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Banjan B, Koshy AJ, Kalath H, John L, Soman S, Raju R, Revikumar A. Potential protein kinase inhibitors that target G-quadruplex DNA structures in the human telomeric regions. Mol Divers 2024:10.1007/s11030-023-10768-7. [PMID: 38509417 DOI: 10.1007/s11030-023-10768-7] [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: 08/28/2023] [Accepted: 11/10/2023] [Indexed: 03/22/2024]
Abstract
Telomeric regions contain Guanine-rich sequences arranged in a planar manner and connected by Hoogsteen hydrogen bonds that can fold into G-quadruplex (G4) DNA structures, and can be stabilized by monovalent metal cations. The presence of G4 DNA holds significance in cancer-related processes, especially due to their regulatory potential at transcriptional and translational levels of oncogene and tumor suppressor genes. The objective of this current research is to explore the evolving realm of FDA-approved protein kinase inhibitors, with a specific emphasis on their capacity to stabilize the G4 DNA structures formed at the human telomeric regions. This involves investigating the possibility of repurposing FDA-approved protein kinase inhibitors as a novel approach for targeting multiple cancer types. In this context, we have selected 16 telomeric G4 DNA structures as targets and 71 FDA-approved small-molecule protein kinase inhibitors as ligands. To investigate their binding affinities, molecular docking of human telomeric G4 DNA with nuclear protein kinase inhibitors and their corresponding co-crystalized ligands were performed. We found that Ponatinib and Lapatinib interact with all the selected G4 targets, the binding free energy calculations, and molecular dynamic simulations confirm their binding efficacy and stability. Thus, it is hypothesized that Ponatinib and Lapatinib may stabilize human telomeric G4 DNA in addition to their ability to inhibit BCR-ABL and the other members of the EGFR family. As a result, we also hypothesize that the stabilization of G4 DNA might represent an additional underlying mechanism contributing to their efficacy in exerting anti-cancer effects.
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Affiliation(s)
- Bhavya Banjan
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to Be University), Mangalore, Karnataka, 575018, India
| | - Abel John Koshy
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to Be University), Mangalore, Karnataka, 575018, India
| | - Haritha Kalath
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to Be University), Mangalore, Karnataka, 575018, India
| | - Levin John
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to Be University), Mangalore, Karnataka, 575018, India
| | - Sowmya Soman
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to Be University), Mangalore, Karnataka, 575018, India
| | - Rajesh Raju
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to Be University), Mangalore, Karnataka, 575018, India.
| | - Amjesh Revikumar
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to Be University), Mangalore, Karnataka, 575018, India.
- Kerala Genome Data Centre, Kerala Development and Innovation Strategic Council, Vazhuthacaud, Thiruvananthapuram, Kerala, 695014, India.
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2
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Wang J, Qiao JQ, Zheng WJ, Lian HZ. Effect of ionic liquids as mobile phase additives on retention behaviors of G-quadruplexes in reversed-phase high performance liquid chromatography. J Chromatogr A 2024; 1715:464604. [PMID: 38176351 DOI: 10.1016/j.chroma.2023.464604] [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: 10/24/2023] [Revised: 12/20/2023] [Accepted: 12/22/2023] [Indexed: 01/06/2024]
Abstract
G-quadruplexes (G4s) play an important role in a variety of biological processes and have extensive application prospects. Due to the significance of G4s in physiology and biosensing, studies on G4s have attracted much attention, stimulating the development or improvement of methods for G4 structures and polymorphism analysis. In this work, ionic liquids (ILs) were involved as mobile phase additives in reversed-phase high performance liquid chromatography (RP-HPLC) to analyse G4s with various conformations for the first time. How ILs affected the retention behaviors of G4s was investigated comprehensively. It was found that the addition of ILs markedly enhanced G4 retention, along with obvious amelioration on chromatographic peak shapes and separation. The influence of pH of mobile phase and types of ILs were also included in order to acquire an in-depth understanding. It appeared that the effect of ILs on G4 retention behaviors was the result of a combination of various interactions between G4s with the hydrophobic stationary phase and with the IL-containing mobile phase, where ion pair mechanism and enhanced hydrophobic interaction dominated. The findings of this work revealed that ILs could effectively improve the separation of G4s in RP-HPLC, which was conducive to G4 structural analysis, especially for G4s polymorphism elucidation.
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Affiliation(s)
- Ju Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering and Center of Materials Analysis, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China
| | - Jun-Qin Qiao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering and Center of Materials Analysis, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China.
| | - Wei-Juan Zheng
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China
| | - Hong-Zhen Lian
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering and Center of Materials Analysis, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China.
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3
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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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4
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Nguyen LTA, Nguyen TTT, Dang DT. Specific binding of G-quadruplex in SARS-CoV-2 RNA by RHAU peptide. Curr Res Struct Biol 2024; 7:100126. [PMID: 38292819 PMCID: PMC10824680 DOI: 10.1016/j.crstbi.2024.100126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 01/04/2024] [Accepted: 01/04/2024] [Indexed: 02/01/2024] Open
Abstract
G-quadruplexes (G4s) are reported to present on the SARS-CoV-2 RNA genome and control various viral activities. Specific ligands targeting those viral nucleic acid structures could be investigated as promising detection methods or antiviral reagents to suppress this menacing virus. Herein, we demonstrate the binding between a G4 structure in the RNA of SARS-CoV-2 and a fluorescent probe created by fusing a parallel-G4 specific RHAU53 and a cyan fluorescent protein. The specific binding of G4 in SARS-CoV-2 by RHAU peptide was easily detected under the fluorescence spectrometer. The drawbacks of this approach and potential solutions are also discussed.
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Affiliation(s)
| | | | - Dung Thanh Dang
- Faculty of Biotechnology, Ho Chi Minh City Open University, HCMC, Viet Nam
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5
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Xu Y, Komiyama M. G-Quadruplexes in Human Telomere: Structures, Properties, and Applications. Molecules 2023; 29:174. [PMID: 38202757 PMCID: PMC10780218 DOI: 10.3390/molecules29010174] [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: 11/27/2023] [Revised: 12/20/2023] [Accepted: 12/25/2023] [Indexed: 01/12/2024] Open
Abstract
G-quadruplexes, intricate four-stranded structures composed of G-tetrads formed by four guanine bases, are prevalent in both DNA and RNA. Notably, these structures play pivotal roles in human telomeres, contributing to essential cellular functions. Additionally, the existence of DNA:RNA hybrid G-quadruplexes adds a layer of complexity to their structural diversity. This review provides a comprehensive overview of recent advancements in unraveling the intricacies of DNA and RNA G-quadruplexes within human telomeres. Detailed insights into their structural features are presented, encompassing the latest developments in chemical approaches designed to probe these G-quadruplex structures. Furthermore, this review explores the applications of G-quadruplex structures in targeting human telomeres. Finally, the manuscript outlines the imminent challenges in this evolving field, setting the stage for future investigations.
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Affiliation(s)
- Yan Xu
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Makoto Komiyama
- Research Center for Advanced Science and Technology (RCAST), The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904, Japan
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Haddad-Mashadrizeh A, Mirahmadi M, Taghavizadeh Yazdi ME, Gholampour-Faroji N, Bahrami A, Zomorodipour A, Moghadam Matin M, Qayoomian M, Saebnia N. Introns and Their Therapeutic Applications in Biomedical Researches. IRANIAN JOURNAL OF BIOTECHNOLOGY 2023; 21:e3316. [PMID: 38269198 PMCID: PMC10804063 DOI: 10.30498/ijb.2023.334488.3316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 03/23/2023] [Indexed: 01/26/2024]
Abstract
Context Although for a long time, it was thought that intervening sequences (introns) were junk DNA without any function, their critical roles and the underlying molecular mechanisms in genome regulation have only recently come to light. Introns not only carry information for splicing, but they also play many supportive roles in gene regulation at different levels. They are supposed to function as useful tools in various biological processes, particularly in the diagnosis and treatment of diseases. Introns can contribute to numerous biological processes, including gene silencing, gene imprinting, transcription, mRNA metabolism, mRNA nuclear export, mRNA localization, mRNA surveillance, RNA editing, NMD, translation, protein stability, ribosome biogenesis, cell growth, embryonic development, apoptosis, molecular evolution, genome expansion, and proteome diversity through various mechanisms. Evidence Acquisition In order to fulfill the objectives of this study, the following databases were searched: Medline, Scopus, Web of Science, EBSCO, Open Access Journals, and Google Scholar. Only articles published in English were included. Results & Conclusions The intervening sequences of eukaryotic genes have critical functions in genome regulation, as well as in molecular evolution. Here, we summarize recent advances in our understanding of how introns influence genome regulation, as well as their effects on molecular evolution. Moreover, therapeutic strategies based on intron sequences are discussed. According to the obtained results, a thorough understanding of intron functional mechanisms could lead to new opportunities in disease diagnosis and therapies, as well as in biotechnology applications.
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Affiliation(s)
- Aliakbar Haddad-Mashadrizeh
- Industrial Biotechnology Research Group, Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mahdi Mirahmadi
- Stem Cell and Regenerative Medicine Research Group, Iranian Academic Center for Education, Culture and Research (ACECR), Khorasan Razavi Branch, Mashhad, Iran
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Nazanin Gholampour-Faroji
- Industrial Biotechnology Research Group, Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Ahmadreza Bahrami
- Industrial Biotechnology Research Group, Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | | | - Maryam Moghadam Matin
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mohsen Qayoomian
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Neda Saebnia
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
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Zalar M, Wang B, Plavec J, Šket P. Insight into Tetramolecular DNA G-Quadruplexes Associated with ALS and FTLD: Cation Interactions and Formation of Higher-Ordered Structure. Int J Mol Sci 2023; 24:13437. [PMID: 37686239 PMCID: PMC10487854 DOI: 10.3390/ijms241713437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/24/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023] Open
Abstract
The G4C2 hexanucleotide repeat expansion in the c9orf72 gene is a major genetic cause of familial amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD), with the formation of G-quadruplexes directly linked to the development of these diseases. Cations play a crucial role in the formation and structure of G-quadruplexes. In this study, we investigated the impact of biologically relevant potassium ions on G-quadruplex structures and utilized 15N-labeled ammonium cations as a substitute for K+ ions to gain further insights into cation binding and exchange dynamics. Through nuclear magnetic resonance spectroscopy and molecular dynamics simulations, we demonstrate that the single d(G4C2) repeat, in the presence of 15NH4+ ions, adopts a tetramolecular G-quadruplex with an all-syn quartet at the 5'-end. The movement of 15NH4+ ions through the central channel of the G-quadruplex, as well as to the bulk solution, is governed by the vacant cation binding site, in addition to the all-syn quartet at the 5'-end. Furthermore, the addition of K+ ions to G-quadruplexes folded in the presence of 15NH4+ ions induces stacking of G-quadruplexes via their 5'-end G-quartets, leading to the formation of stable higher-ordered species.
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Affiliation(s)
- Matja Zalar
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia; (M.Z.); (B.W.); (J.P.)
| | - Baifan Wang
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia; (M.Z.); (B.W.); (J.P.)
| | - Janez Plavec
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia; (M.Z.); (B.W.); (J.P.)
- EN-FIST Center of Excellence, Trg OF 13, SI-1000 Ljubljana, Slovenia
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia
| | - Primož Šket
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia; (M.Z.); (B.W.); (J.P.)
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8
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Trizna L, Osif B, Víglaský V. G-QINDER Tool: Bioinformatically Predicted Formation of Different Four-Stranded DNA Motifs from (GT) n and (GA) n Repeats. Int J Mol Sci 2023; 24:ijms24087565. [PMID: 37108727 DOI: 10.3390/ijms24087565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/10/2023] [Accepted: 04/18/2023] [Indexed: 04/29/2023] Open
Abstract
The recently introduced semi-orthogonal system of nucleic acid imaging offers a greatly improved method of identifying DNA sequences that are capable of adopting noncanonical structures. This paper uses our newly developed G-QINDER tool to identify specific repeat sequences that adopt unique structural motifs in DNA: TG and AG repeats. The structures were found to adopt a left-handed G-quadruplex form under extreme crowding conditions and a unique tetrahelical motif under certain other conditions. The tetrahelical structure likely consists of stacked AGAG-tetrads but, unlike G-quadruplexes, their stability does not appear to be dependent on the type of monovalent cation present. The occurrence of TG and AG repeats in genomes is not rare, and they are also found frequently in the regulatory regions of nucleic acids, so it is reasonable to assume that putative structural motifs, like other noncanonical forms, could play an important regulatory role in cells. This hypothesis is supported by the structural stability of the AGAG motif; its unfolding can occur even at physiological temperatures since the melting temperature is primarily dependent on the number of AG repeats in the sequence.
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Affiliation(s)
- Lukáš Trizna
- Department of Biochemistry, Institute of Chemistry, Faculty of Sciences, Pavol Jozef Šafárik University, 04001 Košice, Slovakia
| | - Branislav Osif
- Department of Biochemistry, Institute of Chemistry, Faculty of Sciences, Pavol Jozef Šafárik University, 04001 Košice, Slovakia
| | - Viktor Víglaský
- Department of Biochemistry, Institute of Chemistry, Faculty of Sciences, Pavol Jozef Šafárik University, 04001 Košice, Slovakia
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Nguyen LTA, Dang DT. RHAU Peptides Specific for Parallel G-Quadruplexes: Potential Applications in Chemical Biology. Mol Biotechnol 2023; 65:291-299. [PMID: 35984625 DOI: 10.1007/s12033-022-00552-7] [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: 05/13/2022] [Accepted: 08/09/2022] [Indexed: 11/28/2022]
Abstract
G-quadruplexes (G4s) are non-canonical nucleic acid structures formed by guanine (G)-rich sequences, which are ubiquitously found in the human genome and transcriptome. Targeting G4s by specific ligands provides a powerful tool to monitor and regulate G4s-associated biological processes. RHAU peptides, derived from the G4-binding motif of "RNA Helicase associated with AU-rich element" (RHAU), have emerged as extraordinary ligands for specific recognition of parallel G4s. This review highlights the significances of recent studies investigating potential applications of the engineered RHAU peptides incorporated to different functional moieties.
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Affiliation(s)
- Le Tuan Anh Nguyen
- Faculty of Biotechnology, Ho Chi Minh City Open University, Ho Chi Minh City, Vietnam
| | - Dung Thanh Dang
- Faculty of Biotechnology, Ho Chi Minh City Open University, Ho Chi Minh City, Vietnam.
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10
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Wang J, Qiao J, Zheng W, Lian H. Study on the Interaction of a Peptide Targeting Specific G-Quadruplex Structures Based on Chromatographic Retention Behavior. Int J Mol Sci 2023; 24:ijms24021438. [PMID: 36674950 PMCID: PMC9866954 DOI: 10.3390/ijms24021438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/01/2023] [Accepted: 01/09/2023] [Indexed: 01/12/2023] Open
Abstract
G-quadruplexes (G4s) are of vital biological significance and G4-specific ligands with conformational selectivity show great application potential in disease treatment and biosensing. RHAU, a RNA helicase associated with AU-rich element, exerts biological functions through the mediation of G4s and has been identified to be a G4 binder. Here, we investigated the interactions between the RHAU peptide and G4s with different secondary structures using size exclusion chromatography (SEC) in association with circular dichroism (CD), ultraviolet-visible (UV-Vis) absorption, and native polyacrylamide gel electrophoresis (Native-PAGE). Spectral results demonstrated that the RHAU peptide did not break the main structure of G4s, making it more reliable for G4 structural analysis. The RHAU peptide was found to display a structural selectivity for a preferential binding to parallel G4s as reflected by the distinct chromatographic retention behaviors. In addition, the RHAU peptide exhibited different interactions with intermolecular parallel G4s and intramolecular parallel G4s, providing a novel recognition approach to G4 structures. The findings of this study enriched the insight into the binding of RHAU to G4s with various conformations. It is noteworthy that SEC technology can be easy and reliable for elucidating G4-peptide interactions, especially for a multiple G4 coexisting system, which supplied an alternative strategy to screen novel specific ligands for G4s.
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Affiliation(s)
- Ju Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering and Center of Materials Analysis, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China
| | - Junqin Qiao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering and Center of Materials Analysis, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China
- Correspondence: (J.Q.); (H.L.)
| | - Weijuan Zheng
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China
| | - Hongzhen Lian
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering and Center of Materials Analysis, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China
- Correspondence: (J.Q.); (H.L.)
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Shitikov EA, Bespiatykh DA, Bodoev IN, Zaychikova MV. G-Quadruplex Structures in Bacteria: Functional Properties and Prospects for Use as Biotargets. BIOCHEMISTRY (MOSCOW), SUPPLEMENT SERIES B: BIOMEDICAL CHEMISTRY 2022. [DOI: 10.1134/s1990750822040084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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12
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Bazzicalupi C, Bonardi A, Biver T, Ferraroni M, Papi F, Savastano M, Lombardi P, Gratteri P. Probing the Efficiency of 13-Pyridylalkyl Berberine Derivatives to Human Telomeric G-Quadruplexes Binding: Spectroscopic, Solid State and In Silico Analysis. Int J Mol Sci 2022; 23:ijms232214061. [PMID: 36430540 PMCID: PMC9693123 DOI: 10.3390/ijms232214061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022] Open
Abstract
The interaction between the series of berberine derivatives 1-5 (NAX071, NAX120, NAX075, NAX077 and NAX079) and human telomeric G-quadruplexes (G4), which are able to inhibit the Telomerase enzyme's activity in malignant cells, was investigated. The derivatives bear a pyridine moiety connected by a hydrocarbon linker of varying length (n = 1-5, with n number of aliphatic carbon atoms) to the C13 position of the parent berberine. As for the G4s, both bimolecular 5'-TAGGGTTAGGGT-3' (Tel12) and monomolecular 5'-TAGGGTTAGGGTTAGGGTTAGGG-3' (Tel23) DNA oligonucleotides were considered. Spectrophotometric titrations, melting tests, X-ray diffraction solid state analysis and in silico molecular dynamics (MD) simulations were used to describe the different systems. The results were compared in search of structure-activity relationships. The analysis pointed out the formation of 1:1 complexes between Tel12 and all ligands, whereas both 1:1 and 2:1 ligand/G4 stoichiometries were found for the adduct formed by NAX071 (n = 1). Tel12, with tetrads free from the hindrance by the loop, showed a higher affinity. The details of the different binding geometries were discussed, highlighting the importance of H-bonds given by the berberine benzodioxole group and a correlation between the strength of binding and the hydrocarbon linker length. Theoretical (MD) and experimental (X-ray) structural studies evidence the possibility for the berberine core to interact with one or both G4 strands, depending on the constraints given by the linker length, thus affecting the G4 stabilization effect.
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Affiliation(s)
- Carla Bazzicalupi
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Firenze, Italy
- Correspondence: (C.B.); (P.G.)
| | - Alessandro Bonardi
- Laboratory of Molecular Modeling Cheminformatics & QSAR, Department NEUROFARBA—Pharmaceutical and Nutraceutical Section, University of Firenze, Via Ugo Schiff 6, 50019 Firenze, Italy
| | - Tarita Biver
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Marta Ferraroni
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Firenze, Italy
| | - Francesco Papi
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Firenze, Italy
- Laboratory of Molecular Modeling Cheminformatics & QSAR, Department NEUROFARBA—Pharmaceutical and Nutraceutical Section, University of Firenze, Via Ugo Schiff 6, 50019 Firenze, Italy
| | - Matteo Savastano
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Firenze, Italy
| | - Paolo Lombardi
- Naxospharma srl, Via G. Di Vittorio 70, Novate Milanese, 20026 Milano, Italy
| | - Paola Gratteri
- Laboratory of Molecular Modeling Cheminformatics & QSAR, Department NEUROFARBA—Pharmaceutical and Nutraceutical Section, University of Firenze, Via Ugo Schiff 6, 50019 Firenze, Italy
- Correspondence: (C.B.); (P.G.)
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13
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Stipaničev N, Raabe K, Rozas I. Aiming to Improve Binding of Porphyrin Diphenyl Guanidinium Conjugates to Guanine-Quadruplexes: When Size Matters. Bioorg Med Chem Lett 2022; 75:128954. [PMID: 36031019 DOI: 10.1016/j.bmcl.2022.128954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/12/2022] [Accepted: 08/22/2022] [Indexed: 11/28/2022]
Abstract
Aiming to improve the binding to Guanine quadruplexes of different topologies, docking studies of porphyrin diphenyl guanidine conjugates previously prepared with an O or a S bridge between the diphenyl moiety and a newly design derivative with an SO2 bridge were carried out using different guanine quadruplexes of different topologies (four parallel, one antiparallel and one hybrid). Positive results were obtained from these computational studies drove us to prepare the SO2 bridge conjugate improving the synthetic route previously reported by us. Biophysical experiments such as UV-thermal melting and circular dichroism indicated the lack of binding to the double stranded DNA and poor binding of the new derivative prepared to any of the guanine quadruplexes studied. These results show that the size of this SO2 bridge could be responsible of the poor experimental binding to guanine quadruplexes.
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Affiliation(s)
- Nikolina Stipaničev
- School of Chemistry, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Konstantin Raabe
- School of Chemistry, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Isabel Rozas
- School of Chemistry, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland.
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Sharma T, Kundu N, Kaur S, Chakraborty A, Mahto AK, Dewangan RP, Shankaraswamy J, Saxena S. Recognition and unfolding of human telomeric G-quadruplex by short peptide binding identified from the HRDC domain of BLM helicase. RSC Adv 2022; 12:21760-21769. [PMID: 36043100 PMCID: PMC9358547 DOI: 10.1039/d2ra03646k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 07/17/2022] [Indexed: 11/24/2022] Open
Abstract
Research in recent decades has revealed that the guanine (G)-quadruplex secondary structure in DNA modulates a variety of cellular events that are mostly related to serious diseases. Systems capable of regulating DNA G-quadruplex structures would therefore be useful for the modulation of various cellular events to produce biological effects. A high specificity for recognition of telomeric G-quadruplex has been observed for BLM helicase. We identified peptides from the HRDC domain of BLM using a molecular docking approach with various available solutions and crystal structures of human telomeres and recently created a peptide library. Herein, we tested one peptide (BLM HRDC peptide) from the library and examined its interaction with human telomeric variant-1 (HTPu-var-1) to understand the basis of G4-protein interactions. Our circular dichroism (CD) data showed that HTPu-var-1 folded into an anti-parallel G-quadruplex, and the CD intensity significantly decreased upon increasing the peptide concentration. There was a significant decrease in hypochromicity due to the formation of G-quadruplex-peptide complex at 295 nm, which indicated the unfolding of structure due to the decrease in stacking interactions. The fluorescence data showed quenching upon titrating the peptide with HTPu-var-1-G4. Electrophoretic mobility shift assay confirmed the unfolding of the G4 structure. Cell viability was significantly reduced in the presence of the BLM peptide, with IC50 values of 10.71 μM and 11.83 μM after 72 and 96 hours, respectively. These results confirmed that the selected peptide has the ability to bind to human telomeric G-quadruplex and unfold it. This is the first report in which a peptide was identified from the HRDC domain of the BLM G4-binding protein for the exploration of the G4-binding motif, which suggests a novel strategy to target G4 using natural key peptide segments. Schematic representation of (HTPu–var-1-G4) located at the 3′ end, formation of G-quadruplex, model of the G-quadruplex structure, base stacking between G-quadruplex planes, G-quadruplex structure-peptide complex and twisting of G-quadruplex planes upon peptide binding.![]()
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Affiliation(s)
- Taniya Sharma
- Structural Biology Lab, Amity Institute of Biotechnology, Amity University Uttar Pradesh Sector-125, Expressway Highway Noida 201313 India +0120-4735600
| | - Nikita Kundu
- Structural Biology Lab, Amity Institute of Biotechnology, Amity University Uttar Pradesh Sector-125, Expressway Highway Noida 201313 India +0120-4735600
| | - Sarvpreet Kaur
- Structural Biology Lab, Amity Institute of Biotechnology, Amity University Uttar Pradesh Sector-125, Expressway Highway Noida 201313 India +0120-4735600
| | - Amlan Chakraborty
- Division of Immunology, Immunity to Infection and Respiratory Medicine (DIIRM), School of Biological Sciences, University of Manchester Manchester England
| | - Aman Kumar Mahto
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard New Delhi India
| | - Rikeshwer Prasad Dewangan
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard New Delhi India
| | - Jadala Shankaraswamy
- Department of Fruit Science, College of Horticulture, Sri Konda Laxman Telangana State Horticultural University Mojerla 509382 Telangana India
| | - Sarika Saxena
- Structural Biology Lab, Amity Institute of Biotechnology, Amity University Uttar Pradesh Sector-125, Expressway Highway Noida 201313 India +0120-4735600
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15
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Zhao CL, Qiao X, Liu XM, Song XQ, Zou YH, Li DQ, Yu XW, Bao WG, Xu JY. Rapid DNA interstrand cross-linking of Pt(IV) compound. Eur J Pharmacol 2022; 925:174985. [PMID: 35489419 DOI: 10.1016/j.ejphar.2022.174985] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 04/23/2022] [Accepted: 04/25/2022] [Indexed: 11/30/2022]
Abstract
Pt(IV) anticancer compounds have been developed for several decades to overcome the drawbacks of their Pt(II) congeners, and the reduction of Pt(IV) to Pt(II) has been commonly regarded as a necessary step in the activation of Pt(IV) compounds prior to targeting DNA. However, blockage of glutathione (GSH) biosynthesis resulted in a slight effect on the cytotoxicity of oxoplatin in yeast Saccharomyces cerevisiae strains, urging us to reconsider the mechanism of actions for the "inert" Pt(IV) complexes. Using X-ray absorption near-edge spectroscopy (XANES), our data demonstrated that Pt(IV) complex oxoplatin could bind to DNA in a tetravalent state. Both alkaline denaturing agarose electrophoresis and thermal denaturation-renaturation assay revealed that oxoplatin could rapidly produce stable interstrand crosslinks (ICLs), which can further translate into a fast cell-killing process in cancer cells. Using quantitative real-time PCR and immunofluorescence analysis, we also proved that Pt(IV) complex oxoplatin could induce a quick intracellular response of the FA/BRCA pathway in cancer cells that involves the DNA interstrand crosslinking repair system, and this quick response to ICLs was independent with the intracellular GSH levels. Cell cycle analysis showed that short incubation with oxoplatin can induce a strong S phase arrest in HeLa cells, indicating that the rapid interstrand crosslinks produced by oxoplatin might stall the replication fork, result in the double-strand breaks, and eventually induce cell death. Our results implied that, besides the reduction mechanism to release the Pt(II) congeners, direct and rapid interstrand cross-linking with DNA by Pt(IV) compounds might be a unique mechanism for Pt(IV) compounds, which may provide new insight for the development of next-generation platinum-based drugs.
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Affiliation(s)
- Chun-Lai Zhao
- Department of Chemical Biology and Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Xin Qiao
- Department of Chemical Biology and Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Xiao-Meng Liu
- Department of Chemical Biology and Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Xue-Qing Song
- Department of Chemical Biology and Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Yun-Hong Zou
- Department of Chemical Biology and Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Dan-Qing Li
- Department of Chemical Biology and Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Xia-Wen Yu
- Department of Chemical Biology and Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Wei-Guo Bao
- Department of Chemical Biology and Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China.
| | - Jing-Yuan Xu
- Department of Chemical Biology and Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China.
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16
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Shitikov EA, Bespiatykh DA, Bodoev IN, Zaychikova MV. [G-quadruplex structures in bacteria: functional properties and prospects for use as biotargets]. BIOMEDITSINSKAIA KHIMIIA 2022; 68:93-103. [PMID: 35485483 DOI: 10.18097/pbmc20226802093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
G-quadruplexes (G4), non-canonical secondary DNA structures, are intensively investigated for a long time. In eukaryotic organisms they play an important role in the regulation of gene expression and DNA repair. G4 have also been found in the genomes of numerous bacteria and archaea, but their functional role has not yet been fully explored. Nevertheless, their participation in the formation of antigenic variability, pathogenicity, antibiotic resistance and survival in extreme conditions has been established. Currently, many tools have been developed to detect potential G4 sequences and confirm their formation ability. Since the controlled formation and resolution of the quadruplex are significant means for the regulation of genes critical for survival, a promising direction is the search for ligands - compounds that can have a stabilizing effect on the quadruplex structure and thereby alter gene expression. Currently, a number of ligands are already known, their use stops the growth of pathogenic microorganisms. G4 ligands are of interest as potential antibiotics, which are extremely relevant due to the wide spread of drug resistant pathogens.
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Affiliation(s)
- E A Shitikov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - D A Bespiatykh
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - I N Bodoev
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - M V Zaychikova
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
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17
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McQuaid KT, Takahashi S, Baumgaertner L, Cardin DJ, Paterson NG, Hall JP, Sugimoto N, Cardin CJ. Ruthenium Polypyridyl Complex Bound to a Unimolecular Chair-Form G-Quadruplex. J Am Chem Soc 2022; 144:5956-5964. [PMID: 35324198 PMCID: PMC8991003 DOI: 10.1021/jacs.2c00178] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
![]()
The DNA G-quadruplex
is known for forming a range of topologies
and for the observed lability of the assembly, consistent with its
transient formation in live cells. The stabilization of a particular
topology by a small molecule is of great importance for therapeutic
applications. Here, we show that the ruthenium complex Λ-[Ru(phen)2(qdppz)]2+ displays enantiospecific G-quadruplex
binding. It crystallized in 1:1 stoichiometry with a modified human
telomeric G-quadruplex sequence, GGGTTAGGGTTAGGGTTTGGG (htel21T18), in an antiparallel chair topology, the first structurally
characterized example of ligand binding to this topology. The lambda
complex is bound in an intercalation cavity created by a terminal
G-quartet and the central narrow lateral loop formed by T10–T11–A12. The two remaining wide
lateral loops are linked through a third K+ ion at the
other end of the G-quartet stack, which also coordinates three thymine
residues. In a comparative ligand-binding study, we showed, using
a Klenow fragment assay, that this complex is the strongest observed
inhibitor of replication, both using the native human telomeric sequence
and the modified sequence used in this work.
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Affiliation(s)
- Kane T McQuaid
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, U.K
| | - Shuntaro Takahashi
- FIBER (Frontier Institute for Biomolecular Engineering Research), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Lena Baumgaertner
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, U.K
| | - David J Cardin
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, U.K
| | - Neil G Paterson
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, U.K
| | - James P Hall
- School of Pharmacy, University of Reading, Whiteknights, Reading RG6 6AD, U.K
| | - Naoki Sugimoto
- FIBER (Frontier Institute for Biomolecular Engineering Research), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan.,FIRST (Graduate School of Frontiers of Innovative Research in Science and Technology), Konan University, 7-1-20 Minatojima-Minamimashi, Chuo-Ku, Kobe 650-0047, Japan
| | - Christine J Cardin
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, U.K
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18
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Yılmaz HE, Bağda E, Bağda E, Durmuş M. Interaction of water soluble cationic gallium(III) phthalocyanines with different G-quadruplex DNAs. Polyhedron 2021. [DOI: 10.1016/j.poly.2021.115404] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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19
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Yang J, Zhang Y, Zhao J, Ma J, Yi C. Development of gold nanoparticles-aptamer nanocomposite for multiplexed analysis of antibiotics and design of molecular logic gates. NANOTECHNOLOGY 2021; 33:015501. [PMID: 34598169 DOI: 10.1088/1361-6528/ac2c41] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 10/01/2021] [Indexed: 06/13/2023]
Abstract
The widespread use of antibiotics caused severe problems of antibiotic residues in foodstuffs and water, posing a serious threat to public health and thus urging the development of sensitive, selective, and rapid detection methods for antibiotics. In this study, a fluorescence resonance energy transfer (FRET)-based system is developed for the multiplexed analysis of chloramphenicol (CAP) and streptomycin (Strep) with detection limits of 2.51 and 8.69μg l-1, respectively. The FRET-based system consists of Cy3-tagged anti-CAP aptamer-conjugated gold nanoparticles (AuNPs) (referred to as AuNPs-AptCAP) and Cy5-tagged anti-Strep aptamer-conjugated AuNPs (referred to as AuNPs-AptStrep). In addition, AuNPs-AptCAP and AuNPs-AptStrep have been demonstrated to serve as signal transducers for implementing a series of logic operations such as YES, NOT, INH, OR, (2-4)-Decoder and even more complicated multi-level logic gates (OR-INH). Based on the outputs of logic operations, it could be figured out whether targeted analytes were present or not, thus enabling multiplex sensing and evaluation of pollution status. This proof of concept study might provide a new route for the enhanced sensing performance to distinguish different pollution status as well as the design of molecular mimics of logic elements to demonstrate better applicability.
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Affiliation(s)
- Jun Yang
- Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, People's Republic of China
| | - Yali Zhang
- Shenzhen Second People's Hospital, Shenzhen 518035, People's Republic of China
- Guangdong Provincial Engineering and Technology Center of Advanced and Portable Medical Devices, School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen 518107, People's Republic of China
| | - Junkai Zhao
- Guangdong Provincial Engineering and Technology Center of Advanced and Portable Medical Devices, School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen 518107, People's Republic of China
| | - Junping Ma
- Guangdong Provincial Engineering and Technology Center of Advanced and Portable Medical Devices, School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen 518107, People's Republic of China
| | - Changqing Yi
- Guangdong Provincial Engineering and Technology Center of Advanced and Portable Medical Devices, School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen 518107, People's Republic of China
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20
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Largy E, König A, Ghosh A, Ghosh D, Benabou S, Rosu F, Gabelica V. Mass Spectrometry of Nucleic Acid Noncovalent Complexes. Chem Rev 2021; 122:7720-7839. [PMID: 34587741 DOI: 10.1021/acs.chemrev.1c00386] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nucleic acids have been among the first targets for antitumor drugs and antibiotics. With the unveiling of new biological roles in regulation of gene expression, specific DNA and RNA structures have become very attractive targets, especially when the corresponding proteins are undruggable. Biophysical assays to assess target structure as well as ligand binding stoichiometry, affinity, specificity, and binding modes are part of the drug development process. Mass spectrometry offers unique advantages as a biophysical method owing to its ability to distinguish each stoichiometry present in a mixture. In addition, advanced mass spectrometry approaches (reactive probing, fragmentation techniques, ion mobility spectrometry, ion spectroscopy) provide more detailed information on the complexes. Here, we review the fundamentals of mass spectrometry and all its particularities when studying noncovalent nucleic acid structures, and then review what has been learned thanks to mass spectrometry on nucleic acid structures, self-assemblies (e.g., duplexes or G-quadruplexes), and their complexes with ligands.
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Affiliation(s)
- Eric Largy
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Alexander König
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Anirban Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Debasmita Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Sanae Benabou
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Frédéric Rosu
- Univ. Bordeaux, CNRS, INSERM, IECB, UMS 3033, F-33600 Pessac, France
| | - Valérie Gabelica
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
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21
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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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22
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Abiri A, Lavigne M, Rezaei M, Nikzad S, Zare P, Mergny JL, Rahimi HR. Unlocking G-Quadruplexes as Antiviral Targets. Pharmacol Rev 2021; 73:897-923. [PMID: 34045305 DOI: 10.1124/pharmrev.120.000230] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Guanine-rich DNA and RNA sequences can fold into noncanonical nucleic acid structures called G-quadruplexes (G4s). Since the discovery that these structures may act as scaffolds for the binding of specific ligands, G4s aroused the attention of a growing number of scientists. The versatile roles of G4 structures in viral replication, transcription, and translation suggest direct applications in therapy or diagnostics. G4-interacting molecules (proteins or small molecules) may also affect the balance between latent and lytic phases, and increasing evidence reveals that G4s are implicated in generally suppressing viral processes, such as replication, transcription, translation, or reverse transcription. In this review, we focus on the discovery of G4s in viruses and the role of G4 ligands in the antiviral drug discovery process. After assessing the role of viral G4s, we argue that host G4s participate in immune modulation, viral tumorigenesis, cellular pathways involved in virus maturation, and DNA integration of viral genomes, which can be potentially employed for antiviral therapeutics. Furthermore, we scrutinize the impediments and shortcomings in the process of studying G4 ligands and drug discovery. Finally, some unanswered questions regarding viral G4s are highlighted for prospective future projects. SIGNIFICANCE STATEMENT: G-quadruplexes (G4s) are noncanonical nucleic acid structures that have gained increasing recognition during the last few decades. First identified as relevant targets in oncology, their importance in virology is now increasingly clear. A number of G-quadruplex ligands are known: viral transcription and replication are the main targets of these ligands. Both viral and cellular G4s may be targeted; this review embraces the different aspects of G-quadruplexes in both host and viral contexts.
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Affiliation(s)
- Ardavan Abiri
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (A.A., S.N.); Institut Pasteur, Department of Virology, UMR 3569 CNRS, Paris, France (M.L.); Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran (M.R.); Dioscuri Center of Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland (P.Z.); Faculty of Medicine, Cardinal Stefan Wyszyński University in Warsaw, Warsaw, Poland (P.Z.); Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, Palaiseau cedex, France (J.-L.M.); Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.); and Department of Pharmacology and Toxicology, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.)
| | - Marc Lavigne
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (A.A., S.N.); Institut Pasteur, Department of Virology, UMR 3569 CNRS, Paris, France (M.L.); Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran (M.R.); Dioscuri Center of Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland (P.Z.); Faculty of Medicine, Cardinal Stefan Wyszyński University in Warsaw, Warsaw, Poland (P.Z.); Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, Palaiseau cedex, France (J.-L.M.); Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.); and Department of Pharmacology and Toxicology, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.)
| | - Masoud Rezaei
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (A.A., S.N.); Institut Pasteur, Department of Virology, UMR 3569 CNRS, Paris, France (M.L.); Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran (M.R.); Dioscuri Center of Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland (P.Z.); Faculty of Medicine, Cardinal Stefan Wyszyński University in Warsaw, Warsaw, Poland (P.Z.); Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, Palaiseau cedex, France (J.-L.M.); Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.); and Department of Pharmacology and Toxicology, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.)
| | - Sanaz Nikzad
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (A.A., S.N.); Institut Pasteur, Department of Virology, UMR 3569 CNRS, Paris, France (M.L.); Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran (M.R.); Dioscuri Center of Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland (P.Z.); Faculty of Medicine, Cardinal Stefan Wyszyński University in Warsaw, Warsaw, Poland (P.Z.); Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, Palaiseau cedex, France (J.-L.M.); Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.); and Department of Pharmacology and Toxicology, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.)
| | - Peyman Zare
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (A.A., S.N.); Institut Pasteur, Department of Virology, UMR 3569 CNRS, Paris, France (M.L.); Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran (M.R.); Dioscuri Center of Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland (P.Z.); Faculty of Medicine, Cardinal Stefan Wyszyński University in Warsaw, Warsaw, Poland (P.Z.); Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, Palaiseau cedex, France (J.-L.M.); Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.); and Department of Pharmacology and Toxicology, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.)
| | - Jean-Louis Mergny
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (A.A., S.N.); Institut Pasteur, Department of Virology, UMR 3569 CNRS, Paris, France (M.L.); Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran (M.R.); Dioscuri Center of Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland (P.Z.); Faculty of Medicine, Cardinal Stefan Wyszyński University in Warsaw, Warsaw, Poland (P.Z.); Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, Palaiseau cedex, France (J.-L.M.); Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.); and Department of Pharmacology and Toxicology, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.)
| | - Hamid-Reza Rahimi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (A.A., S.N.); Institut Pasteur, Department of Virology, UMR 3569 CNRS, Paris, France (M.L.); Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran (M.R.); Dioscuri Center of Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland (P.Z.); Faculty of Medicine, Cardinal Stefan Wyszyński University in Warsaw, Warsaw, Poland (P.Z.); Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, Palaiseau cedex, France (J.-L.M.); Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.); and Department of Pharmacology and Toxicology, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.)
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23
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Maddah M, Karami L. An atomistic investigation on the interaction of distamycin A and its derivative with the telomeric G-Quadruplex as anticancer agents by molecular dynamics simulation. Arch Biochem Biophys 2021; 701:108797. [PMID: 33607110 DOI: 10.1016/j.abb.2021.108797] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 02/05/2021] [Accepted: 02/06/2021] [Indexed: 10/22/2022]
Abstract
Human telomerase that activates within cancer cells has a telomeric sequence at the 3' end. Each factor that stabilizes the G-quadruplex in guanine-rich telomeric sequences can inhibit the regular telomerase activity. Therefore, the telomeric G-quadruplex is known as a promising target in cancer treatment. In this work, we studied the binding of positively charged distamycin A and its uncharged derivative to the G-quadruplex in a solution environment by Molecular Dynamics (MD) simulation. The binding mechanism and subtle conformational changes were investigated as a result of the ligand attachment. Moreover, binding free energy and clustering analysis describe the stability and flexibility of G-quadruplexes upon ligand binding. Structural analyses displayed that the favorable binding of both ligands imposes significant stability and rigidity in G-quadruplex conformation compared to free G-quadruplex, especially charged distamycin. Hydration pattern and ion distribution were different for free G-quadruplex and both of the ligand complexes. Energy decomposition reveals the electrostatic effect on the stability of G-quadruplex. The radial distribution function displayed the solvent shell and ion moving away from the groove. The hydrogen bond played an essential role in the binding of both ligands, especially for the charged derivative. van der Waals interaction is the only factor that is more important in binding uncharged distamycin into G-quadruplex than the charged one. The calculated ΔGbind showed the stability of both ligands within grooves and good agreement with the experimental binding free energy data. Finally, the results suggest that ligand modification improves the binding mode toward stabilizing G-quadruplexes.
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Affiliation(s)
- Mina Maddah
- Depatment of Chemistry, K. N. Toosi University of Technology, Tehran, Iran; Super Computing Institute, University of Tehran, Tehran, Iran.
| | - Leila Karami
- Department of Cell and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran.
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24
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Xie Y, Wang Y, Xiang W, Wang Q, Cao Y. Molecular Mechanisms of the Action of Myricetin in Cancer. Mini Rev Med Chem 2020; 20:123-133. [PMID: 31648635 DOI: 10.2174/1389557519666191018112756] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 03/31/2019] [Accepted: 09/26/2019] [Indexed: 02/07/2023]
Abstract
Natural compounds, such as paclitaxel and camptothecin, have great effects on the treatment of tumors. Such natural chemicals often achieve anti-tumor effects through a variety of mechanisms. Therefore, it is of great significance to conduct further studies on the anticancer mechanism of natural anticancer agents to lay a solid foundation for the development of new drugs. Myricetin, originally isolated from Myrica nagi, is a natural pigment of flavonoids that can inhibit the growth of cancer cells (such as liver cancer, rectal cancer, skin cancer and lung cancer, etc.). It can regulate many intracellular activities (such as anti-inflammatory and blood lipids regulation) and can even be bacteriostatic. The purpose of this paper is to outline the molecular pathways of the anticancer effects of myricetin, including the effect on cancer cell death, proliferation, angiogenesis, metastasis and cell signaling pathway.
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Affiliation(s)
- Yutao Xie
- Department of Pharmacy, Nanchong Center Hospital, The Second Clinical Medical College, North Sichuan Medical College (University), Nanchong, 637000, Sichuan, China
| | - Yunlong Wang
- Department of Pharmacy, Nanchong Center Hospital, The Second Clinical Medical College, North Sichuan Medical College (University), Nanchong, 637000, Sichuan, China
| | - Wei Xiang
- Department of Pharmacy, Nanchong Center Hospital, The Second Clinical Medical College, North Sichuan Medical College (University), Nanchong, 637000, Sichuan, China
| | - Qiaoying Wang
- Department of Cardiothoracic Surgery, Nanchong Center Hospital, The Second Clinical Medical College, North Sichuan Medical College (University), Nanchong, 637000, Sichuan, China
| | - Yajun Cao
- Department of Pharmacy, Nanchong Center Hospital, The Second Clinical Medical College, North Sichuan Medical College (University), Nanchong, 637000, Sichuan, China
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25
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Yum JH, Sugiyama H, Park S. Modular quadruplex-duplex hybrids as biomolecular scaffolds for asymmetric Michael addition reactions. Org Biomol Chem 2020; 18:6812-6817. [PMID: 32870219 DOI: 10.1039/d0ob01362e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Asymmetric synthesis based on DNA scaffolds has been actively exploited because of the advantages of DNA such as diverse tertiary structures, chemical stability, and easy handling. Since duplex DNA-based hybrid catalysts have demonstrated this remarkable capability, efforts have been made to investigate new biomolecular scaffolds. Herein, we report modular quadruplex-duplex (QD) hybrid DNA catalysts containing bipyridine ligands and hydrogen donor moieties. The conformation, thermal stability, and metal-binding ability of modified QD hybrid DNA were characterized using spectroscopy. The QD hybrid-based DNA catalysts were successfully applied to asymmetric Michael addition reactions (86% conversion and 76% ee). This study describes a new type of DNA hybrid catalyst produced by the construction of a cooperative active site with a Lewis acid and a H-bond donor.
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Affiliation(s)
- Ji Hye Yum
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku Kyoto 606-8502, Japan.
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26
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Zhang Y, Li CW, Zhou L, Chen Z, Yi C. "Plug and Play" logic gate construction based on chemically triggered fluorescence switching of gold nanoparticles conjugated with Cy3-tagged aptamer. Mikrochim Acta 2020; 187:437. [PMID: 32647943 DOI: 10.1007/s00604-020-04421-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 06/30/2020] [Indexed: 11/29/2022]
Abstract
Gold nanoparticles (AuNPs) conjugated with Cy3-tagged aptamer which can specifically recognize chloramphenicol (CAP) (referred to as AuNPs-AptCAP) are described. CAP can trigger the configuration change of CAP binding aptamer, and thus switching the fluorescence of AuNPs-AptCAP through changing the efficiency of the fluorescence resonance energy transfer (FRET) system with Cy3 as donors and AuNPs as recipients. AuNPs-AptCAP exhibits a linear range of CAP concentrations from 26.0 to 277 μg L-1 with a limit of detection of 8.1 μg L-1 when Cy3 was excited at 530 nm and emission was measured at 570 nm. More importantly, AuNPs-AptCAP can be utilized as signal transducers for the build-up of a series of logic gates including YES, PASS 0, INH, NOT, PASS 1, and NAND. Utilizing the principle of a metal ion-mediated fluorescence switch together with a strong metal ion chelator, the fluorescence of AuNPs-AptCAP could be modulated by adding metal ions and EDTA sequentially. Therefore, a "Plug and Play" logic system based on AuNPs-AptCAP has been realized by simply adding other components to create new logic functions. This work highlights the advantages of simple synthesis and facile fluorescence switching properties, which will provide useful knowledge for the establishment of molecular logic systems. Graphical abstract.
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Affiliation(s)
- Yali Zhang
- Key Laboratory of Sensing Technology and Biomedical Instruments (Guangdong Province), School of Biomedical Engineering, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Cheuk-Wing Li
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK
| | - Lefei Zhou
- Key Laboratory of Sensing Technology and Biomedical Instruments (Guangdong Province), School of Biomedical Engineering, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Zhanpeng Chen
- Key Laboratory of Sensing Technology and Biomedical Instruments (Guangdong Province), School of Biomedical Engineering, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Changqing Yi
- Key Laboratory of Sensing Technology and Biomedical Instruments (Guangdong Province), School of Biomedical Engineering, Sun Yat-Sen University, Guangzhou, 510006, China. .,Research Institute of Sun Yat-Sen University in Shenzhen, Shenzhen, 518057, China.
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27
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Park S, Matsui H, Fukumoto K, Yum JH, Sugiyama H. Histidine-conjugated DNA as a biomolecular depot for metal ions. RSC Adv 2020; 10:9717-9722. [PMID: 35497221 PMCID: PMC9050151 DOI: 10.1039/d0ra01267j] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 02/26/2020] [Indexed: 12/18/2022] Open
Abstract
Histidine is a versatile amino acid residue that plays a critical role in the active sites of many metalloenzymes. DNA is an attractive biomolecular scaffold owing to its chemical and thermal stability and easy accessibility. Herein, we report histidine-conjugated DNA oligonucleotides, which were synthesized by combining DNA alphabets and natural metal-binding amino acids, as novel biohybrid materials and demonstrate their use as molecular depots for various metal ions. Moreover, histidine-conjugated DNA oligonucleotides could be successfully used in asymmetric catalysis (up to 90% conversion and 95% ee) as DNA metalloenzymes and in 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) oxidation reactions as horseradish-peroxidase (HRP)-mimicking DNAzymes with suitable metal cofactors. Nature-inspired histidine-DNA hybrids will become an attractive strategy to construct fine-tuned coordination environments as an alternative to bioremediation and the development of multimetal enzymes. Histidine is a versatile amino acid residue that plays a critical role in the active sites of many metalloenzymes.![]()
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Affiliation(s)
- Soyoung Park
- Department of Chemistry
- Graduate School of Science
- Kyoto University
- Kyoto 606-8502
- Japan
| | - Haruka Matsui
- Department of Chemistry
- Graduate School of Science
- Kyoto University
- Kyoto 606-8502
- Japan
| | - Koyuki Fukumoto
- Department of Chemistry
- Graduate School of Science
- Kyoto University
- Kyoto 606-8502
- Japan
| | - Ji Hye Yum
- Department of Chemistry
- Graduate School of Science
- Kyoto University
- Kyoto 606-8502
- Japan
| | - Hiroshi Sugiyama
- Department of Chemistry
- Graduate School of Science
- Kyoto University
- Kyoto 606-8502
- Japan
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28
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Chaconas G, Castellanos M, Verhey TB. Changing of the guard: How the Lyme disease spirochete subverts the host immune response. J Biol Chem 2019; 295:301-313. [PMID: 31753921 DOI: 10.1074/jbc.rev119.008583] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Lyme disease, also known as Lyme borreliosis, is the most common tick-transmitted disease in the Northern Hemisphere. The disease is caused by the bacterial spirochete Borrelia burgdorferi and other related Borrelia species. One of the many fascinating features of this unique pathogen is an elaborate system for antigenic variation, whereby the sequence of the surface-bound lipoprotein VlsE is continually modified through segmental gene conversion events. This perpetual changing of the guard allows the pathogen to remain one step ahead of the acquired immune response, enabling persistent infection. Accordingly, the vls locus is the most evolutionarily diverse genetic element in Lyme disease-causing borreliae. Small stretches of information are transferred from a series of silent cassettes in the vls locus to generate an expressed mosaic vlsE gene version that contains genetic information from several different silent cassettes, resulting in ∼1040 possible vlsE sequences. Yet, despite its extreme evolutionary flexibility, the locus has rigidly conserved structural features. These include a telomeric location of the vlsE gene, an inverse orientation of vlsE and the silent cassettes, the presence of nearly perfect inverted repeats of ∼100 bp near the 5' end of vlsE, and an exceedingly high concentration of G runs in vlsE and the silent cassettes. We discuss the possible roles of these evolutionarily conserved features, highlight recent findings from several studies that have used next-generation DNA sequencing to unravel the switching process, and review advances in the development of a mini-vls system for genetic manipulation of the locus.
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Affiliation(s)
- George Chaconas
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta T2N 4N1, Canada; Department of Microbiology, Immunology, and Infectious Diseases, University of Calgary, Calgary, Alberta T2N 4N1, Canada; Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta T2N 4N1, Canada.
| | - Mildred Castellanos
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta T2N 4N1, Canada; Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Theodore B Verhey
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta T2N 4N1, Canada; Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta T2N 4N1, Canada
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Doria F, Salvati E, Pompili L, Pirota V, D'Angelo C, Manoli F, Nadai M, Richter SN, Biroccio A, Manet I, Freccero M. Dyads of G‐Quadruplex Ligands Triggering DNA Damage Response and Tumour Cell Growth Inhibition at Subnanomolar Concentration. Chemistry 2019; 25:11085-11097. [DOI: 10.1002/chem.201900766] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 06/18/2019] [Indexed: 02/05/2023]
Affiliation(s)
- Filippo Doria
- Department of ChemistryUniversity of Pavia V. le Taramelli 10 27100 Pavia Italy
| | - Erica Salvati
- Oncogenomic and Epigenetic UnitIRCCS Regina Elena National Cancer Institute Via Elio Chianes 53 00144 Rome Italy
- Present address: Institute of Molecular Biology and Pathology (IBPM)National Research Council (CNR) Via degli Apuli 4 00185 Rome Italy
| | - Luca Pompili
- Oncogenomic and Epigenetic UnitIRCCS Regina Elena National Cancer Institute Via Elio Chianes 53 00144 Rome Italy
| | - Valentina Pirota
- Department of ChemistryUniversity of Pavia V. le Taramelli 10 27100 Pavia Italy
| | - Carmen D'Angelo
- Oncogenomic and Epigenetic UnitIRCCS Regina Elena National Cancer Institute Via Elio Chianes 53 00144 Rome Italy
| | - Francesco Manoli
- Institute for Organic Synthesis and Photoreactivity (ISOF)National Research Council (CNR) Via P. Gobetti 101 40129 Bologna Italy
| | - Matteo Nadai
- Department of Molecular MedicineUniversity of Padua Via Gabelli 63 35121 Padua Italy
| | - Sara N. Richter
- Department of Molecular MedicineUniversity of Padua Via Gabelli 63 35121 Padua Italy
| | - Annamaria Biroccio
- Oncogenomic and Epigenetic UnitIRCCS Regina Elena National Cancer Institute Via Elio Chianes 53 00144 Rome Italy
| | - Ilse Manet
- Institute for Organic Synthesis and Photoreactivity (ISOF)National Research Council (CNR) Via P. Gobetti 101 40129 Bologna Italy
| | - Mauro Freccero
- Department of ChemistryUniversity of Pavia V. le Taramelli 10 27100 Pavia Italy
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30
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Fong P, Wong HK. Evaluation of Scoring Function Performance on DNA-ligand Complexes. THE OPEN MEDICINAL CHEMISTRY JOURNAL 2019. [DOI: 10.2174/1874104501913010040] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Background:
DNA has been a pharmacological target for different types of treatment, such as antibiotics and chemotherapy agents, and is still a potential target in many drug discovery processes. However, most docking and scoring approaches were parameterised for protein-ligand interactions; their suitability for modelling DNA-ligand interactions is uncertain.
Objective:
This study investigated the performance of four scoring functions on DNA-ligand complexes.
Material & Methods:
Here, we explored the ability of four docking protocols and scoring functions to discriminate the native pose of 33 DNA-ligand complexes over a compiled set of 200 decoys for each DNA-ligand complexes. The four approaches were the AutoDock, ASP@GOLD, ChemScore@GOLD and GoldScore@GOLD.
Results:
Our results indicate that AutoDock performed the best when predicting binding mode and that ChemScore@GOLD achieved the best discriminative power. Rescoring of AutoDock-generated decoys with ChemScore@GOLD further enhanced their individual discriminative powers. All four approaches have no discriminative power in some DNA-ligand complexes, including both minor groove binders and intercalators.
Conclusion:
This study suggests that the evaluation for each DNA-ligand complex should be performed in order to obtain meaningful results for any drug discovery processes. Rescoring with different scoring functions can improve discriminative power.
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31
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Li Y, Liu W, Zhu Y, Diao L. A fluorescence method for homogeneous detection of influenza A DNA sequence based on guanine-quadruplex-N-methylmesoporphyrin IX complex and assistance-DNA inhibition. J Med Virol 2019; 91:979-985. [PMID: 30715734 DOI: 10.1002/jmv.25422] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 11/20/2018] [Accepted: 12/07/2018] [Indexed: 12/31/2022]
Abstract
In his study, we report a fluorescence method for homogeneous detection of influenza A (H1N1) DNA sequence based on G-quadruplex-NMM complex and assistance-DNA (A-DNA) inhibition. The quadruplex-based functional DNA (QBF-DNA), composed of a complementary probe to the target H1N1 DNA sequence and G-rich fragment, was designed as the signal DNA. The A-DNA consisted of two parts, one part was complementary to target H1N1 DNA and the other part was complementary to the signal DNA. In the absence of target H1N1 DNA, the G-rich fragment of QBF-DNA can form G-quadruplex-NMM complex, which outputted a fluorescent signal. With the presence of target H1N1 DNA, QBF-DNA, and A-DNA can simultaneously hybridize with target H1N1 DNA to form double-helix structure. In this case, the A-DNA partially hybridized with the QBF-DNA, which inhibited the formation of G-quadruplex-NMM complex, leading to the decrease of fluorescent signal. Under the optimum conditions, the fluorescence intensity was inversely proportional to the concentration of target H1N1 DNA over the range from 25 to 700 pmol/L with a detection limit of 8 pmol/L. In addition, the method is target specific and practicability, and would become a new diagnostic assay for H1N1 DNA sequence and other infectious diseases.
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Affiliation(s)
- Yubin Li
- School of Chemistry and Environment, Guangdong Ocean University, Zhanjiang, China
| | - Wanshan Liu
- School of Chemistry and Environment, Guangdong Ocean University, Zhanjiang, China
| | - Yinling Zhu
- School of Chemistry and Environment, Guangdong Ocean University, Zhanjiang, China
| | - Liping Diao
- School of Chemistry and Environment, Guangdong Ocean University, Zhanjiang, China
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32
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Xu H, Zhu X, Wang J, Lin Z, Chen G. Electrochemiluminescent functional nucleic acids‐based sensors for food analysis. LUMINESCENCE 2019; 34:308-315. [DOI: 10.1002/bio.3596] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 12/20/2018] [Accepted: 12/23/2018] [Indexed: 12/15/2022]
Affiliation(s)
- Huifeng Xu
- Academy of Integrative MedicineFujian University of Traditional Chinese Medicine Fuzhou Fujian P. R. China
| | - Xi Zhu
- College of Life SciencesFujian Agriculture and Forestry University Fuzhou Fujian P. R. China
| | - Jian Wang
- Ministry of Education Key Laboratory of Analysis and Detection for Food Safety, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, Department of ChemistryFuzhou University Fuzhou Fujian P. R. China
| | - Zhenyu Lin
- Ministry of Education Key Laboratory of Analysis and Detection for Food Safety, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, Department of ChemistryFuzhou University Fuzhou Fujian P. R. China
| | - Guonan Chen
- Ministry of Education Key Laboratory of Analysis and Detection for Food Safety, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, Department of ChemistryFuzhou University Fuzhou Fujian P. R. China
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33
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Asamitsu S, Obata S, Yu Z, Bando T, Sugiyama H. Recent Progress of Targeted G-Quadruplex-Preferred Ligands Toward Cancer Therapy. Molecules 2019; 24:E429. [PMID: 30682877 PMCID: PMC6384606 DOI: 10.3390/molecules24030429] [Citation(s) in RCA: 192] [Impact Index Per Article: 38.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 01/22/2019] [Accepted: 01/23/2019] [Indexed: 02/07/2023] Open
Abstract
A G-quadruplex (G4) is a well-known nucleic acid secondary structure comprising guanine-rich sequences, and has profound implications for various pharmacological and biological events, including cancers. Therefore, ligands interacting with G4s have attracted great attention as potential anticancer therapies or in molecular probe applications. To date, a large variety of DNA/RNA G4 ligands have been developed by a number of laboratories. As protein-targeting drugs face similar situations, G-quadruplex-interacting drugs displayed low selectivity to the targeted G-quadruplex structure. This low selectivity could cause unexpected effects that are usually reasons to halt the drug development process. In this review, we address the recent research on synthetic G4 DNA-interacting ligands that allow targeting of selected G4s as an approach toward the discovery of highly effective anticancer drugs.
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Affiliation(s)
- Sefan Asamitsu
- Department of Chemistry, Graduate School of Science Kyoto University, Kitashirakawa-Oiwakecho, Sakyo, Kyoto, 606-8502, Japan.
| | - Shunsuke Obata
- Department of Chemistry, Graduate School of Science Kyoto University, Kitashirakawa-Oiwakecho, Sakyo, Kyoto, 606-8502, Japan.
| | - Zutao Yu
- Department of Chemistry, Graduate School of Science Kyoto University, Kitashirakawa-Oiwakecho, Sakyo, Kyoto, 606-8502, Japan.
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science Kyoto University, Kitashirakawa-Oiwakecho, Sakyo, Kyoto, 606-8502, Japan.
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science Kyoto University, Kitashirakawa-Oiwakecho, Sakyo, Kyoto, 606-8502, Japan.
- Institute for Integrated Cell-Material Science (WPI-iCeMS) Kyoto University, Yoshida-Ushinomiyacho, Sakyo, Kyoto, 606-8501, Japan.
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34
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Yum JH, Park S, Sugiyama H. G-quadruplexes as versatile scaffolds for catalysis. Org Biomol Chem 2019; 17:9547-9561. [DOI: 10.1039/c9ob01876j] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
This review summarizes the beginning, progress, and prospects of non-canonical DNA-based hybrid catalysts focusing on G-quadruplexes as versatile scaffolds for catalysis.
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Affiliation(s)
- Ji Hye Yum
- Department of Chemistry
- Graduate School of Science
- Kyoto University
- Kyoto 606-8502
- Japan
| | - Soyoung Park
- Department of Chemistry
- Graduate School of Science
- Kyoto University
- Kyoto 606-8502
- Japan
| | - Hiroshi Sugiyama
- Department of Chemistry
- Graduate School of Science
- Kyoto University
- Kyoto 606-8502
- Japan
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35
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Azargun M, Meister PJ, Gauld JW, Fridgen TD. The K2(9-ethylguanine)122+ quadruplex is more stable to unimolecular dissociation than the K(9-ethylguanine)8+ quadruplex in the gas phase: a BIRD, energy resolved SORI-CID, IRMPD spectroscopic, and computational study. Phys Chem Chem Phys 2019; 21:15319-15326. [DOI: 10.1039/c9cp01651a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A combination of experimental trapped-ion mass spectrometric studies and computational chemistry has been used to assess the intrinsic properties of the potassiated 9-ethylguanine (9eG) self-assembled quadruplex, K2(9eG)122+, in the gas phase.
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Affiliation(s)
- Mohammad Azargun
- Department of Chemistry
- Memorial University of Newfoundland
- St. John's
- Canada
| | - Paul J. Meister
- Department of Chemistry and Biochemistry
- University of Windsor
- Windsor
- Canada
| | - James W. Gauld
- Department of Chemistry and Biochemistry
- University of Windsor
- Windsor
- Canada
| | - Travis D. Fridgen
- Department of Chemistry
- Memorial University of Newfoundland
- St. John's
- Canada
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36
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Non-duplex G-Quadruplex Structures Emerge as Mediators of Epigenetic Modifications. Trends Genet 2018; 35:129-144. [PMID: 30527765 DOI: 10.1016/j.tig.2018.11.001] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 10/10/2018] [Accepted: 11/02/2018] [Indexed: 12/16/2022]
Abstract
The role of non-duplex DNA, the guanine-quadruplex structure in particular, is becoming widely appreciated. Increasing evidence in the last decade implicates quadruplexes in important processes such as transcription and replication. Interestingly, more recent work suggests roles for quadruplexes, in association with quadruplex-interacting proteins, in epigenetics through both DNA and histone modifications. Here, we review the effect of the quadruplex structure on post-replication epigenetic memory and quadruplex-induced promoter DNA/histone modifications. Furthermore, we highlight the epigenetic state of the telomerase promoter where quadruplexes could play a key regulatory role. Finally, we discuss the possibility that DNA structures such as quadruplexes, within a largely duplex DNA background, could act as molecular anchors for locally induced epigenetic modifications.
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37
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Asamitsu S, Bando T, Sugiyama H. Ligand Design to Acquire Specificity to Intended G-Quadruplex Structures. Chemistry 2018; 25:417-430. [PMID: 30051593 DOI: 10.1002/chem.201802691] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 07/14/2018] [Indexed: 12/17/2022]
Abstract
A G-quadruplex is a nucleic acid secondary structure that is adopted by guanine-rich sequences, and is considered to be relevant in various pharmacological and biological contexts. G-Quadruplexes have also attracted great attention in the field of DNA nanotechnology because of their extremely high thermal stability and the availability of many defined structures. To date, a large repertory of DNA/RNA G-quadruplex-interactive ligands has been developed by numerous laboratories. Several relevant reviews have also been published that have helped researchers to grasp the full scope of G-quadruplex research from its outset to the present. This review focuses on the G-quadruplex ligands that allow targeting of specific G-quadruplexes. Moreover, unique ligands, successful methodologies, and future perspectives in relation to specific G-quadruplex recognition are also addressed.
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Affiliation(s)
- Sefan Asamitsu
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo, Kyoto, 606-8502, Japan
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo, Kyoto, 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo, Kyoto, 606-8502, Japan.,Institute for Integrated Cell-Material Science (WPI-iCeMS), Kyoto University, Sakyo, Kyoto, 606-8501, Japan
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38
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Liu C, Zhou B, Geng Y, Yan Tam D, Feng R, Miao H, Xu N, Shi X, You Y, Hong Y, Tang BZ, Kwan Lo P, Kuryavyi V, Zhu G. A chair-type G-quadruplex structure formed by a human telomeric variant DNA in K + solution. Chem Sci 2018; 10:218-226. [PMID: 30713633 PMCID: PMC6330691 DOI: 10.1039/c8sc03813a] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Accepted: 10/03/2018] [Indexed: 01/15/2023] Open
Abstract
The chair-type G-quadruplex structure formed by human telomeric variant DNA.
Guanine tracts of human telomeric DNA sequences are known to fold into eight different four-stranded structures that vary by the conformation of guanine nucleotides arranged in the stack of G-tetrads in their core and by different kinds and orders of connecting loops, called G-quadruplexes. Here, we present a novel G-quadruplex structure formed in K+ solution by a human telomeric variant d[(GGGTTA)2GGGTTTGGG], htel21T18. This variant DNA is located in the subtelomeric regions of human chromosomes 8, 11, 17, and 19 as well as in the DNase hypersensitive region and in the subcentromeric region of chromosome 5. Interestingly, single A18T substitution that makes htel21T18 different from the human telomeric sequence results in the formation of a three-layer chair-type G-quadruplex, a fold previously unknown among human telomeric repeats, with two loops interacting through the reverse Watson–Crick A6·T18 base pair. The loops are edgewise; glycosidic conformation of guanines is syn·anti·syn·anti around each tetrad, and each strand of the core has two antiparallel adjacent strands. Our results expand the repertoire of known G-quadruplex folding topologies and may provide a potential target for structure-based anticancer drug design.
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Affiliation(s)
- Changdong Liu
- Division of Life Science , The Hong Kong University of Science and Technology , Clear Water Bay , Kowloon , Hong Kong SAR , China .
| | - Bo Zhou
- Division of Life Science , The Hong Kong University of Science and Technology , Clear Water Bay , Kowloon , Hong Kong SAR , China . .,Institute for Advanced Study , The Hong Kong University of Science and Technology , Clear Water Bay , Kowloon , Hong Kong SAR , China
| | - Yanyan Geng
- Division of Life Science , The Hong Kong University of Science and Technology , Clear Water Bay , Kowloon , Hong Kong SAR , China .
| | - Dick Yan Tam
- Department of Biology and Chemistry , City University of Hong Kong , 83 Tat Chee Avenue , Kowloon Tong , Hong Kong SAR , China
| | - Rui Feng
- Division of Life Science , The Hong Kong University of Science and Technology , Clear Water Bay , Kowloon , Hong Kong SAR , China .
| | - Haitao Miao
- Division of Life Science , The Hong Kong University of Science and Technology , Clear Water Bay , Kowloon , Hong Kong SAR , China .
| | - Naining Xu
- Division of Life Science , The Hong Kong University of Science and Technology , Clear Water Bay , Kowloon , Hong Kong SAR , China .
| | - Xiao Shi
- Division of Life Science , The Hong Kong University of Science and Technology , Clear Water Bay , Kowloon , Hong Kong SAR , China .
| | - Yingying You
- Division of Life Science , The Hong Kong University of Science and Technology , Clear Water Bay , Kowloon , Hong Kong SAR , China .
| | - Yuning Hong
- Department of Chemistry , The Hong Kong University of Science and Technology , Clear Water Bay , Kowloon , Hong Kong SAR , China
| | - Ben Zhong Tang
- Department of Chemistry , The Hong Kong University of Science and Technology , Clear Water Bay , Kowloon , Hong Kong SAR , China
| | - Pik Kwan Lo
- Department of Biology and Chemistry , City University of Hong Kong , 83 Tat Chee Avenue , Kowloon Tong , Hong Kong SAR , China
| | - Vitaly Kuryavyi
- Structural Biology Program , Memorial Sloan-Kettering Cancer Center , New York , NY , USA .
| | - Guang Zhu
- Division of Life Science , The Hong Kong University of Science and Technology , Clear Water Bay , Kowloon , Hong Kong SAR , China . .,Institute for Advanced Study and State Key Laboratory of Molecular Neuroscience , The Hong Kong University of Science and Technology , Clear Water Bay , Kowloon , Hong Kong SAR , China
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Ghoshdastidar D, Bansal M. Dynamics of physiologically relevant noncanonical DNA structures: an overview from experimental and theoretical studies. Brief Funct Genomics 2018; 18:192-204. [DOI: 10.1093/bfgp/ely026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 06/23/2018] [Accepted: 07/09/2018] [Indexed: 12/23/2022] Open
Abstract
Abstract
DNA is a complex molecule with phenomenal inherent plasticity and the ability to form different hydrogen bonding patterns of varying stabilities. These properties enable DNA to attain a variety of structural and conformational polymorphic forms. Structurally, DNA can exist in single-stranded form or as higher-order structures, which include the canonical double helix as well as the noncanonical duplex, triplex and quadruplex species. Each of these structural forms in turn encompasses an ensemble of dynamically heterogeneous conformers depending on the sequence composition and environmental context. In vivo, the widely populated canonical B-DNA attains these noncanonical polymorphs during important cellular processes. While several investigations have focused on the structure of these noncanonical DNA, studying their dynamics has remained nontrivial. Here, we outline findings from some recent advanced experimental and molecular simulation techniques that have significantly contributed toward understanding the complex dynamics of physiologically relevant noncanonical forms of DNA.
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Affiliation(s)
| | - Manju Bansal
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
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40
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Fu X, Zhang H, Zhang J, Wen ST, Deng XC. A Highly Sensitive and Label-Free Microbead-Based ‘Turn-On’ Colorimetric Sensor for the Detection of Mercury(II) in Urine Using a Peroxidase-Like Split G-Quadruplex–Hemin DNAzyme. Aust J Chem 2018. [DOI: 10.1071/ch18302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A highly sensitive and label-free microbead-based ‘turn-on’ assay was developed for the detection of Hg2+ in urine based on the Hg2+-mediated formation of intermolecular split G-quadruplex–hemin DNAzymes. In the presence of Hg2+, T–T mismatches between the two partial cDNA strands were stabilized by a T–Hg2+–T base pair, and can cause the G-rich sequences of the two oligonucleotides to associate to form a split G-quadruplex which is able to bind hemin to form the catalytically active G-quadruplex–hemin DNAzyme. This microbead-based ‘turn-on’ process allows the detection of Hg2+ in urine samples at concentrations as low as 0.5 pM. The relative standard deviation and recovery are 1.2–3.9 and 98.7–103.2%, respectively. The remarkable sensitivity for Hg2+ is mainly attributed to the enhanced mass transport ability that is inherent in homogeneous microbead-based assays. Compared with previous developments of intermolecular split G-quardruplex–hemin DNAzymes for the homogeneous detection of Hg2+ (the limit of detection was 19nM), a signal enhancement of ~1000 times is obtained when such an assay is performed on the surface of microbeads.
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41
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Scalabrin M, Palumbo M, Richter SN. Highly Improved Electrospray Ionization-Mass Spectrometry Detection of G-Quadruplex-Folded Oligonucleotides and Their Complexes with Small Molecules. Anal Chem 2017; 89:8632-8637. [PMID: 28787153 PMCID: PMC5588092 DOI: 10.1021/acs.analchem.7b01282] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
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G-quadruplexes
are nucleic acids structures stabilized by physiological
concentration of potassium ions. Because low stability G-quadruplexes
are hardly detectable by mass spectrometry, we optimized solvent conditions:
isopropanol in a triethylamine/hexafluoroisopropanol mixture highly
increased G-quadruplex sensitivity with no modification of the physiological
G-quadruplex conformation. G-quadruplexes/G-quadruplex-ligand complexes
were also correctly detected at concentration as low as 40 nM. Detection
of the physiological conformation of G4s and their complexes opens
up the possibility to perform high-throughput screening of G-quadruplex
ligands for the development of drug molecules effective against critical
human diseases.
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Affiliation(s)
- Matteo Scalabrin
- Department of Molecular Medicine, University of Padua , via Gabelli 63, 35121 Padua, Italy
| | - Manlio Palumbo
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua , via Marzolo 5, 35131 Padua, Italy
| | - Sara N Richter
- Department of Molecular Medicine, University of Padua , via Gabelli 63, 35121 Padua, Italy
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42
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Synthesis and structure of dihydroberberine nitroaryl derivatives – potential ligands for G-quadruplexes. Chem Heterocycl Compd (N Y) 2017. [DOI: 10.1007/s10593-017-2055-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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43
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Rajczak E, Pecoraro VL, Juskowiak B. Sm(iii)[12-MCGa(III)shi-4] as a luminescent probe for G-quadruplex structures. Metallomics 2017; 9:1735-1744. [DOI: 10.1039/c7mt00232g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The luminescent anionic metallacrown Sm12-MC-4 exhibits similarity in shape and size to the guanine tetrad and is able to form complexes with G-quadruplex assembly.
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Affiliation(s)
- Ewa Rajczak
- Faculty of Chemistry
- Adam Mickiewicz University in Poznan
- 61-614 Poznan
- Poland
| | | | - Bernard Juskowiak
- Faculty of Chemistry
- Adam Mickiewicz University in Poznan
- 61-614 Poznan
- Poland
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44
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Kumar V, kashav T, Islam A, Ahmad F, Hassan MI. Structural insight into C9orf72 hexanucleotide repeat expansions: Towards new therapeutic targets in FTD-ALS. Neurochem Int 2016; 100:11-20. [DOI: 10.1016/j.neuint.2016.08.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 08/12/2016] [Accepted: 08/12/2016] [Indexed: 12/12/2022]
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Bhattacharjee S, Chakraborty S, Sengupta PK, Bhowmik S. Exploring the Interactions of the Dietary Plant Flavonoids Fisetin and Naringenin with G-Quadruplex and Duplex DNA, Showing Contrasting Binding Behavior: Spectroscopic and Molecular Modeling Approaches. J Phys Chem B 2016; 120:8942-52. [DOI: 10.1021/acs.jpcb.6b06357] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Snehasish Bhattacharjee
- Department of Biophysics, Molecular Biology & Bioinformatics, University of Calcutta, 92 Acharya Prafulla Chandra Road, Kolkata 700009, India
| | - Sandipan Chakraborty
- Department
of Microbiology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata 700019, India
| | - Pradeep K. Sengupta
- Department of Biophysics, Molecular Biology & Bioinformatics, University of Calcutta, 92 Acharya Prafulla Chandra Road, Kolkata 700009, India
| | - Sudipta Bhowmik
- Department of Biophysics, Molecular Biology & Bioinformatics, University of Calcutta, 92 Acharya Prafulla Chandra Road, Kolkata 700009, India
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46
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Nelissen FHT, Tessari M, Wijmenga SS, Heus HA. Stable isotope labeling methods for DNA. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2016; 96:89-108. [PMID: 27573183 DOI: 10.1016/j.pnmrs.2016.06.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 06/02/2016] [Accepted: 06/02/2016] [Indexed: 06/06/2023]
Abstract
NMR is a powerful method for studying proteins and nucleic acids in solution. The study of nucleic acids by NMR is far more challenging than for proteins, which is mainly due to the limited number of building blocks and unfavorable spectral properties. For NMR studies of DNA molecules, (site specific) isotope enrichment is required to facilitate specific NMR experiments and applications. Here, we provide a comprehensive review of isotope-labeling strategies for obtaining stable isotope labeled DNA as well as specifically stable isotope labeled building blocks required for enzymatic DNA synthesis.
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Affiliation(s)
- Frank H T Nelissen
- Institute for Molecules and Materials, Radboud University, 6525 AJ Nijmegen, The Netherlands.
| | - Marco Tessari
- Institute for Molecules and Materials, Radboud University, 6525 AJ Nijmegen, The Netherlands.
| | - Sybren S Wijmenga
- Institute for Molecules and Materials, Radboud University, 6525 AJ Nijmegen, The Netherlands.
| | - Hans A Heus
- Institute for Molecules and Materials, Radboud University, 6525 AJ Nijmegen, The Netherlands.
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47
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Garg R, Aggarwal J, Thakkar B. Genome-wide discovery of G-quadruplex forming sequences and their functional relevance in plants. Sci Rep 2016; 6:28211. [PMID: 27324275 PMCID: PMC4914980 DOI: 10.1038/srep28211] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 05/18/2016] [Indexed: 11/22/2022] Open
Abstract
DNA, in addition to the canonical B-form, can acquire a variety of alternate structures, such as G-quadruplexes. These structures have been implicated in several cellular processes in animals. In this study, we identified different types of G-quadruplex forming sequences (GQSes) in 15 sequenced plants and analyzed their distribution in various genomic features, including gene body, coding, intergenic and promoter regions. G2-type GQSes were most abundant in all the plant species analyzed. A strong association of G3-type GQSes with intergenic, promoter and intronic regions was found. However, G2-type GQSes were enriched in genic, CDS, exonic and untranslated regions. Further, we identified GQSes present in the conserved genes among monocots and dicots. The genes involved in development, cell growth and size, transmembrane transporter, and regulation of gene expression were found to be significantly enriched. In the promoter region, we detected strong co-occurrence of Telobox, ERF, MYB, RAV1B and E2F motifs with GQSes. Further, we validated the structure formation of several plant GQSes, demonstrated their effect on stalling in-vitro replication and revealed their interaction with plant nuclear proteins. Our data provide insights into the prevalence of GQSes in plants, establish their association with different genomic features and functional relevance.
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Affiliation(s)
- Rohini Garg
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
| | - Jyoti Aggarwal
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
| | - Bijal Thakkar
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
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48
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Liu W, Lin M, Yang X, Wu B, Chen N, Wang Q, Wang K, Qin S. Investigation of newly identified G-quadruplexes and their application to DNA detection. Analyst 2016; 141:4463-9. [PMID: 27215424 DOI: 10.1039/c6an00987e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
G-quadruplexes are guanine-rich nucleic acid sequences that can act as universal signal-transducers and generate colorimetric, fluorescence, and chemiluminescence signals when complexed with different ligands. Due to their merits including easy modification and low cost, it is of great importance to explore new G-quadruplexes with improved performance. Herein the properties of newly identified G-quadruplexes 9th-3-35 and 10th-2-40 were investigated in detail with UV-vis spectra, circular dichroism (CD) spectra and fluorescence spectra. The results indicated that 9th-3-35 and 10th-2-40 exhibited excellent peroxidase-like activity, as well as fluorescence enhancement of thioflavin T (ThT). Furthermore, the application of G-quadruplexes to DNA detection was performed on account of the ThT fluorescence enhancement, and the limit of detection was as low as 8 pM. This study implied that 9th-3-35 and 10th-2-40 are competitive candidates as signal-transducers in the design of bioassays.
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Affiliation(s)
- Wenjing Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Hunan University, Changsha, 410082, China.
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49
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Tang W, Robles AI, Beyer RP, Gray LT, Nguyen GH, Oshima J, Maizels N, Harris CC, Monnat RJ. The Werner syndrome RECQ helicase targets G4 DNA in human cells to modulate transcription. Hum Mol Genet 2016; 25:2060-2069. [PMID: 26984941 DOI: 10.1093/hmg/ddw079] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 03/07/2016] [Indexed: 11/12/2022] Open
Abstract
The Werner syndrome (WS) is a prototypic adult Mendelian progeroid syndrome in which signs of premature aging are associated with genomic instability and an elevated risk of cancer. The WRN RECQ helicase protein binds and unwinds G-quadruplex (G4) DNA substrates in vitro, and we identified significant enrichment in G4 sequence motifs at the transcription start site and 5' ends of first introns (false discovery rate < 0.001) of genes down-regulated in WS patient fibroblasts. This finding provides strong evidence that WRN binds G4 DNA structures at many chromosomal sites to modulate gene expression. WRN appears to bind a distinct subpopulation of G4 motifs in human cells, when compared with the related Bloom syndrome RECQ helicase protein. Functional annotation of the genes and miRNAs altered in WS provided new insight into WS disease pathogenesis. WS patient fibroblasts displayed altered expression of multiple, mechanistically distinct, senescence-associated gene expression programs, with altered expression of disease-associated miRNAs, and dysregulation of canonical pathways that regulate cell signaling, genome stability and tumorigenesis. WS fibroblasts also displayed a highly statistically significant and distinct gene expression signature, with coordinate overexpression of nearly all of the cytoplasmic tRNA synthetases and associated ARS-interacting multifunctional protein genes. The 'non-canonical' functions of many of these upregulated tRNA charging proteins may together promote WS disease pathogenesis. Our results identify the human WRN RECQ protein as a G4 helicase that modulates gene expression in G4-dependent fashion at many chromosomal sites and provide several new and unexpected mechanistic insights into WS disease pathogenesis.
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Affiliation(s)
| | - Ana I Robles
- Laboratory of Human Carcinogenesis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA and
| | | | | | - Giang H Nguyen
- Laboratory of Human Carcinogenesis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA and
| | - Junko Oshima
- Department of Pathology, Department of Medicine, Chiba University, Chiba, Japan
| | - Nancy Maizels
- Department of Pathology, Department of Immunology, Department of Biochemistry
| | - Curtis C Harris
- Laboratory of Human Carcinogenesis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA and
| | - Raymond J Monnat
- Department of Pathology, Department of Genome Sciences, University of Washington, Seattle, WA, USA,
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50
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Carvalho J, Ferreira J, Pereira P, Coutinho E, Guédin A, Nottelet P, Salgado GF, Mergny JL, Queiroz J, Sousa F, Cabrita EJ, Cruz C. Stabilization of novel immunoglobulin switch regions G-quadruplexes by naphthalene and quinoline-based ligands. Tetrahedron 2016. [DOI: 10.1016/j.tet.2016.01.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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