1
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Tao S, Run Y, Monchaud D, Zhang W. i-Motif DNA: identification, formation, and cellular functions. Trends Genet 2024:S0168-9525(24)00133-1. [PMID: 38902139 DOI: 10.1016/j.tig.2024.05.011] [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: 04/24/2024] [Revised: 05/29/2024] [Accepted: 05/29/2024] [Indexed: 06/22/2024]
Abstract
An i-motif (iM) is a four-stranded (quadruplex) DNA structure that folds from cytosine (C)-rich sequences. iMs can fold under many different conditions in vitro, which paves the way for their formation in living cells. iMs are thought to play key roles in various DNA transactions, notably in the regulation of genome stability, gene transcription, mRNA translation, DNA replication, telomere and centromere functions, and human diseases. We summarize the different techniques used to assess the folding of iMs in vitro and provide an overview of the internal and external factors that affect their formation and stability in vivo. We describe the possible biological relevance of iMs and propose directions towards their use as target in biology.
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Affiliation(s)
- Shentong Tao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production (CIC-MCP), Nanjing Agricultural University, 1 Weigang, Nanjing, Jiangsu 210095, China
| | - Yonghang Run
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production (CIC-MCP), Nanjing Agricultural University, 1 Weigang, Nanjing, Jiangsu 210095, China
| | - David Monchaud
- Institut de Chimie Moleculaire de l'Université de Bourgogne (ICMUB), Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 6302, Université Bourgogne Franche Comté (UBFC), Dijon, France
| | - Wenli Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production (CIC-MCP), Nanjing Agricultural University, 1 Weigang, Nanjing, Jiangsu 210095, China.
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2
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Chaudhuri R, Bhattacharya S, Dash J. Bioorthogonal Chemistry in Translational Research: Advances and Opportunities. Chembiochem 2023; 24:e202300474. [PMID: 37800582 DOI: 10.1002/cbic.202300474] [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: 06/24/2023] [Revised: 09/19/2023] [Indexed: 10/07/2023]
Abstract
Bioorthogonal chemistry is a rapidly expanding field of research that involves the use of small molecules that can react selectively with biomolecules in living cells and organisms, without causing any harm or interference with native biochemical processes. It has made significant contributions to the field of biology and medicine by enabling selective labeling, imaging, drug targeting, and manipulation of bio-macromolecules in living systems. This approach offers numerous advantages over traditional chemistry-based methods, including high specificity, compatibility with biological systems, and minimal interference with biological processes. In this review, we provide an overview of the recent advancements in bioorthogonal chemistry and their current and potential applications in translational research. We present an update on this innovative chemical approach that has been utilized in cells and living systems during the last five years for biomedical applications. We also highlight the nucleic acid-templated synthesis of small molecules by using bioorthogonal chemistry. Overall, bioorthogonal chemistry provides a powerful toolset for studying and manipulating complex biological systems, and holds great potential for advancing translational research.
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Affiliation(s)
- Ritapa Chaudhuri
- School of Chemical Sciences Indian Association for the Cultivation of Science, 2A and 2B Raja S.C. Mullick Road, Jadavpur, Kolkata, 700099, India
| | - Semantee Bhattacharya
- School of Chemical Sciences Indian Association for the Cultivation of Science, 2A and 2B Raja S.C. Mullick Road, Jadavpur, Kolkata, 700099, India
| | - Jyotirmayee Dash
- School of Chemical Sciences Indian Association for the Cultivation of Science, 2A and 2B Raja S.C. Mullick Road, Jadavpur, Kolkata, 700099, India
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3
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Bhattacharya S, Bhattacharyya T, Khanra S, Banerjee R, Dash J. Nucleoside-Derived Metallohydrogel Induces Cell Death in Leishmania Parasites. ACS Infect Dis 2023; 9:1676-1684. [PMID: 37606735 DOI: 10.1021/acsinfecdis.2c00635] [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] [Indexed: 08/23/2023]
Abstract
Self-assembled hydrogels by virtue of their unique 3D network and tunability have extensively been explored for bio-medical applications like tissue engineering, delivery and release of therapeutic agents, etc. Herein, we demonstrate for the first-time nucleoside-based biocompatible hydrogels with a remarkable leishmanicidal effect against both Leishmania major promastigotes and amastigotes and no cytotoxic effect on the macrophage cell line. In this work, a series of biocompatible hydrogels have been synthesized by silver ion-driven self-assembly of natural nucleoside and nucleotide-like cytidine and 5'-GMP. The supramolecular metallogel obtained from the assembly of cytidine and boronic acid is capable of inducing apoptotic-like cell death of protozoan parasite by causing damage to the membrane as well as DNA. These hydrogels could find promising applications in combating cutaneous leishmaniasis by topical treatment.
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Affiliation(s)
- Semantee Bhattacharya
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Tanima Bhattacharyya
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Supriya Khanra
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Kolkata 700064, India
| | - Rahul Banerjee
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Kolkata 700064, India
| | - Jyotirmayee Dash
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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4
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Wei Z, Lin X, Wang S, Zhang J, Ji D, Gong X, Huang ZS, Shu B, Li D. Syntheses and evaluation of acridone derivatives as anticancer agents targeting Kras promoter i-motif structure. Bioorg Chem 2023; 136:106526. [PMID: 37058782 DOI: 10.1016/j.bioorg.2023.106526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/26/2023] [Accepted: 04/03/2023] [Indexed: 04/16/2023]
Abstract
Two series of novel acridone derivatives were designed and synthesized, with their anticancer activity evaluated. Most of these compounds showed potent antiproliferative activity against cancer cell lines. Among them, compound C4 with dual 1,2,3-triazol moieties exhibited the most potent activity against Hep-G2 cells with IC50 value determined to be 6.29 ± 0.93 μM. Subsequent experiments showed that C4 could bind to and destabilize Kras gene promoter i-motif structure without significant interaction with its corresponding G-quadruplex. C4 could down-regulate Kras expression in Hep-G2 cells, possibly due to its interaction with the Kras i-motif. Further cellular studies indicated that C4 could induce apoptosis of Hep-G2 cells, possibly related to its effect on mitochondrial dysfunction. These results indicated that C4 could be further developed as a promising anticancer agent.
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Affiliation(s)
- Zuzhuang Wei
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, 132 Waihuan East Road, Guangzhou 510006, PR China
| | - Xiaomin Lin
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, 132 Waihuan East Road, Guangzhou 510006, PR China
| | - Siyi Wang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, 132 Waihuan East Road, Guangzhou 510006, PR China
| | - Jiahui Zhang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, 132 Waihuan East Road, Guangzhou 510006, PR China
| | - Dongsheng Ji
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, 132 Waihuan East Road, Guangzhou 510006, PR China
| | - Xue Gong
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, 132 Waihuan East Road, Guangzhou 510006, PR China
| | - Zhi-Shu Huang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, 132 Waihuan East Road, Guangzhou 510006, PR China
| | - Bing Shu
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, PR China.
| | - Ding Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, 132 Waihuan East Road, Guangzhou 510006, PR China.
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5
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Singh M, Gupta R, Comez L, Paciaroni A, Rani R, Kumar V. BCL2 G quadruplex-binding small molecules: Current status and prospects for the development of next-generation anticancer therapeutics. Drug Discov Today 2022; 27:2551-2561. [PMID: 35709931 DOI: 10.1016/j.drudis.2022.06.002] [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: 12/01/2021] [Revised: 06/01/2022] [Accepted: 06/08/2022] [Indexed: 11/03/2022]
Abstract
B cell lymphoma 2 (BCL2) overexpression in a range of human tumors is often related to chemotherapy resistance and poor prognosis. GC-rich regions upstream of the P1 promoter in human BCL2 can form G-quadruplex (G4) structures through the stacking of four Hoogsteen-paired guanine bases. Stabilizing the G4 fold implies the inhibition of BCL2 expression and, thus, small molecules that selectively bind to the G4 are promising anticancer candidates. In this review, we discuss the structural aspects, binding affinity, selectivity, and biological activity of well-characterized BCL2 G4 binding ligands in vitro and in vivo. We also explore future directions in the research and development of G4-based anticancer therapeutics.
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Affiliation(s)
- Mamta Singh
- Amity Institute of Molecular Medicine and Stem Cell Research, Amity University, Noida, UP, 201303, India
| | - Rajat Gupta
- Amity Institute of Molecular Medicine and Stem Cell Research, Amity University, Noida, UP, 201303, India
| | - Lucia Comez
- IOM-CNR National Research Council, Via Pascoli, Perugia I-06123, Italy
| | - Alessandro Paciaroni
- Department of Physics and Geology, University of Perugia, via Pascoli, 06123, Italy
| | - Reshma Rani
- Drug Discovery Unit, Jubilant Biosys Ltd, Sector 58, Noida, UP 201301, India.
| | - Vinit Kumar
- Amity Institute of Molecular Medicine and Stem Cell Research, Amity University, Noida, UP, 201303, India.
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6
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Development of a Smart Fluorescent Probe Specifically Interacting with C-Myc I-Motif. Int J Mol Sci 2022; 23:ijms23073872. [PMID: 35409230 PMCID: PMC8998492 DOI: 10.3390/ijms23073872] [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: 03/04/2022] [Revised: 03/27/2022] [Accepted: 03/28/2022] [Indexed: 11/17/2022] Open
Abstract
I-motifs play key regulatory roles in biological processes, holding great potential as attractive therapeutic targets. In the present study, we developed a novel fluorescent probe G59 with strong and selective binding to the c-myc gene promoter i-motif. G59 had an i-motif-binding carbazole moiety conjugated with naphthalimide fluorescent groups. G59 could differentiate the c-myc i-motif from other DNA structures through selective activation of its fluorescence, with its apparent visualization in solution. The smart probe G59 showed excellent sensitivity, with a low fluorescent detection limit of 154 nM and effective stabilization to the c-myc i-motif. G59 could serve as a rapid and sensitive probe for label-free screening of selective c-myc i-motif binding ligands under neutral crowding conditions. To the best of our knowledge, G59 is the first fluorescent probe with high sensitivity for recognizing the i-motif structure and screening for selective binding ligands.
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7
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Stability and context of intercalated motifs (i-motifs) for biological applications. Biochimie 2022; 198:33-47. [PMID: 35259471 DOI: 10.1016/j.biochi.2022.03.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 02/21/2022] [Accepted: 03/03/2022] [Indexed: 11/24/2022]
Abstract
DNA is naturally dynamic and can self-assemble into alternative secondary structures including the intercalated motif (i-motif), a four-stranded structure formed in cytosine-rich DNA sequences. Until recently, i-motifs were thought to be unstable in physiological cellular environments. Studies demonstrating their existence in the human genome and role in gene regulation are now shining light on their biological relevance. Herein, we review the effects of epigenetic modifications on i-motif structure and stability, and biological factors that affect i-motif formation within cells. Furthermore, we highlight recent progress in targeting i-motifs with structure-specific ligands for biotechnology and therapeutic purposes.
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Ma X, Feng Y, Yang Y, Li X, Shi Y, Tao S, Cheng X, Huang J, Wang XE, Chen C, Monchaud D, Zhang W. Genome-wide characterization of i-motifs and their potential roles in the stability and evolution of transposable elements in rice. Nucleic Acids Res 2022; 50:3226-3238. [PMID: 35188565 PMCID: PMC8989525 DOI: 10.1093/nar/gkac121] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 01/13/2022] [Accepted: 02/07/2022] [Indexed: 12/15/2022] Open
Abstract
I-motifs (iMs) are non-canonical DNA secondary structures that fold from cytosine (C)-rich genomic DNA regions termed putative i-motif forming sequences (PiMFSs). The structure of iMs is stabilized by hemiprotonated C-C base pairs, and their functions are now suspected in key cellular processes in human cells such as genome stability and regulation of gene transcription. In plants, their biological relevance is still largely unknown. Here, we characterized PiMFSs with high potential for i-motif formation in the rice genome by developing and applying a protocol hinging on an iMab antibody-based immunoprecipitation (IP) coupled with high-throughput sequencing (seq), consequently termed iM-IP-seq. We found that PiMFSs had intrinsic subgenomic distributions, cis-regulatory functions and an intricate relationship with DNA methylation. We indeed found that the coordination of PiMFSs with DNA methylation may affect dynamics of transposable elements (TEs) among different cultivated Oryza subpopulations or during evolution of wild rice species. Collectively, our study provides first and unique insights into the biology of iMs in plants, with potential applications in plant biotechnology for improving important agronomic rice traits.
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Affiliation(s)
- Xing Ma
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, P.R. China
| | - Yilong Feng
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, P.R. China
| | - Ying Yang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, P.R. China
| | - Xin Li
- Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan410125, P.R. China
| | - Yining Shi
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, P.R. China
| | - Shentong Tao
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, P.R. China
| | - Xuejiao Cheng
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, P.R. China
| | - Jian Huang
- School of Biology & Basic Medical Science, Soochow University, Suzhou, Jiangsu 215123, P.R. China
| | - Xiu-e Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, P.R. China
| | - Caiyan Chen
- Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan410125, P.R. China
| | - David Monchaud
- Institut de Chimie Moleculaire, ICMUB CNRS UMR 6302, UBFC Dijon, France
| | - Wenli Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, P.R. China
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9
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Takahashi S, Kotar A, Tateishi-Karimata H, Bhowmik S, Wang ZF, Chang TC, Sato S, Takenaka S, Plavec J, Sugimoto N. Chemical Modulation of DNA Replication along G-Quadruplex Based on Topology-Dependent Ligand Binding. J Am Chem Soc 2021; 143:16458-16469. [PMID: 34554731 DOI: 10.1021/jacs.1c05468] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Ligands that bind to and stabilize guanine-quadruplex (G4) structures to regulate DNA replication have therapeutic potential for cancer and neurodegenerative diseases. Because there are several G4 topologies, ligands that bind to their specific types may have the ability to preferentially regulate the replication of only certain genes. Here, we demonstrated that binding ligands stalled the replication of template DNA at G4, depending on different topologies. For example, naphthalene diimide derivatives bound to the G-quartet of G4 with an additional interaction between the ligand and the loop region of a hybrid G4 type from human telomeres, which efficiently repressed the replication of the G4. Thus, these inhibitory effects were not only stability-dependent but also topology-selective based on the manner in which G4 structures interacted with G4 ligands. Our original method, referred to as a quantitative study of topology-dependent replication (QSTR), was developed to evaluate correlations between replication rate and G4 stability. QSTR enabled the systematic categorization of ligands based on topology-dependent binding. It also demonstrated accuracy in determining quantitatively how G4 ligands control the intermediate state of replication and the kinetics of G4 unwinding. Hence, the QSTR index would facilitate the design of new drugs capable of controlling the topology-dependent regulation of gene expression.
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Affiliation(s)
- Shuntaro Takahashi
- FIBER (Frontier Institute for Biomolecular Engineering Research), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Anita Kotar
- Slovenian NMR Center, National Institute of Chemistry, SI-1000 Ljubljana, Slovenia
| | - Hisae Tateishi-Karimata
- FIBER (Frontier Institute for Biomolecular Engineering Research), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Sudipta Bhowmik
- Department of Biophysics, Molecular Biology and Bioinformatics, University College of Science, University of Calcutta, 92, A.P.C. Road, Kolkata 700009, India
| | - Zi-Fu Wang
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106, Taiwan
| | - Ta-Chau Chang
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106, Taiwan
| | - Shinobu Sato
- Department of Applied Chemistry, Kyushu Institute of Technology, Fukuoka 804-8550, Japan
| | - Shigeori Takenaka
- Department of Applied Chemistry, Kyushu Institute of Technology, Fukuoka 804-8550, Japan
| | - Janez Plavec
- Slovenian NMR Center, National Institute of Chemistry, SI-1000 Ljubljana, Slovenia
| | - Naoki Sugimoto
- FIBER (Frontier Institute for Biomolecular Engineering Research), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan.,FIRST (Graduate School of Frontiers of Innovative Research in Science and Technology), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
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10
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Müller D, Saha P, Panda D, Dash J, Schwalbe H. Insights from Binding on Quadruplex Selective Carbazole Ligands. Chemistry 2021; 27:12726-12736. [PMID: 34138492 PMCID: PMC8518889 DOI: 10.1002/chem.202101866] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Indexed: 01/11/2023]
Abstract
Polymorphic G-quadruplex (G4) secondary DNA structures have received increasing attention in medicinal chemistry owing to their key involvement in the regulation of the maintenance of genomic stability, telomere length homeostasis and transcription of important proto-oncogenes. Different classes of G4 ligands have been developed for the potential treatment of several human diseases. Among them, the carbazole scaffold with appropriate side chain appendages has attracted much interest for designing G4 ligands. Because of its large and rigid π-conjugation system and ease of functionalization at three different positions, a variety of carbazole derivatives have been synthesized from various natural or synthetic sources for potential applications in G4-based therapeutics and biosensors. Herein, we provide an updated close-up of the literatures on carbazole-based G4 ligands with particular focus given on their detailed binding insights studied by NMR spectroscopy. The structure-activity relationships and the opportunities and challenges of their potential applications as biosensors and therapeutics are also discussed. This review will provide an overall picture of carbazole ligands with remarkable G4 topological preference, fluorescence properties and significant bioactivity; portraying carbazole as a very promising scaffold for assembling G4 ligands with a range of novel functional applications.
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Affiliation(s)
- Diana Müller
- Institute of Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Goethe University FrankfurtMax-von-Laue Strasse 7Frankfurt am Main60438Germany
| | - Puja Saha
- School of Chemical SciencesIndian Association for the Cultivation of ScienceJadavpurKolkata-700032India
| | - Deepanjan Panda
- School of Chemical SciencesIndian Association for the Cultivation of ScienceJadavpurKolkata-700032India
| | - Jyotirmayee Dash
- School of Chemical SciencesIndian Association for the Cultivation of ScienceJadavpurKolkata-700032India
| | - Harald Schwalbe
- Institute of Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Goethe University FrankfurtMax-von-Laue Strasse 7Frankfurt am Main60438Germany
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11
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Sanchez-Martin V, Soriano M, Garcia-Salcedo JA. Quadruplex Ligands in Cancer Therapy. Cancers (Basel) 2021; 13:3156. [PMID: 34202648 PMCID: PMC8267697 DOI: 10.3390/cancers13133156] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/18/2021] [Accepted: 06/20/2021] [Indexed: 02/07/2023] Open
Abstract
Nucleic acids can adopt alternative secondary conformations including four-stranded structures known as quadruplexes. To date, quadruplexes have been demonstrated to exist both in human chromatin DNA and RNA. In particular, quadruplexes are found in guanine-rich sequences constituting G-quadruplexes, and in cytosine-rich sequences forming i-Motifs as a counterpart. Quadruplexes are associated with key biological processes ranging from transcription and translation of several oncogenes and tumor suppressors to telomeres maintenance and genome instability. In this context, quadruplexes have prompted investigations on their possible role in cancer biology and the evaluation of small-molecule ligands as potential therapeutic agents. This review aims to provide an updated close-up view of the literature on quadruplex ligands in cancer therapy, by grouping together ligands for DNA and RNA G-quadruplexes and DNA i-Motifs.
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Affiliation(s)
- Victoria Sanchez-Martin
- Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, PTS Granada, 18016 Granada, Spain;
- Microbiology Unit, Biosanitary Research Institute IBS, University Hospital Virgen de las Nieves, 18014 Granada, Spain
- Department of Biochemistry, Molecular Biology III and Immunology, University of Granada, 18016 Granada, Spain
| | - Miguel Soriano
- Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, PTS Granada, 18016 Granada, Spain;
- Centre for Intensive Mediterranean Agrosystems and Agri-Food Biotechnology (CIAMBITAL), University of Almeria, 04001 Almeria, Spain
| | - Jose Antonio Garcia-Salcedo
- Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, PTS Granada, 18016 Granada, Spain;
- Microbiology Unit, Biosanitary Research Institute IBS, University Hospital Virgen de las Nieves, 18014 Granada, Spain
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12
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Chaudhuri R, Fatma K, Dash J. Regulation of gene expression by targeting DNA secondary structures. J CHEM SCI 2021. [DOI: 10.1007/s12039-021-01898-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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13
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Bhattacharyya T, Panda D, Dash J. Supramolecular Template-Directed In Situ Click Chemistry: A Bioinspired Approach to Synthesize G-Quadruplex DNA Ligands. Org Lett 2021; 23:3004-3009. [PMID: 33830771 DOI: 10.1021/acs.orglett.1c00685] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The assembly of guanosine and boronic acids produces anionic hydrogels (G-B hydrogels) that mimic the topology of the DNA G-quadruplex. We herein demonstrate an unconventional approach of using the G-B hydrogel as a supramolecular template that assembles the irreversible formation of DNA G-quadruplex-selective 1,4-triazole ligands from a pool of alkyne-azide building blocks. These generated ligands could also stabilize and strengthen the gel assembly.
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Affiliation(s)
- Tanima Bhattacharyya
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Deepanjan Panda
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Jyotirmayee Dash
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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14
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Saha P, Panda D, Paul R, Dash J. A DNA nanosensor for monitoring ligand-induced i-motif formation. Org Biomol Chem 2021; 19:1965-1969. [DOI: 10.1039/d1ob00248a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A GNP-based DNA nanosensor has been developed that identifies i-motif inducing ligands at physiological pH from a chemical library.
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Affiliation(s)
- Puja Saha
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata-700032
- India
| | - Deepanjan Panda
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata-700032
- India
| | - Raj Paul
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata-700032
- India
| | - Jyotirmayee Dash
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata-700032
- India
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15
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Chakraborti G, Jana R, Mandal T, Datta A, Dash J. Prolinamide plays a key role in promoting copper-catalyzed cycloaddition of azides and alkynes in aqueous media via unprecedented metallacycle intermediates. Org Chem Front 2021. [DOI: 10.1039/d0qo01150a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Room temperature copper-catalyzed cycloaddition of azides and alkynes (CuAAC) proceeds in the presence of a prolinamide ligand in aqueous media via unique metallacycles.
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Affiliation(s)
- Gargi Chakraborti
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata 700032
- India
| | - Rajkumar Jana
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata 700032
- India
| | - Tirtha Mandal
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata 700032
- India
| | - Ayan Datta
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata 700032
- India
| | - Jyotirmayee Dash
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata 700032
- India
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16
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Mayer L, Kohlbecher R, Müller TJJ. Concatenating Suzuki Arylation and Buchwald-Hartwig Amination by A Sequentially Pd-Catalyzed One-Pot Process-Consecutive Three-Component Synthesis of C,N-Diarylated Heterocycles. Chemistry 2020; 26:15130-15134. [PMID: 32815662 PMCID: PMC7756286 DOI: 10.1002/chem.202003837] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Indexed: 12/20/2022]
Abstract
The concatenation of Suzuki coupling and Buchwald‐Hartwig amination in a consecutive multicomponent reaction opens a concise, modular and efficient one‐pot approach to diversely functionalized heterocycles, as exemplified for 3,10‐diaryl 10H‐phenothiazines, 3,9‐diaryl 9H‐carbazoles, and 1,5‐diaryl 1H‐indoles, in high yields starting from simple staring materials. Moreover, this one‐pot reaction is a sequentially palladium‐catalyzed process that does not require additional catalyst loading after the first coupling step.
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Affiliation(s)
- Laura Mayer
- Institut für Organische Chemie und Makromolekulare Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Regina Kohlbecher
- Institut für Organische Chemie und Makromolekulare Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Thomas J J Müller
- Institut für Organische Chemie und Makromolekulare Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
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17
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Gütschow M, Vanden Eynde JJ, Jampilek J, Kang C, Mangoni AA, Fossa P, Karaman R, Trabocchi A, Scott PJH, Reynisson J, Rapposelli S, Galdiero S, Winum JY, Brullo C, Prokai-Tatrai K, Sharma AK, Schapira M, Azuma YT, Cerchia L, Spetea M, Torri G, Collina S, Geronikaki A, García-Sosa AT, Vasconcelos MH, Sousa ME, Kosalec I, Tuccinardi T, Duarte IF, Salvador JAR, Bertinaria M, Pellecchia M, Amato J, Rastelli G, Gomes PAC, Guedes RC, Sabatier JM, Estévez-Braun A, Pagano B, Mangani S, Ragno R, Kokotos G, Brindisi M, González FV, Borges F, Miloso M, Rautio J, Muñoz-Torrero D. Breakthroughs in Medicinal Chemistry: New Targets and Mechanisms, New Drugs, New Hopes-7. Molecules 2020; 25:E2968. [PMID: 32605268 PMCID: PMC7412072 DOI: 10.3390/molecules25132968] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 06/23/2020] [Indexed: 02/06/2023] Open
Abstract
Breakthroughs in Medicinal Chemistry [...].
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Affiliation(s)
- Michael Gütschow
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany;
| | - Jean Jacques Vanden Eynde
- Formerly head of the Department of Organic Chemistry (FS), University of Mons-UMONS, 7000 Mons, Belgium;
| | - Josef Jampilek
- Department of Analytical Chemistry, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, 842 15 Bratislava, Slovakia;
| | - CongBao Kang
- Experimental Drug Development Centre, Agency for Science, Technology and Research, 10 Biopolis Road, Chromos, 05-01, Singapore 138670, Singapore;
| | - Arduino A. Mangoni
- Discipline of Clinical Pharmacology, College of Medicine and Public Health, Flinders University and Flinders Medical Centre, Bedford Park, Adelaide 5042, Australia;
- Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, 01069 Dresden, Germany
| | - Paola Fossa
- Department of Pharmacy, School of Medical and Pharmaceutical Sciences, University of Genova, 16132 Genova, Italy;
| | - Rafik Karaman
- Pharmaceutical & Medicinal Chemistry Department, Faculty of Pharmacy, Al-Quds University, Jerusalem P.O. Box 20002, Palestine;
- Department of Sciences, University of Basilicata, Viadell’Ateneo Lucano 10, 85100 Potenza, Italy
| | - Andrea Trabocchi
- Department of Chemistry “Ugo Schiff”, University of Florence, via della Lastruccia 13, I-50019 Sesto Fiorentino, Florence, Italy;
| | - Peter J. H. Scott
- Department of Radiology, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Jóhannes Reynisson
- School of Pharmacy and Bioengineering, Keele University, Keele, Staffordshire ST5 5BG, UK;
| | - Simona Rapposelli
- Laboratory of Medicinal Chemistry, Department of Pharmacy, University of Pisa, 56126 Pisa, Italy;
- Interdepartmental Research Centre of Ageing Biology and Pathology, University of Pisa, 56126 Pisa, Italy
| | - Stefania Galdiero
- Department of Pharmacy, University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy; (S.G.); (J.A.); (B.P.); (M.B.)
| | - Jean-Yves Winum
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247 CNRS, ENSCM, Université de Montpellier, CEDEX 05, 34296 Montpellier, France;
| | - Chiara Brullo
- Department of Pharmacy, Section of Medicinal Chemistry, University of Genoa, V.le Benedetto XV 3, I-16132 Genova, Italy;
| | - Katalin Prokai-Tatrai
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, Fort Worth, TX 76107, USA;
| | - Arun K. Sharma
- Department of Pharmacology, Penn State Cancer Institute, CH72, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, USA;
| | - Matthieu Schapira
- Structural Genomics Consortium, University of Toronto, MaRS Centre, South Tower, 101 College St., Suite 700, Toronto, ON M5G 1L7, Canada;
- Department of Pharmacology and Toxicology, University of Toronto, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
| | - Yasu-Taka Azuma
- Laboratory of Veterinary Pharmacology, Division of Veterinary Science, Osaka Prefecture University Graduate School of Life and Environmental Sciences, 1-58 Rinku-ohraikita, Izumisano, Osaka 598-8531, Japan;
| | - Laura Cerchia
- Institute of Experimental Endocrinology and Oncology “G. Salvatore” (IEOS), National Research Council (CNR), 80131 Naples, Italy;
| | - Mariana Spetea
- Department of Pharmaceutical Chemistry, Institute of Pharmacy and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria;
| | - Giangiacomo Torri
- Istituto di Ricerche Chimiche e Biochimiche “G. Ronzoni”, via Giuseppe Colombo 81, 20133 Milano, Italy;
| | - Simona Collina
- Department of Drug Sciences, Medicinal Chemistry and Pharmaceutical Technology Section, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy;
| | - Athina Geronikaki
- Department of Pharmaceutical Chemistry, School of Pharmacy, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | | | - M. Helena Vasconcelos
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal;
- Cancer Drug Resistance Group-IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, Rua Júlio Amaral de Carvalho, 45, 4200-135 Porto, Portugal
- Department of Biological Sciences, FFUP-Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Maria Emília Sousa
- Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências, Químicas, Faculdade de Farmácia, Universidade do Porto, Rua Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal;
- Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR/CIMAR), Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N 4450-208 Matosinhos, Portugal
| | - Ivan Kosalec
- Faculty of Pharmacy and Biochemistry, University of Zagreb, A. Kovačića 1, HR-10000 Zagreb, Croatia;
| | - Tiziano Tuccinardi
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy;
| | - Iola F. Duarte
- Department of Chemistry, CICECO—Aveiro Institute of Materials, University of Aveiro, 3810-193 Aveiro, Portugal;
| | - Jorge A. R. Salvador
- Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal;
| | - Massimo Bertinaria
- Dipartimento di Scienza e Tecnologia del Farmaco, Università degli Studi di Torino, Via P. Giuria 9, 10125 Torino, Italy;
| | - Maurizio Pellecchia
- Division of Biomedical Sciences, School of Medicine, University of California Riverside, Riverside, CA 92521, USA;
| | - Jussara Amato
- Department of Pharmacy, University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy; (S.G.); (J.A.); (B.P.); (M.B.)
| | - Giulio Rastelli
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125 Modena, Italy;
| | - Paula A. C. Gomes
- LAQV-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre 687, 4169-007 Porto, Portugal;
| | - Rita C. Guedes
- iMed.Ulisboa and Faculdade de Farmácia, Universidade de Lisboa, 1649-003 Lisbon, Portugal;
| | - Jean-Marc Sabatier
- Institute of NeuroPhysiopathology, UMR 7051, Faculté de Médecine Secteur Nord, 51, Boulevard Pierre Dramard-CS80011, CEDEX 15, 13344-Marseille, France;
| | - Ana Estévez-Braun
- Departamento de Química Orgánica, Instituto Universitario de Bio-Orgánica (CIBICAN), Universidad de La Laguna, 38206 Tenerife, Spain;
| | - Bruno Pagano
- Department of Pharmacy, University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy; (S.G.); (J.A.); (B.P.); (M.B.)
| | - Stefano Mangani
- Department of Biotechnology, Chemistry and Pharmacy, DoE 2018-2022, University of Siena, via Aldo Moro 2, 53100 Siena, Italy;
| | - Rino Ragno
- Department of Drug Chemistry and Technology, Rome Center for Molecular Design, Sapienza University, P.le Aldo Moro 5, 00185 Rome, Italy;
| | - George Kokotos
- Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, 15771 Athens, Greece;
| | - Margherita Brindisi
- Department of Pharmacy, University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy; (S.G.); (J.A.); (B.P.); (M.B.)
| | - Florenci V. González
- Departament de Química Inorgànica i Orgànica, Universitat Jaume I, 12080 Castelló, Spain;
| | - Fernanda Borges
- CIQUP/Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, R. Campo Alegre 1021/1055, 4169-007 Porto, Portugal;
| | - Mariarosaria Miloso
- School of Medicine and Surgery, Experimental Neurology Unit, University of Milano-Bicocca, Via Cadore 48, 20900 Monza, MB, Italy;
| | - Jarkko Rautio
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland;
| | - Diego Muñoz-Torrero
- Laboratory of Medicinal Chemistry, Faculty of Pharmacy and Food Sciences, and Institute of Biomedicine (IBUB), University of Barcelona, Av. Joan XXIII, 27-31, E-08028 Barcelona, Spain
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