS oncogene promoters. We determined the structure of the major G-quadruplex formed in the MYC promoter, a prototype for parallel G-quadruplexes. It is the first example of the parallel-stranded G3NG3 structure motif with a 1-nt loop, which is prevalent in promoter sequences and likely evolutionarily selected to initiate folding. Remarkably, the parallel MYC promoter G-quadruplexes are highly stable. Additionally, we determined the molecular structures of G-quadruplexes formed in human BCL2, VEGF, and PDGFR-β promoters, each adopting a unique structure. For example, the BCL2 promoter contains distinct interchangeable G-quadruplexes in two adjacent regions, suggesting precise regulation by different proteins. The PDGFR-β promoter adopts unique "broken-strand" and vacancy G-quadruplexes, which can be recognized by cellular guanine metabolites for a potential regulatory role.Structural information on G-quadruplexes in complex with small-molecules is critical for understanding specific recognition and structure-based rational drug design. Our studies show that many G-quadruplexes contain unique structural features such as capping and loop structures, allowing specific recognition by drugs and protein. This represents a paradigm shift in understanding DNA as a drug target: Rather than a uniform, nonselective binding site in duplex DNA, the G-quadruplex is being pursued as a new class of selectively targetable drug receptors. We focus on targeting the biologically relevant MYC promoter G-quadruplex (MycG4) with small molecules and have determined its first and additional drug complex structures. Very recently, we have discovered clinically tested indenoisoquinolines as strong MycG4 binders and potent MYC inhibitors. We have also discovered drugs targeting the unique dGMP-bound-vG4 formed in the PDGFR-β promoter. Moreover, we determined the complex structures of the first small molecules that specifically recognize the physiologically relevant human telomeric G-quadruplexes. Unlike the previously recognized dogma that the optimal G-quadruplex ligands are large aromatic or cyclic compounds, our results suggest that smaller asymmetric compounds with appropriate functional groups are better choices to specifically bind G-quadruplexes. This body of work lays a strong foundation for future work aimed at understanding the cellular functions of G-quadruplexes and G-quadruplex-targeted drug design.
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Affiliation(s)
- Luying Chen
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Jonathan Dickerhoff
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Saburo Sakai
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
- Biogeochemistry Research Center, Japan Agency for Marine-Earth Science and Technology, 2-15, Natsushima-cho, Yokosuka-city, Kanagawa 237-0061, Japan
| | - Danzhou Yang
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
- Purdue Center for Cancer Research, Purdue University, 201 University Street, West Lafayette, Indiana 47907, United States
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
- Purdue Institute for Drug Discovery, Purdue University, 720 Clinic Drive, West Lafayette, Indiana 47907, United States
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22
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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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23
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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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24
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Sun J, Wu G, Pastor F, Rahman N, Wang WH, Zhang Z, Merle P, Hui L, Salvetti A, Durantel D, Yang D, Andrisani O. RNA helicase DDX5 enables STAT1 mRNA translation and interferon signalling in hepatitis B virus replicating hepatocytes. Gut 2022; 71:991-1005. [PMID: 34021034 PMCID: PMC8606016 DOI: 10.1136/gutjnl-2020-323126] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 05/09/2021] [Indexed: 12/18/2022]
Abstract
OBJECTIVE RNA helicase DDX5 is downregulated during HBV replication and poor prognosis HBV-related hepatocellular carcinoma (HCC). The objective of this study is to investigate the role of DDX5 in interferon (IFN) signalling. We provide evidence of a novel mechanism involving DDX5 that enables translation of transcription factor STAT1 mediating the IFN response. DESIGN AND RESULTS Molecular, pharmacological and biophysical assays were used together with cellular models of HBV replication, HCC cell lines and liver tumours. We demonstrate that DDX5 regulates STAT1 mRNA translation by resolving a G-quadruplex (rG4) RNA structure, proximal to the 5' end of STAT1 5'UTR. We employed luciferase reporter assays comparing wild type (WT) versus mutant rG4 sequence, rG4-stabilising compounds, CRISPR/Cas9 editing of the STAT1-rG4 sequence and circular dichroism determination of the rG4 structure. STAT1-rG4 edited cell lines were resistant to the effect of rG4-stabilising compounds in response to IFN-α, while HCC cell lines expressing low DDX5 exhibited reduced IFN response. Ribonucleoprotein and electrophoretic mobility assays demonstrated direct and selective binding of RNA helicase-active DDX5 to the WT STAT1-rG4 sequence. Immunohistochemistry of normal liver and liver tumours demonstrated that absence of DDX5 corresponded to absence of STAT1. Significantly, knockdown of DDX5 in HBV infected HepaRG cells reduced the anti-viral effect of IFN-α. CONCLUSION RNA helicase DDX5 resolves a G-quadruplex structure in 5'UTR of STAT1 mRNA, enabling STAT1 translation. We propose that DDX5 is a key regulator of the dynamic range of IFN response during innate immunity and adjuvant IFN-α therapy.
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Affiliation(s)
- Jiazeng Sun
- Basic Medical Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Guanhui Wu
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, USA
| | - Florentin Pastor
- International Center for Infectiology Research (CIRI), INSERM U1111-CNRS UMR5308, Lyon, France
| | - Naimur Rahman
- Basic Medical Sciences, Purdue University System, West Lafayette, Indiana, USA
| | - Wen-Hung Wang
- Gene Editing Core, Bindley Biosciences Center, Purdue University, West Lafayette, Indiana, USA
| | - Zhengtao Zhang
- Department of Biochemistry and Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Shanghai, China
| | - Philippe Merle
- Service d'Hépatologie, Hôpital de La Croix-Rousse Centre Livet, Lyon, Rhône-Alpes, France
| | - Lijian Hui
- Department of Biochemistry and Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Shanghai, China
| | - Anna Salvetti
- International Center for Infectiology Research (CIRI), INSERM U1111-CNRS UMR5308, Lyon, France
| | - David Durantel
- INSERM U1111-CNRS UMR5308 International Center for Infectiology Research (CIRI), Lyon, France
| | - Danzhou Yang
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, USA
| | - Ourania Andrisani
- Basic Medical Sciences, Purdue University, West Lafayette, Indiana, USA
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25
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Jamroskovic J, Deiana M, Sabouri N. Probing the folding pathways of four-stranded intercalated cytosine-rich motifs at single base-pair resolution. Biochimie 2022; 199:81-91. [PMID: 35452743 DOI: 10.1016/j.biochi.2022.04.007] [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: 03/06/2022] [Revised: 04/13/2022] [Accepted: 04/13/2022] [Indexed: 11/24/2022]
Abstract
Cytosine-rich DNA can fold into four-stranded intercalated structures called i-motifs (iMs) under acidic conditions through the formation of hemi-protonated C:C+ base pairs. However, the folding and stability of iMs rely on many other factors that are not yet fully understood. Here, we combined biochemical and biophysical approaches to determine the factors influencing iM stability under a wide range of experimental conditions. By using high-resolution primer extension assays, circular dichroism, and absorption spectroscopies, we demonstrate that the stabilities of three different biologically relevant iMs are not dependent on molecular crowding agents. Instead, some of the crowding agents affected overall DNA synthesis. We also tested a range of small molecules to determine their effect on iM stabilization at physiological temperature and demonstrated that the G-quadruplex-specific molecule CX-5461 is also a promising candidate for selective iM stabilization. This work provides important insights into the requirements needed for different assays to accurately study iM stabilization, which will serve as important tools for understanding the contribution of iMs in cell regulation and their potential as therapeutic targets.
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Affiliation(s)
- Jan Jamroskovic
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87, Umeå, Sweden.
| | - Marco Deiana
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87, Umeå, Sweden
| | - Nasim Sabouri
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87, Umeå, Sweden.
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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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Jiang J, Teunens T, Tisaun J, Denuit L, Moucheron C. Ruthenium(II) Polypyridyl Complexes and Their Use as Probes and Photoreactive Agents for G-quadruplexes Labelling. Molecules 2022; 27:1541. [PMID: 35268640 PMCID: PMC8912042 DOI: 10.3390/molecules27051541] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/21/2022] [Accepted: 02/22/2022] [Indexed: 02/01/2023] Open
Abstract
Due to their optical and electrochemical properties, ruthenium(II) polypyridyl complexes have been used in a wide array of applications. Since the discovery of the light-switch ON effect of [Ru(bpy)2dppz]2+ when interacting with DNA, the design of new Ru(II) complexes as light-up probes for specific regions of DNA has been intensively explored. Amongst them, G-quadruplexes (G4s) are of particular interest. These structures formed by guanine-rich parts of DNA and RNA may be associated with a wide range of biological events. However, locating them and understanding their implications in biological pathways has proven challenging. Elegant approaches to tackle this challenge relies on the use of photoprobes capable of marking, reversibly or irreversibly, these G4s. Indeed, Ru(II) complexes containing ancillary π-deficient TAP ligands can create a covalently linked adduct with G4s after a photoinduced electron transfer from a guanine residue to the excited complex. Through careful design of the ligands, high selectivity of interaction with G4 structures can be achieved. This allows the creation of specific Ru(II) light-up probes and photoreactive agents for G4 labelling, which is at the core of this review composed of an introduction dedicated to a brief description of G-quadruplex structures and two main sections. The first one will provide a general picture of ligands and metal complexes interacting with G4s. The second one will focus on an exhaustive and comprehensive overview of the interactions and (photo)reactions of Ru(II) complexes with G4s.
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Affiliation(s)
- Julie Jiang
- Laboratoire de Chimie Organique et Photochimie, Service de Chimie et PhysicoChimie Organiques, Université Libre de Bruxelles, Avenue F. D. Roosevelt 50-CP 160/08, 1050 Brussels, Belgium; (J.J.); (T.T.); (J.T.); (L.D.)
| | - Titouan Teunens
- Laboratoire de Chimie Organique et Photochimie, Service de Chimie et PhysicoChimie Organiques, Université Libre de Bruxelles, Avenue F. D. Roosevelt 50-CP 160/08, 1050 Brussels, Belgium; (J.J.); (T.T.); (J.T.); (L.D.)
- Laboratoire de Chimie des Matériaux Nouveaux, Université de Mons, Place du Parc 20, 7000 Mons, Belgium
| | - Jérôme Tisaun
- Laboratoire de Chimie Organique et Photochimie, Service de Chimie et PhysicoChimie Organiques, Université Libre de Bruxelles, Avenue F. D. Roosevelt 50-CP 160/08, 1050 Brussels, Belgium; (J.J.); (T.T.); (J.T.); (L.D.)
| | - Laura Denuit
- Laboratoire de Chimie Organique et Photochimie, Service de Chimie et PhysicoChimie Organiques, Université Libre de Bruxelles, Avenue F. D. Roosevelt 50-CP 160/08, 1050 Brussels, Belgium; (J.J.); (T.T.); (J.T.); (L.D.)
| | - Cécile Moucheron
- Laboratoire de Chimie Organique et Photochimie, Service de Chimie et PhysicoChimie Organiques, Université Libre de Bruxelles, Avenue F. D. Roosevelt 50-CP 160/08, 1050 Brussels, Belgium; (J.J.); (T.T.); (J.T.); (L.D.)
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Joshi S, Singh A, Kukreti S. Porphyrin induced structural destabilization of a parallel DNA G-quadruplex in human MRP1 gene promoter. J Mol Recognit 2022; 35:e2950. [PMID: 34990028 DOI: 10.1002/jmr.2950] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/21/2021] [Accepted: 12/22/2021] [Indexed: 01/01/2023]
Abstract
Porphyrins are among the first ligands that have been tested for their quadruplex binding and stabilization potential. We report the differential interaction of the positional cationic porphyrin isomers TMPyP3 and TMPyP4 with a parallel G-quadruplex (GQ) formed by 33-mer (TP) regulatory sequence present in the promoter region of the human multidrug resistance protein 1 (MRP1) transporter gene. This GQ element encompasses the three evolutionary conserved SP1 transcription factor binding sites. Taking into account that SP1 binds to a non-canonical GQ motif with higher affinity than to a canonical duplex DNA consensus motif, it is suggestive that GQ distortion by cationic porphyrin will have important implications in the regulation of MRP1 expression. Herein, we employed biophysical analysis using circular dichroism, visible absorption, UV-thermal melting and steady-state fluorescence spectroscopy, reporting destabilization of MRP1 GQ by cationic porphyrins. Results suggest that TMPyP4 and TMPyP3 interact with GQ with a binding affinity of 106 to 107 M-1 . Thermodynamic analysis indicated a significant decrease in melting temperature of GQ (ΔTm of 15.5°C-23.5°C), in the presence of 2 times excess of porphyrins. This study provides the biophysical evidence indicating the destabilisation of a parallel DNA G-quadruplex by cationic porphyrins.
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Affiliation(s)
- Savita Joshi
- Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi (North Campus), Delhi, India
| | - Anju Singh
- Department of Chemistry, Ramjas College, University of Delhi, Delhi, India
| | - Shrikant Kukreti
- Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi (North Campus), Delhi, India
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29
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Ruggiero E, Zanin I, Terreri M, Richter SN. G-Quadruplex Targeting in the Fight against Viruses: An Update. Int J Mol Sci 2021; 22:ijms222010984. [PMID: 34681641 PMCID: PMC8538215 DOI: 10.3390/ijms222010984] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/07/2021] [Accepted: 10/08/2021] [Indexed: 12/16/2022] Open
Abstract
G-quadruplexes (G4s) are noncanonical nucleic acid structures involved in the regulation of key cellular processes, such as transcription and replication. Since their discovery, G4s have been mainly investigated for their role in cancer and as targets in anticancer therapy. More recently, exploration of the presence and role of G4s in viral genomes has led to the discovery of G4-regulated key viral pathways. In this context, employment of selective G4 ligands has helped to understand the complexity of G4-mediated mechanisms in the viral life cycle, and highlighted the possibility to target viral G4s as an emerging antiviral approach. Research in this field is growing at a fast pace, providing increasing evidence of the antiviral activity of old and new G4 ligands. This review aims to provide a punctual update on the literature on G4 ligands exploited in virology. Different classes of G4 binders are described, with emphasis on possible antiviral applications in emerging diseases, such as the current COVID-19 pandemic. Strengths and weaknesses of G4 targeting in viruses are discussed.
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30
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Libera V, Andreeva EA, Martel A, Thureau A, Longo M, Petrillo C, Paciaroni A, Schirò G, Comez L. Porphyrin Binding and Irradiation Promote G-Quadruplex DNA Dimeric Structure. J Phys Chem Lett 2021; 12:8096-8102. [PMID: 34406777 DOI: 10.1021/acs.jpclett.1c01840] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Nucleic acid sequences rich in guanines can organize into noncanonical DNA G-quadruplexes (G4s) of variable size. The design of small molecules stabilizing the structure of G4s is a rapidly growing area for the development of novel anticancer therapeutic strategies and bottom-up nanotechnologies. Among a multitude of binders, porphyrins are very attractive due to their light activation that can make them valuable conformational regulators of G4s. Here, a structure-based strategy, integrating complementary probes, is employed to study the interaction between TMPyP4 porphyrin and a 22-base human telomeric sequence (Tel22) before and after irradiation with blue light. Porphyrin binding is discovered to promote Tel22 dimerization, while light irradiation of the Tel22-TMPyP4 complex controls dimer fraction. Such a change in quaternary structure is found to be strictly correlated with modifications at the secondary structure level, thus providing an unprecedented link between the degree of dimerization and the underlying conformational changes in G4s.
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Affiliation(s)
- Valeria Libera
- Dipartimento di Fisica e Geologia, Università di Perugia, Via Pascoli, 06123 Perugia, Italy
- Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
- CNR-IOM c/o Dipartimento di Fisica e Geologia, Università di Perugia, Via Pascoli, 06123 Perugia, Italy
| | - Elena A Andreeva
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, F-38000 Grenoble, France
| | - Anne Martel
- Institut Laue-Langevin, 71 avenue des Martyrs, 38042 Grenoble Cedex 9, France
| | - Aurelien Thureau
- Swing Beamline, Synchrotron SOLEIL, 91192 Gif sur Yvette, France
| | - Marialucia Longo
- Jülich Centre for Neutron Science at Heinz Maier-Leibnitz Zentrum, Lichtenbergstraße 1, 85748 Garching, Germany
| | - Caterina Petrillo
- Dipartimento di Fisica e Geologia, Università di Perugia, Via Pascoli, 06123 Perugia, Italy
| | - Alessandro Paciaroni
- Dipartimento di Fisica e Geologia, Università di Perugia, Via Pascoli, 06123 Perugia, Italy
| | - Giorgio Schirò
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, F-38000 Grenoble, France
| | - Lucia Comez
- CNR-IOM c/o Dipartimento di Fisica e Geologia, Università di Perugia, Via Pascoli, 06123 Perugia, Italy
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31
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Mitteaux J, Lejault P, Wojciechowski F, Joubert A, Boudon J, Desbois N, Gros CP, Hudson RHE, Boulé JB, Granzhan A, Monchaud D. Identifying G-Quadruplex-DNA-Disrupting Small Molecules. J Am Chem Soc 2021; 143:12567-12577. [PMID: 34346684 DOI: 10.1021/jacs.1c04426] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The quest for small molecules that strongly bind to G-quadruplex-DNA (G4), so-called G4 ligands, has invigorated the G4 research field from its very inception. Massive efforts have been invested to discover or rationally design G4 ligands, evaluate their G4-interacting properties in vitro through a series of now widely accepted and routinely implemented assays, and use them as innovative chemical biology tools to interrogate cellular networks that might involve G4s. In sharp contrast, only uncoordinated efforts aimed at developing small molecules that destabilize G4s have been invested to date, even though it is now recognized that such molecular tools would have tremendous application in neurobiology as many genetic and age-related diseases are caused by an overrepresentation of G4s. Herein, we report on our efforts to develop in vitro assays to reliably identify molecules able to destabilize G4s. This workflow comprises the newly designed G4-unfold assay, adapted from the G4-helicase assay implemented with Pif1, as well as a series of biophysical and biochemical techniques classically used to study G4/ligand interactions (CD, UV-vis, PAGE, and FRET-melting), and a qPCR stop assay, adapted from a Taq-based protocol recently used to identify G4s in the genomic DNA of Schizosaccharomyces pombe. This unique, multipronged approach leads to the characterization of a phenylpyrrolocytosine (PhpC)-based G-clamp analog as a prototype of G4-disrupting small molecule whose properties are validated through many different and complementary in vitro evaluations.
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Affiliation(s)
- Jérémie Mitteaux
- Institut de Chimie Moléculaire, ICMUB CNRS UMR 6302, UBFC, 21078 Dijon, France
| | - Pauline Lejault
- Institut de Chimie Moléculaire, ICMUB CNRS UMR 6302, UBFC, 21078 Dijon, France
| | - Filip Wojciechowski
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Alexandra Joubert
- Genome Structure and Instability Laboratory, CNRS UMR 7196, INSERM U1154, National Museum of Natural History, Alliance Sorbonne Université, 75005 Paris, France
| | - Julien Boudon
- Laboratoire Interdisciplinaire Carnot de Bourgogne, ICB CNRS UMR 6303, UBFC, 21078 Dijon, France
| | - Nicolas Desbois
- Institut de Chimie Moléculaire, ICMUB CNRS UMR 6302, UBFC, 21078 Dijon, France
| | - Claude P Gros
- Institut de Chimie Moléculaire, ICMUB CNRS UMR 6302, UBFC, 21078 Dijon, France
| | - Robert H E Hudson
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Jean-Baptiste Boulé
- Genome Structure and Instability Laboratory, CNRS UMR 7196, INSERM U1154, National Museum of Natural History, Alliance Sorbonne Université, 75005 Paris, France
| | - Anton Granzhan
- Institut Curie, CNRS UMR 9187, INSERM U1196, PSL Research University, 91405 Orsay, France.,Université Paris Saclay, CNRS UMR 9187, INSERM U1196, 91405 Orsay, France
| | - David Monchaud
- Institut de Chimie Moléculaire, ICMUB CNRS UMR 6302, UBFC, 21078 Dijon, France
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Photoinduced Electron Transfer Reactions of Water Soluble Porphyrins in Zeolite Environment. J Fluoresc 2021; 31:1575-1585. [PMID: 34338967 DOI: 10.1007/s10895-021-02747-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 05/04/2021] [Indexed: 10/20/2022]
Abstract
Excited state interactions of zeolite adsorbed porphyrins have been investigated by steady state luminescence quenching technique with certain antioxidants such as reduced glutathione, ascorbic acid and L-cysteine. The zeolite supported porphyrins, meso-tetra (N-methyl-4-pyridyl) porphyrin (H2TMPyP4+) and zinc tetra(N-methyl-4-pyridyl) porphyrin (ZnTMPyP4+) were prepared and characterized by various techniques such as Diffuse Reflectance Spectra (DRS), Scanning Electron Microscope (SEM), powder X-Ray Diffraction (XRD) and BET surface area. The interaction of zeolites with porphyrins are shown to increase the lifetime of the singlet excited state of porphyrins and decays are biphasic in nature. The splitting of the emission band of porphyrins occurs in 1:1 glycerol: water solution due to the changes in the dielectric of the solvation sphere associated with porphyrin. The Stern-Volmer plots of I0/I vs quencher concentration [Q] were linear in the whole range of [Q] used. These studies revealed the effective quenching for zinc porphyrin compared to free base porphyrin. The effect of quenchers and zeolite acidity has also been studied and the quenching rate constant (kq) is found in the order of 109 M-1 s-1. The quenching reaction obeys Rehm-Weller Equation and is shown to be due to thermodynamically favoured electron transfer from quenchers to the excited singlet state of porphyrins (reductive quenching).
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Hori D, Yum JH, Sugiyama H, Park S. Tropylium Derivatives as New Entrants that Sense Quadruplex Structures. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20210123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Daisuke Hori
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Ji Hye Yum
- 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 (iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Soyoung Park
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
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34
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Malina J, Kostrhunova H, Scott P, Brabec V. Fe II Metallohelices Stabilize DNA G-Quadruplexes and Downregulate the Expression of G-Quadruplex-Regulated Oncogenes. Chemistry 2021; 27:11682-11692. [PMID: 34048082 DOI: 10.1002/chem.202101388] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Indexed: 12/15/2022]
Abstract
DNA G-quadruplexes (G4s) have been identified within the promoter regions of many proto-oncogenes. Thus, G4s represent attractive targets for cancer therapy, and the design and development of new drugs as G4 binders is a very active field of medicinal chemistry. Here, molecular biophysics and biology methods were employed to investigate the interaction of chiral metallohelices with a series of four DNA G4s (hTelo, c-myc, c-kit1, c-kit2) that are formed by the human telomeric sequence (hTelo) and in the promoter regions of c-MYC and c-KIT proto-oncogenes. We show that the investigated water-compatible, optically pure metallohelices, which are made by self-assembly of simple nonpeptidic organic components around FeII ions and exhibit bioactivity emulating the natural systems, bind with high affinity to G4 DNA and much lower affinity to duplex DNA. Notably, both enantiomers of a metallohelix containing a m-xylenyl bridge (5 b) were found to effectively inhibit primer elongation catalyzed by Taq DNA polymerase by stabilizing G4 structures formed in the template strands containing c-myc and c-kit2 G4-forming sequences. Moreover, both enantiomers of 5 b downregulated the expression of c-MYC and c-KIT oncogenes in human embryonic kidney cells at mRNA and protein levels. As metallohelices also bind alternative nucleic acid structures, they hold promise as potential multitargeted drugs.
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Affiliation(s)
- Jaroslav Malina
- Institute of Biophysics, Czech Academy of Sciences, Kralovopolska 135, 61265, Brno, Czech Republic
| | - Hana Kostrhunova
- Institute of Biophysics, Czech Academy of Sciences, Kralovopolska 135, 61265, Brno, Czech Republic
| | - Peter Scott
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| | - Viktor Brabec
- Institute of Biophysics, Czech Academy of Sciences, Kralovopolska 135, 61265, Brno, Czech Republic
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35
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Onodera M, Sueyoshi K, Umetsu M. Fluorescence Quenching by Complex of a DNA Aptamer and Porphyrin for Sensitive Detection of Porphyrins by Capillary Electrophoresis. CHEM LETT 2021. [DOI: 10.1246/cl.200729] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Mari Onodera
- Tohoku University, 6-6-11 Aramaki-Aza-Aoba, Aoba-ku, Sendai, Miyagi 980-8579, Japan
- Panasonic Corporation, 8-21-1 Ginza, Chuo-ku, Tokyo 140-0061, Japan
| | - Kenji Sueyoshi
- Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| | - Mitsuo Umetsu
- Tohoku University, 6-6-11 Aramaki-Aza-Aoba, Aoba-ku, Sendai, Miyagi 980-8579, Japan
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Tassinari M, Richter SN, Gandellini P. Biological relevance and therapeutic potential of G-quadruplex structures in the human noncoding transcriptome. Nucleic Acids Res 2021; 49:3617-3633. [PMID: 33721024 PMCID: PMC8053107 DOI: 10.1093/nar/gkab127] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 02/10/2021] [Accepted: 02/15/2021] [Indexed: 12/11/2022] Open
Abstract
Noncoding RNAs are functional transcripts that are not translated into proteins. They represent the largest portion of the human transcriptome and have been shown to regulate gene expression networks in both physiological and pathological cell conditions. Research in this field has made remarkable progress in the comprehension of how aberrations in noncoding RNA drive relevant disease-associated phenotypes; however, the biological role and mechanism of action of several noncoding RNAs still need full understanding. Besides fulfilling its function through sequence-based mechanisms, RNA can form complex secondary and tertiary structures which allow non-canonical interactions with proteins and/or other nucleic acids. In this context, the presence of G-quadruplexes in microRNAs and long noncoding RNAs is increasingly being reported. This evidence suggests a role for RNA G-quadruplexes in controlling microRNA biogenesis and mediating noncoding RNA interaction with biological partners, thus ultimately regulating gene expression. Here, we review the state of the art of G-quadruplexes in the noncoding transcriptome, with their structural and functional characterization. In light of the existence and further possible development of G-quadruplex binders that modulate G-quadruplex conformation and protein interactions, we also discuss the therapeutic potential of G-quadruplexes as targets to interfere with disease-associated noncoding RNAs.
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Affiliation(s)
- Martina Tassinari
- Department of Biosciences, University of Milan, via G. Celoria 26, 20133 Milano, Italy
| | - Sara N Richter
- Department of Molecular Medicine, University of Padua, via A. Gabelli 63, 35121 Padova, Italy
| | - Paolo Gandellini
- Department of Biosciences, University of Milan, via G. Celoria 26, 20133 Milano, Italy
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Liu J, Ding G, Chen S, Xue C, Chen M, Wu X, Yuan Q, Zheng J, Yang R. Multifunctional Programmable DNA Nanotrain for Activatable Hypoxia Imaging and Mitochondrion-Targeted Enhanced Photodynamic Therapy. ACS APPLIED MATERIALS & INTERFACES 2021; 13:9681-9690. [PMID: 33606499 DOI: 10.1021/acsami.0c21681] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Programmable DNA-based nanostructures (e.g., nanotrains, nanoflowers, and DNA dendrimers) provide new approaches for safe and effective biological imaging and tumor therapy. However, few studies have reported that DNA-based nanostructures respond to the hypoxic microenvironment for activatable imaging and organelle-targeted tumor therapy. Herein, we innovatively report an azoreductase-responsive, mitochondrion-targeted multifunctional programmable DNA nanotrain for activatable hypoxia imaging and enhanced efficacy of photodynamic therapy (PDT). Cyanine structural dye (Cy3) and black hole quencher 2 (BHQ2), which were employed as a fluorescent mitochondrion-targeted molecule and azoreductase-responsive element, respectively, covalently attached to the DNA hairpin monomers. The extended guanine (G)-rich sequence at the end of the DNA hairpin monomer served as a nanocarrier for the photosensitizer 5,10,15,20-tetrakis(4-N-methylpyridiniumyl) porphyrin (TMPyP4). Upon initiation between the DNA hairpin monomer and initiation probe, the fluorescence of Cy3 and the singlet oxygen (1O2) generation of TMPyP4 in the programmable nanotrain were effectively quenched by BHQ2 through the fluorescence resonance energy transfer (FRET) process. Once the programmable nanotrain entered cancer cells, the azo bond in BHQ2 will be reduced to amino groups by the high expression of azoreductase under hypoxia conditions; then, the fluorescence of Cy3 and the 1O2 generation of TMPyP4 will significantly be restored. Furthermore, due to the mitochondrion-targeting characteristic endowed by Cy3, the TMPyP4-loaded nanotrain would accumulate in the mitochondria of cancer cells and then demonstrate enhanced PDT efficacy under light irradiation. We expect that this programmable DNA nanotrain-based multifunctional nanoplatform could be effectively used for activatable imaging and high performance of PDT in hypoxia-related biomedical field.
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Affiliation(s)
- Jin Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Institute of Chemical Biology and Nanomedicine (ICBN), Hunan University, Changsha 410082, China
| | - Ge Ding
- National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, Health Science Center, School of Biomedical Engineering, Shenzhen University, Shenzhen 518055, China
| | - Shiya Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Institute of Chemical Biology and Nanomedicine (ICBN), Hunan University, Changsha 410082, China
| | - Caoye Xue
- Hunan Institute of Sports Science, Changsha 410003, China
| | - Mian Chen
- National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, Health Science Center, School of Biomedical Engineering, Shenzhen University, Shenzhen 518055, China
| | - Xu Wu
- NHC Key Laboratory of Carcinogenesis and Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha 410083, China
| | - Quan Yuan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Institute of Chemical Biology and Nanomedicine (ICBN), Hunan University, Changsha 410082, China
| | - Jing Zheng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Institute of Chemical Biology and Nanomedicine (ICBN), Hunan University, Changsha 410082, China
| | - Ronghua Yang
- School of Chemistry and Biological Engineering, Changsha University of Science and Technology, Changsha 410004, 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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YY1 interacts with guanine quadruplexes to regulate DNA looping and gene expression. Nat Chem Biol 2021; 17:161-168. [PMID: 33199912 PMCID: PMC7854983 DOI: 10.1038/s41589-020-00695-1] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 08/30/2020] [Accepted: 10/14/2020] [Indexed: 01/28/2023]
Abstract
The DNA guanine quadruplexes (G4) play important roles in multiple cellular processes, including DNA replication, transcription and maintenance of genome stability. Here, we showed that Yin and Yang 1 (YY1) can bind directly to G4 structures. ChIP-seq results revealed that YY1-binding sites overlap extensively with G4 structure loci in chromatin. We also observed that the dimerization of YY1 and its binding with G4 structures contribute to YY1-mediated long-range DNA looping. Displacement of YY1 from G4 structure sites disrupts substantially the YY1-mediated DNA looping. Moreover, treatment with G4-stabilizing ligands modulates the expression of not only those genes with G4 structures in their promoters, but also those associated with distal G4 structures that are brought to close proximity via YY1-mediated DNA looping. Together, we identified YY1 as a DNA G4-binding protein, and revealed that YY1-mediated long-range DNA looping requires its dimerization and occurs, in part, through its recognition of G4 structure.
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40
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Antiviral Activity of the G-Quadruplex Ligand TMPyP4 against Herpes Simplex Virus-1. Viruses 2021; 13:v13020196. [PMID: 33525505 PMCID: PMC7911665 DOI: 10.3390/v13020196] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/17/2021] [Accepted: 01/25/2021] [Indexed: 02/06/2023] Open
Abstract
The herpes simplex virus 1 (HSV-1) genome is extremely rich in guanine tracts that fold into G-quadruplexes (G4s), nucleic acid secondary structures implicated in key biological functions. Viral G4s were visualized in HSV-1 infected cells, with massive virus cycle-dependent G4-formation peaking during viral DNA replication. Small molecules that specifically interact with G4s have been shown to inhibit HSV-1 DNA replication. We here investigated the antiviral activity of TMPyP4, a porphyrin known to interact with G4s. The analogue TMPyP2, with lower G4 affinity, was used as control. We showed by biophysical analysis that TMPyP4 interacts with HSV-1 G4s, and inhibits polymerase progression in vitro; in infected cells, it displayed good antiviral activity which, however, was independent of inhibition of virus DNA replication or entry. At low TMPyP4 concentration, the virus released by the cells was almost null, while inside the cell virus amounts were at control levels. TEM analysis showed that virus particles were trapped inside cytoplasmatic vesicles, which could not be ascribed to autophagy, as proven by RT-qPCR, western blot, and immunofluorescence analysis. Our data indicate a unique mechanism of action of TMPyP4 against HSV-1, and suggest the unprecedented involvement of currently unknown G4s in viral or antiviral cellular defense pathways.
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41
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Andreeva DV, Tikhomirov AS, Shchekotikhin AE. Ligands of G-quadruplex nucleic acids. RUSSIAN CHEMICAL REVIEWS 2021. [DOI: 10.1070/rcr4968] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Stanojević A, Milovanović B, Stanković I, Etinski M, Petković M. The significance of the metal cation in guanine-quartet – metalloporphyrin complexes. Phys Chem Chem Phys 2021; 23:574-584. [DOI: 10.1039/d0cp05798c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The distinct positions of the divalent metal ions with respect to the porphyrin ring are responsible for different interaction energies between metalloporphyrins and the guanine quartet.
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Affiliation(s)
- Ana Stanojević
- University of Belgrade – Faculty of Physical Chemistry
- 11 158 Belgrade
- Serbia
| | | | - Ivana Stanković
- Institute of Chemistry
- Technology and Metallurgy
- 11 000 Belgrade
- Serbia
| | - Mihajlo Etinski
- University of Belgrade – Faculty of Physical Chemistry
- 11 158 Belgrade
- Serbia
| | - Milena Petković
- University of Belgrade – Faculty of Physical Chemistry
- 11 158 Belgrade
- Serbia
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Li L, Williams P, Gao Z, Wang Y. VEZF1-guanine quadruplex DNA interaction regulates alternative polyadenylation and detyrosinase activity of VASH1. Nucleic Acids Res 2020; 48:11994-12003. [PMID: 33231681 PMCID: PMC7708047 DOI: 10.1093/nar/gkaa1092] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 10/22/2020] [Accepted: 11/20/2020] [Indexed: 11/14/2022] Open
Abstract
Vascular endothelial zinc finger 1 (VEZF1) plays important roles in endothelial lineage definition and angiogenesis. Vasohibins 1 and 2 (VASH1 and VASH2) can form heterodimers with small vasohibin-binding protein (SVBP) and were recently shown to regulate angiogenesis by acting as tubulin detyrosinases. Here, we showed that VEZF1 binds directly with DNA guanine quadruplex (G quadruplex, G4) structures in vitro and in cells, which modulates the levels of the two isoforms of VASH1 mRNA. Disruption of this interaction, through genetic depletion of VEZF1 or treatment of cells with G4-stabilizing small molecules, led to increased production of the long over short isoform of VASH1 (i.e. VASH1A and VASH1B, respectively) mRNA and elevated tubulin detyrosinase activity in cells. Moreover, disruption of VEZF1-G4 interactions in human umbilical vein endothelial cells resulted in diminished angiogenesis. These results suggest that the interaction between VEZF1 and G4 structures assumes a crucial role in angiogenesis, which occurs through regulating the relative levels of the two isoforms of VASH1 mRNA and the detyrosinase activity of the VASH1-SVBP complex. Together, our work revealed VEZF1 as a G4-binding protein, identified a novel regulatory mechanism for tubulin detyrosinase, and illustrated that the VEZF1- and VASH1-mediated angiogenesis pathways are functionally connected.
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Affiliation(s)
- Lin Li
- Department of Chemistry, University of California, Riverside, CA 92521, USA
| | - Preston Williams
- Department of Chemistry, University of California, Riverside, CA 92521, USA
| | - Zi Gao
- Department of Chemistry, University of California, Riverside, CA 92521, USA
| | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside, CA 92521, USA
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44
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Cao Y, Yang L, Ding P, Li W, Pei R. Ligand Selectivity by Inserting GCGC‐Tetrads into G‐Quadruplex Structures. Chemistry 2020; 26:14730-14737. [DOI: 10.1002/chem.202003004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/22/2020] [Indexed: 12/22/2022]
Affiliation(s)
- Yanwei Cao
- CAS Key Laboratory of Nano-Bio Interface Division of Nanobiomedicine Suzhou Institute of Nano-Tech and Nano-Bionics Chinese Academy of Sciences Suzhou 215123 P. R. China
| | - Luyan Yang
- CAS Key Laboratory of Nano-Bio Interface Division of Nanobiomedicine Suzhou Institute of Nano-Tech and Nano-Bionics Chinese Academy of Sciences Suzhou 215123 P. R. China
| | - Pi Ding
- CAS Key Laboratory of Nano-Bio Interface Division of Nanobiomedicine Suzhou Institute of Nano-Tech and Nano-Bionics Chinese Academy of Sciences Suzhou 215123 P. R. China
| | - Wenjing Li
- CAS Key Laboratory of Nano-Bio Interface Division of Nanobiomedicine Suzhou Institute of Nano-Tech and Nano-Bionics Chinese Academy of Sciences Suzhou 215123 P. R. China
| | - Renjun Pei
- CAS Key Laboratory of Nano-Bio Interface Division of Nanobiomedicine Suzhou Institute of Nano-Tech and Nano-Bionics Chinese Academy of Sciences Suzhou 215123 P. R. China
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45
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Chalikian TV, Liu L, Macgregor RB. Duplex-tetraplex equilibria in guanine- and cytosine-rich DNA. Biophys Chem 2020; 267:106473. [PMID: 33031980 DOI: 10.1016/j.bpc.2020.106473] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 09/03/2020] [Indexed: 02/07/2023]
Abstract
Noncanonical four-stranded DNA structures, including G-quadruplexes and i-motifs, have been discovered in the cell and are implicated in a variety of genomic regulatory functions. The tendency of a specific guanine- and cytosine-rich region of genomic DNA to adopt a four-stranded conformation depends on its ability to overcome the constraints of duplex base-pairing by undergoing consecutive duplex-to-coil and coil-to-tetraplex transitions. The latter ability is determined by the balance between the free energies of participating ordered and disordered structures. In this review, we present an overview of the literature on the stability of G-quadruplex and i-motif structures and discuss the extent of duplex-tetraplex competition as a function of the sequence context of the DNA and environmental conditions including temperature, pH, salt, molecular crowding, and the presence of G-quadruplex-binding ligands. We outline how the results of in vitro studies can be expanded to understanding duplex-tetraplex equilibria in vivo.
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Affiliation(s)
- Tigran V Chalikian
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada.
| | - Lutan Liu
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Robert B Macgregor
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
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46
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Singh M, Wang S, Joo H, Ye Z, Christison KM, Hekman R, Vierra C, Xue L. Use of neomycin as a structured amino-containing side chain motif for phenanthroline-based G-quadruplex ligands and telomerase inhibitors. Chem Biol Drug Des 2020; 96:1292-1304. [PMID: 32516846 DOI: 10.1111/cbdd.13741] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 05/05/2020] [Accepted: 05/31/2020] [Indexed: 01/05/2023]
Abstract
In this paper, we report the synthesis of a phenanthroline and neomycin conjugate (7). Compound 7 binds to a human telomeric G-quadruplex (G1) with a higher affinity compared with its parent compounds (phenanthroline and neomycin), which is determined by several biophysical studies. Compound 7 shows good selectivity for G-quadruplex (G4) DNA over duplex DNA. The binding of 7 with G1 is predominantly enthalpy-driven, and the binding stoichiometry of 7 with G1 is one for the tight-binding event as determined by ESI mass spectrometry. A plausible binding mode is a synergistic effect of end-stacking and groove interactions, as indicated by docking studies. Compound 7 can inhibit human telomerase activity at low micromolar concentrations, which is more potent than previously reported 5-substituted phenanthroline derivatives.
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Affiliation(s)
- Mandeep Singh
- Department of Chemistry, University of the Pacific, Stockton, CA, USA
| | - Siwen Wang
- Department of Chemistry, University of the Pacific, Stockton, CA, USA
| | - Hyun Joo
- Department of Chemistry, University of the Pacific, Stockton, CA, USA
| | - Zhihan Ye
- Department of Chemistry, University of the Pacific, Stockton, CA, USA
| | | | - Ryan Hekman
- Department of Biological Sciences, University of the Pacific, Stockton, CA, USA
| | - Craig Vierra
- Department of Biological Sciences, University of the Pacific, Stockton, CA, USA
| | - Liang Xue
- Department of Chemistry, University of the Pacific, Stockton, CA, USA
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Carvalho J, Cruz C. Forster resonance energy transfer for studying nucleic acids denaturation: A chemical and biological sciences laboratory experiment. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2020; 48:329-336. [PMID: 32268010 DOI: 10.1002/bmb.21353] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 02/25/2020] [Accepted: 03/29/2020] [Indexed: 06/11/2023]
Abstract
The Förster resonance energy transfer (FRET) melting assay intends to evaluate the unfolding, denaturation process of DNA secondary structures, and its stabilization using compounds known as DNA binders, some of which are highly specific for G-quadruplex DNAs versus duplex DNAs. First, students determined the melting temperature (Tm ) of DNA sequences double labeled with 5'-FAM (fluorescein) and 3'-TAMRA (tetramethylrhodamine) in the absence of DNA binders. Second, they determined the melting temperature of the DNAs in the presence of DNA binders by monitoring fluorescence. After completing this experiment, students understood that this method allows a semiquantitative analysis to test a variety of DNA binders against DNA secondary structures, and it can be used to rapidly identify the most promising drug candidates in the drug development stages at the basic research level.
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Affiliation(s)
- Josué Carvalho
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Covilhã, Portugal
| | - Carla Cruz
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Covilhã, Portugal
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48
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Zagami R, Franco D, Pipkin JD, Antle V, De Plano L, Patanè S, Guglielmino S, Monsù Scolaro L, Mazzaglia A. Sulfobutylether-β-cyclodextrin/5,10,15,20-tetrakis(1-methylpyridinium-4-yl)porphine nanoassemblies with sustained antimicrobial phototherapeutic action. Int J Pharm 2020; 585:119487. [PMID: 32492506 DOI: 10.1016/j.ijpharm.2020.119487] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 05/27/2020] [Accepted: 05/28/2020] [Indexed: 12/11/2022]
Abstract
Nowadays, novel less-expensive nanoformulations for in situ-controlled and safe delivery of photosensitisers (PSs) against opportunistic pathogens in body-infections areas need to be developed. Antimicrobial photodynamic therapy (aPDT) is a promising approach to treat bacterial infections that are recalcitrant to antibiotics. In this paper, we propose the design and characterization of a novel nanophototherapeutic based on the trade cyclodextrin CAPTISOL® (sulfobutylether-beta-cyclodextrin, SBE-βCD) and 5,10,15,20-tetrakis(1-methylpyridinium-4-yl)porphine tetrakis(p-toluenesulfonate) (TMPyP) to fabricate efficient biocompatible systems for aPDT. Spherical nanoassemblies of about 360 nm based on CAPTISOL®/TMPyP supramolecular complexes with 1:1 stoichiometry and apparent equilibrium binding constant (Kb ≅ 1.32 × 105 M-1) were prepared with entrapment efficiency of ≅ 100% by simple mixing in aqueous media and freeze-drying. These systems have been characterized by complementary spectroscopy and microscopy techniques. Time resolved fluorescence pointed out the strong interaction of porphyrin monomer within nanoassemblies (τ2 ≅ 11 ns with an amount of ca 90%) and scarce self-aggregation of porphyrins have been observed. Singlet oxygen comparative determination (ϕΔ CAPTISOL®/TMPyP = 0.58) assessed their photodynamic potential. Release and photostability studies have been carried out under physiological conditions pointing out the role of CAPTISOL® to sustain porphyrin release for more than 2 weeks and to protect PS from photodegradation. Finally, photoantimicrobial activity of nanoassemblies vs free porphyrin have been investigated against Gram-negative P. aeruginosa, E. coli and Gram-positive S. aureus. The proposed nanosystems were able to photokill both Gram-positive and -negative bacterial cells similarly to TMPyP at MBC90 = 6 µM of TMPyP and at 42 J/cm2 light dose. However, with respect to the less selective free TMPyP in biological sites, nanoassemblies exhibit sustained release properties and a higher photostability thus optimizing the PDT effect at the site of action. These results can open routes for in vivo translational studies on nano(photo)drugs and nanotheranostics based on less expensive formulations of CD and PS.
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Affiliation(s)
- Roberto Zagami
- CNR-ISMN, Istituto per lo Studio dei Materiali Nanostrutturati c/o Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali dell'Università di Messina, Viale F. Stagno d'Alcontres 31, Messina 98166, Italy.
| | - Domenico Franco
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali dell'Università di Messina, Viale F. Stagno d'Alcontres 31, Messina 98166, Italy
| | | | - Vince Antle
- Ligand Pharmaceuticals Incorporated, San Diego, CA, USA
| | - Laura De Plano
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali dell'Università di Messina, Viale F. Stagno d'Alcontres 31, Messina 98166, Italy
| | - Salvatore Patanè
- Dipartimento di Scienze Matematiche e Informatiche, Scienze Fisiche e Scienze della Terra, Università di Messina, Viale F. Stagno d'Alcontres, 31, 98166 Messina, Italy
| | - Salvatore Guglielmino
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali dell'Università di Messina, Viale F. Stagno d'Alcontres 31, Messina 98166, Italy
| | - Luigi Monsù Scolaro
- CNR-ISMN, Istituto per lo Studio dei Materiali Nanostrutturati c/o Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali dell'Università di Messina, Viale F. Stagno d'Alcontres 31, Messina 98166, Italy; Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali dell'Università di Messina, Viale F. Stagno d'Alcontres 31, Messina 98166, Italy; C.I.R.C.M.S.B, Unity of Messina, Messina, Italy
| | - Antonino Mazzaglia
- CNR-ISMN, Istituto per lo Studio dei Materiali Nanostrutturati c/o Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali dell'Università di Messina, Viale F. Stagno d'Alcontres 31, Messina 98166, Italy.
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G-quadruplex, Friend or Foe: The Role of the G-quartet in Anticancer Strategies. Trends Mol Med 2020; 26:848-861. [PMID: 32467069 DOI: 10.1016/j.molmed.2020.05.002] [Citation(s) in RCA: 166] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/13/2020] [Accepted: 05/06/2020] [Indexed: 02/07/2023]
Abstract
The clinical applicability of G-quadruplexes (G4s) as anticancer drugs is currently being evaluated. Several G4 ligands and aptamers are undergoing clinical trials following the notable examples of quarfloxin and AS1411, respectively. In this review, we summarize the latest achievements and breakthroughs in the use of G4 nucleic acids as both therapeutic tools ('friends', as healing anticancer drugs) and targets ('foes', within the harmful cancer cell), particularly using aptamers and quadruplex-targeted ligands, respectively. We explore the recent research on synthetic G4 ligands toward the discovery of anticancer therapeutics and their mechanism of action. Additionally, we highlight recent advances in chemical and structural biology that enable the design of specific G4 aptamers to be used as novel anticancer agents.
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Phthalocyanines for G-quadruplex aptamers binding. Bioorg Chem 2020; 100:103920. [PMID: 32413624 DOI: 10.1016/j.bioorg.2020.103920] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 05/05/2020] [Accepted: 05/06/2020] [Indexed: 01/02/2023]
Abstract
The G-quadruplex (G4)-forming sequence within the AS1411 derivatives with alternative nucleobases and backbones can improve the chemical and biological properties of AS1411. Zn(II) phthalocyanine (ZnPc) derivatives have potential as high-affinity G4 ligands because they have similar size and shape to the G-quartets. The interactions of four Zn(II) phthalocyanines with the G4 AS1411 aptamer and its derivatives were determined by biophysical techniques, molecular docking and gel electrophoresis. Cell viability assay was carried out to evaluate the antiproliferative effects of Zn(II) phthalocyanines and complexes. CD experiments showed structural changes after addition of ZnPc 4, consistent with multiple binding modes and conformations shown by NMR and gel electrophoresis. CD melting confirmed that ZnPc 2 and ZnPc 4, both containing eight positive charges, are able to stabilize the AT11 G4 structure (ΔTm > 30 °C and 18.5 °C, respectively). Molecular docking studies of ZnPc 3 and ZnPc 4 suggested a preferential binding to the 3'- and 5'-end, respectively, of the AT11 G4. ZnPc 3 and its AT11 and AT11-L0 complexes revealed pronounced cytotoxic effect against cervical cancer cells and no cytotoxicity to normal human cells. Zn(II) phthalocyanines provide the basis for the development of effective therapeutic agents as G4 ligands.
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