1
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Massalha L, Levin AR, Adiram-Filiba N, Golub E. Selective binding of c-MYC G-quadruplex caged in a dsDNA by a hemopeptide. Chem Commun (Camb) 2024; 60:7769-7772. [PMID: 38973676 DOI: 10.1039/d4cc01389a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2024]
Abstract
The microperoxidase-11 hemopeptide exhibits configuration-dependent selectivity for guanine-quadruplexes by specifically uncaging c-MYC guanine-quadruplexes from a duplex DNA.
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Affiliation(s)
- Leen Massalha
- Department of Chemistry, Faculty of Exact Sciences and Institute of Nanotechnology and Advanced Materials, Bar Ilan University, 5290002, Israel.
| | - Adiel Richter Levin
- Department of Chemistry, Faculty of Exact Sciences and Institute of Nanotechnology and Advanced Materials, Bar Ilan University, 5290002, Israel.
| | - Nurit Adiram-Filiba
- Department of Chemistry, Faculty of Exact Sciences and Institute of Nanotechnology and Advanced Materials, Bar Ilan University, 5290002, Israel.
| | - Eyal Golub
- Department of Chemistry, Faculty of Exact Sciences and Institute of Nanotechnology and Advanced Materials, Bar Ilan University, 5290002, Israel.
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2
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Teng X, Hu D, Dai Y, Jing H, Hu W, Zhang Q, Zhang N, Li J. Discovery of A G-Quadruplex Unwinder That Unleashes the Translation of G-Quadruplex-Containing mRNA without Inducing DNA Damage. Angew Chem Int Ed Engl 2024:e202407353. [PMID: 38953247 DOI: 10.1002/anie.202407353] [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: 04/17/2024] [Revised: 06/28/2024] [Accepted: 07/01/2024] [Indexed: 07/03/2024]
Abstract
To explore the mechanisms and therapeutic strategies for G-quadruplex (G4) mediated diseases, it is crucial to manipulate and intervene in intracellular G4 structures using small molecular tools. While hundreds of G4 stabilizers have been developed, there is a significant gap in the availability of G4 unwinding agents. Here, we propose a strategy to disrupt G-quadruplexes by forming G-C hydrogen bonds with chemically modified cytidine trimers. We validated a good G4 unwinder, the 2'-F cytidine trimer (2'-F C3). 2'-F C3 does not inhibit cell growth nor cause severe DNA damage at a concentration below 10 μM. Moreover, 2'-F C3 does not affect gene transcription nor RNA splicing, while it significantly enhances the translation of G4-containing mRNA and upregulates RNA splicing, RNA processing and cell cycle pathways. The discovery of this G4 unwinder provides a functional tool for the chemical modulation of G4s in living cells.
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Affiliation(s)
- Xucong Teng
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
- New Cornerstone Science Laboratory, Shenzhen, 518054, China
- Beijing Life Science Academy, Beijing, 102209, China
- Center for BioAnalytical Chemistry, Hefei National Laboratory of Physical Science at Microscale, University of Science and Technology of China, Hefei, 230026, China
| | - Difei Hu
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
| | - Yicong Dai
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
| | - Haitao Jing
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, China
| | - Wenxuan Hu
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, China
| | - Qiushuang Zhang
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
| | - Na Zhang
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, China
| | - Jinghong Li
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
- New Cornerstone Science Laboratory, Shenzhen, 518054, China
- Beijing Life Science Academy, Beijing, 102209, China
- Center for BioAnalytical Chemistry, Hefei National Laboratory of Physical Science at Microscale, University of Science and Technology of China, Hefei, 230026, China
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3
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Bednarz A, Rosendal RT, Lund LM, Birkedal V. Probing G-quadruplex-ligand binding using DNA intrinsic fluorescence. Biochimie 2024:S0300-9084(24)00145-7. [PMID: 38936685 DOI: 10.1016/j.biochi.2024.06.009] [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: 12/07/2023] [Revised: 06/24/2024] [Accepted: 06/24/2024] [Indexed: 06/29/2024]
Abstract
G-quadruplexes (G4s) are helical four-stranded nucleic acid structures that can form in guanine-rich sequences, which are mostly found in functional cellular regions, such as telomeres, promoters, and DNA replication origins. Great efforts are being made to target these structures towards the development of specific small molecule G4 binders for novel anti-cancer, neurological, and viral therapies. Here, we introduce an optical assay based on quenching of the intrinsic fluorescence of DNA G-quadruplexes for assessing and comparing the G4 binding affinity of various small molecule ligands in solutions. We show that the approach allows direct quantification of ligand binding to distinctive G4 topologies. We believe that this method will facilitate quick and reliable evaluation of small molecule G4 ligands and support their development.
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Affiliation(s)
- Aleksandra Bednarz
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Denmark; Department of Chemistry, Aarhus University, Denmark
| | - Rebecca Torp Rosendal
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Denmark; Department of Chemistry, Aarhus University, Denmark
| | - Line Mørkholt Lund
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Denmark; Department of Chemistry, Aarhus University, Denmark
| | - Victoria Birkedal
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Denmark; Department of Chemistry, Aarhus University, Denmark.
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4
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Fujii S, Sato S, Hidaka R, Takenaka S. Biotinylated cyclic naphthalene diimide as a searching tool for G4 sites on the genome. ANAL SCI 2024; 40:943-950. [PMID: 38609708 PMCID: PMC11035424 DOI: 10.1007/s44211-024-00551-5] [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: 12/25/2023] [Accepted: 02/28/2024] [Indexed: 04/14/2024]
Abstract
A biotinyl cyclic naphthalene diimide (biotinyl cNDI) (1), in which biotin is introduced on the cyclic linker chain of cNDI with high G-quadruplex (G4) specificity, was synthesized. 1 was used for binding analysis to G4 DNAs such as c-myc, c-kit, CEGF, or TA-core. The results showed that 1 bind to G4 DNAs with high affinity and, especially, two molecules of 1 bind to c-myc DNA from top and bottom of G4 site at K = 3.9 × 10-6 M-1 without changing the G4 structure. As a pulldown assay, 1 and streptavidin magnetic beads could be used to recover a c-myc DNA or 120-mer DNA fragment having single c-myc sequence. The qPCR results for the 120-meric DNAs showed that more than 50% of genomic DNA fragments could be recovered by this pulldown assay. The results obtained here might allow the recovery of G4-containing DNA fragments from genomic DNA to analyze the true G4 present in the genome.
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Affiliation(s)
- Satoshi Fujii
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka-Shi, Fukuoka, 820-8502, Japan.
| | - Shinobu Sato
- Department of Applied Chemistry, Kyushu Institute of Technology, 1-1 Sensui-Cho, Tobata-Ku, Kitakyushu-Shi, Fukuoka, 804-8550, Japan.
| | - Ryuki Hidaka
- Department of Applied Chemistry, Kyushu Institute of Technology, 1-1 Sensui-Cho, Tobata-Ku, Kitakyushu-Shi, Fukuoka, 804-8550, Japan
| | - Shigeori Takenaka
- Department of Applied Chemistry, Kyushu Institute of Technology, 1-1 Sensui-Cho, Tobata-Ku, Kitakyushu-Shi, Fukuoka, 804-8550, Japan
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5
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Lourenço P, Miranda A, Campello MPC, Paulo A, Louis-Mergny J, Cruz C. Targeting proto-oncogene B-MYB G-quadruplex with a nucleic acid-based fluorescent probe. Int J Biol Macromol 2024; 266:131055. [PMID: 38522681 DOI: 10.1016/j.ijbiomac.2024.131055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 03/08/2024] [Accepted: 03/10/2024] [Indexed: 03/26/2024]
Abstract
The B-MYB gene encodes a transcription factor (B-MYB) that regulates cell growth and survival. Abnormal expression of B-MYB is frequently observed in lung cancer and poses challenges for targeted drug therapy. Oncogenes often contain DNA structures called G-quadruplexes (G4s) in their promoter regions, and B-MYB is no exception. These G4s play roles in genetic regulation and are potential cancer treatment targets. In this study, a probe was designed to specifically identify a G4 within the promoter region of the B-MYB gene. This probe combines an acridine derivative ligand with a DNA segment complementary to the target sequence, enabling it to hybridize with the adjacent sequence of the G4 being investigated. Biophysical studies demonstrated that the acridine derivative ligands C5NH2 and C8NH2 not only effectively stabilized the G4 structure but also exhibited moderate affinity. They were capable of altering the G4 topology and exhibited enhanced fluorescence emission in the presence of this quadruplex. Additionally, these ligands increased the number of G4s observed in cellular studies. Through various biophysical studies, the target sequence was shown to form a G4 structure, even with an extra nucleotide tail added to its flanking region. Cellular studies confirmed the co-localization between the target sequence and the developed probe.
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Affiliation(s)
- Pedro Lourenço
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal
| | - André Miranda
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal
| | - Maria Paula Cabral Campello
- Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10 (km 139.7), 2695-066 Bobadela, Portugal
| | - António Paulo
- Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10 (km 139.7), 2695-066 Bobadela, Portugal; Departamento de Engenharia e Ciências Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10 (km 139.7), 2695-066 Bobadela, Portugal
| | - Jean Louis-Mergny
- Laboratoire d'Optique et Biosciences, École Polytechnique, Institut Polytechnique de Paris, CNRS, INSERM, 91120 Palaiseau, France
| | - Carla Cruz
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal; Departamento de Química da Faculdade de Ciências da Universidade da Beira Interior, Rua Marquês de Ávila e Bolama, 6201-001 Covilhã, Portugal.
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6
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Bağda E. Insights into the G-quadruplex DNA interaction landscape: Comparative analysis of anionic Zn(II) and Co(II) phthalocyanine-tetrasulfonate complexes. J Mol Recognit 2024; 37:e3082. [PMID: 38471837 DOI: 10.1002/jmr.3082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 02/15/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024]
Abstract
G-quadruplexes play a pivotal role in regulating various cellular processes, including gene expression and replication, making them essential structures in understanding, and manipulating cellular functions. The development of G-quadruplex ligands holds significant promise in therapeutic and research applications, offering targeted tools to modulate G-quadruplex structures and potentially influence critical biological pathways. An exciting frontier in G-quadruplex research lies in the exploration of anionic ligands, and their profound impact on stabilizing and modulating G-quadruplex DNA. In this study, the interaction of two anionic phthalocyanine compounds (Zinc (II) phthalocyanine 3,4',4″,4‴-tetrasulfonic acid, tetrasodium salt, ZnAPC; cobalt (II) phthalocyanine 3,4',4″,4‴-tetrasulfonic acid, tetrasodium salt, CoAPC) and three separate G-quadruplex-forming DNA sequences was investigated. Interactions were carried out by DNA polymerase stop studies along with spectroscopic studies. According to the results of experimental data, it was determined that ZnAPC actively interacts with the G-quadruplex DNA structures. On the other hand, it was thought that the interaction with CoAPC was less and even occurred in simple electrostatic interactions. KD constants and Bmax constants for the interaction with ZnAPC were calculated. The KD constants for ZnAPC were found to be (1.16 ± 0.07) × 10-5, (9.75 ± .24) × 10-6 and (1.00 ± 0.36) × 10-4 M for AS1411, Vegf, and Tel21, respectively. Accordingly, it was concluded that ZnAPC interacts with G-quadruplex DNA ligands effectively.
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Affiliation(s)
- Efkan Bağda
- Molecular Biology and Genetics, Faculty of Science, Sivas Cumhuriyet University, Sivas, Turkey
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7
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Gómez-Bra A, Gude L, Arias-Pérez MS. Synthesis, structural study and antitumor activity of novel alditol-based imidazophenanthrolines (aldo-IPs). Bioorg Med Chem 2024; 99:117563. [PMID: 38215623 DOI: 10.1016/j.bmc.2023.117563] [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: 07/05/2023] [Revised: 11/17/2023] [Accepted: 12/18/2023] [Indexed: 01/14/2024]
Abstract
A series of 1H-imidazo [4,5-f][1,10] phenanthroline derivatives functionalized at 2-position with chiral, and conformationally flexible polyhydroxy alkyl chains derived from carbohydrates (alditol-based imidazophenanthrolines, aldo-IPs) is presented herein. These novel glycomimetics showed relevant and differential cytotoxic activity against several cultured tumor cell lines (PC3, HeLa and HT-29), dependent on the nature and stereochemistry of the polyhydroxy alkyl chain. The mannose-based aldo-IP demonstrated the higher cytotoxicity in the series, substantially better than cisplatin metallo-drug in all cell lines tested, and better than G-quadruplex ligand 360A in HeLa and HT29 cells. Cell cycle experiments and Annexin V-PI assays revealed that aldo-IPs induce apoptosis in HeLa cells. Initial study of DNA interactions by DNA FRET melting assays proved that the aldo-IPs produce only a slight thermal stabilization of DNA secondary structures, more pronounced in the case of quadruplex DNA. Viscosity titrations with CT dsDNA suggest that the compounds behave as DNA groove binders, whereas equilibrium dialysis assays showed that the compounds bind CT with Ka values in the range 104-105 M-1. The aldo-IP derivatives were obtained with synthetically useful yields through a feasible one-pot multistep process, by aerobic oxidative cyclization of 1,10-phenanthroline-5,6-diamine with a selection of unprotected aldoses using (NH4)2SO4 as promoter.
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Affiliation(s)
- Ana Gómez-Bra
- Universidad de Alcalá, Departamento de Química Orgánica y Química Inorgánica, Instituto de Investigación Química "Andrés M. del Río" (IQAR), 28805-Alcalá de Henares, Madrid, Spain; Grupo DISCOBAC, Instituto de Investigación Sanitaria de Castilla-La Mancha (IDISCAM), Spain
| | - Lourdes Gude
- Universidad de Alcalá, Departamento de Química Orgánica y Química Inorgánica, Instituto de Investigación Química "Andrés M. del Río" (IQAR), 28805-Alcalá de Henares, Madrid, Spain; Grupo DISCOBAC, Instituto de Investigación Sanitaria de Castilla-La Mancha (IDISCAM), Spain.
| | - María-Selma Arias-Pérez
- Universidad de Alcalá, Departamento de Química Orgánica y Química Inorgánica, Instituto de Investigación Química "Andrés M. del Río" (IQAR), 28805-Alcalá de Henares, Madrid, Spain.
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8
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Bhat-Ambure J, Ambure P, Serrano-Candelas E, Galiana-Roselló C, Gil-Martínez A, Guerrero M, Martin M, González-García J, García-España E, Gozalbes R. G4-QuadScreen: A Computational Tool for Identifying Multi-Target-Directed Anticancer Leads against G-Quadruplex DNA. Cancers (Basel) 2023; 15:3817. [PMID: 37568632 PMCID: PMC10416877 DOI: 10.3390/cancers15153817] [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: 06/01/2023] [Revised: 07/16/2023] [Accepted: 07/21/2023] [Indexed: 08/13/2023] Open
Abstract
The study presents 'G4-QuadScreen', a user-friendly computational tool for identifying MTDLs against G4s. Also, it offers a few hit MTDLs based on in silico and in vitro approaches. Multi-tasking QSAR models were developed using linear discriminant analysis and random forest machine learning techniques for predicting the responses of interest (G4 interaction, G4 stabilization, G4 selectivity, and cytotoxicity) considering the variations in the experimental conditions (e.g., G4 sequences, endpoints, cell lines, buffers, and assays). A virtual screening with G4-QuadScreen and molecular docking using YASARA (AutoDock-Vina) was performed. G4 activities were confirmed via FRET melting, FID, and cell viability assays. Validation metrics demonstrated the high discriminatory power and robustness of the models (the accuracy of all models is ~>90% for the training sets and ~>80% for the external sets). The experimental evaluations showed that ten screened MTDLs have the capacity to selectively stabilize multiple G4s. Three screened MTDLs induced a strong inhibitory effect on various human cancer cell lines. This pioneering computational study serves a tool to accelerate the search for new leads against G4s, reducing false positive outcomes in the early stages of drug discovery. The G4-QuadScreen tool is accessible on the ChemoPredictionSuite website.
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Affiliation(s)
| | - Pravin Ambure
- ProtoQSAR SL, Centro Europeo de Empresas Innovadoras (CEEI), Parque Tecnológico de Valencia, 46980 Valencia, Spain; (P.A.); (E.S.-C.)
| | - Eva Serrano-Candelas
- ProtoQSAR SL, Centro Europeo de Empresas Innovadoras (CEEI), Parque Tecnológico de Valencia, 46980 Valencia, Spain; (P.A.); (E.S.-C.)
| | - Cristina Galiana-Roselló
- Department of Inorganic Chemistry, Institute of Molecular Science, University of Valencia, 46980 Valencia, Spain; (C.G.-R.); (A.G.-M.); (J.G.-G.); (E.G.-E.)
| | - Ariadna Gil-Martínez
- Department of Inorganic Chemistry, Institute of Molecular Science, University of Valencia, 46980 Valencia, Spain; (C.G.-R.); (A.G.-M.); (J.G.-G.); (E.G.-E.)
| | - Mario Guerrero
- Biochemistry and Molecular Biology Unit, Biomedicine Department, Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain; (M.G.); (M.M.)
| | - Margarita Martin
- Biochemistry and Molecular Biology Unit, Biomedicine Department, Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain; (M.G.); (M.M.)
- Clinical and Experimental Respiratory Immunoallergy (IRCE), Institut d’Investigacions Biomediques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
| | - Jorge González-García
- Department of Inorganic Chemistry, Institute of Molecular Science, University of Valencia, 46980 Valencia, Spain; (C.G.-R.); (A.G.-M.); (J.G.-G.); (E.G.-E.)
| | - Enrique García-España
- Department of Inorganic Chemistry, Institute of Molecular Science, University of Valencia, 46980 Valencia, Spain; (C.G.-R.); (A.G.-M.); (J.G.-G.); (E.G.-E.)
| | - Rafael Gozalbes
- MolDrug AI Systems SL, c/Olimpia Arozena Torres, 46018 Valencia, Spain;
- ProtoQSAR SL, Centro Europeo de Empresas Innovadoras (CEEI), Parque Tecnológico de Valencia, 46980 Valencia, Spain; (P.A.); (E.S.-C.)
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9
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Sasaki S, Ma Y, Hirokawa T, Ikebukuro K, Tera M, Nagasawa K. Regulation of thrombin activity by ligand-induced topological alteration in a thrombin-binding aptamer. Chem Commun (Camb) 2023. [PMID: 37377065 DOI: 10.1039/d3cc02308g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
Thrombin-binding aptamer (TBA), which forms a G-quadruplex (G4) structure with anti-parallel topology, interacts with thrombin to inhibit its enzymatic activity. Here we show that the G4-topology-altering ligand L2H2-2M2EA-6LCO (6LCO) changes the anti-parallel topology of TBA G4 to the parallel topology, thereby abrogating the thrombin-inhibitory activity of TBA. This finding suggests that G4 ligands that alter topology may be promising drug candidates for diseases involving G4-binding proteins.
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Affiliation(s)
- Shogo Sasaki
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.
| | - Yue Ma
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-0062, Japan
- Research Core Center, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Takatsugu Hirokawa
- Transborder Medical Research Center, University of Tsukuba, Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
- Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.
| | - Masayuki Tera
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.
| | - Kazuo Nagasawa
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.
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10
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Holden L, Gkika KS, Burke CS, Long C, Keyes TE. Selective, Disruptive Luminescent Ru(II) Polypyridyl Probes of G-Quadruplex. Inorg Chem 2023; 62:2213-2227. [PMID: 36703307 PMCID: PMC9906756 DOI: 10.1021/acs.inorgchem.2c03903] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Sensors capable of transducing G-quadruplex DNA binding are important both in solution and for imaging and interrogation in cellulo. Ru(II)-based light switches incorporating dipyridylphenazine (dppz) ligands are effective probes for recognition and imaging of DNA and its polymorphs including G-quadruplex, although selectivity is a limitation. While the majority of Ru(II)-based light switches reported to date, stabilize the quadruplex, imaging/theranostic probes that can disrupt G4s are of potentially enormous value in study and therapy for a range of disease states. We report here, on a Ru(II) complex (Ru-PDC3) that assembles the light switch capability of a Ru(II) dipyridylphenazine complex with the well-known G4-selective ligand Phen-DC3, into a single structure. The complex shows the anticipated light switch effect and strong affinity for G4 structures. Affinity depended on the G4 topology and sequence, but across all structures bar one, it was roughly an order of magnitude greater than for duplex or single-stranded DNA. Moreover, photophysical and Raman spectral data showed clear discrimination between duplex DNA and G4-bound structures offering the prospect of discrimination in imaging as well as in solution. Crucially, unlike the constituent components of the probe, Ru-PDC3 is a powerful G4 disrupter. From circular dichroism (CD), a reduction of ellipticity of the G4 between 70 and 95% was observed depending on topology and in many cases was accompanied by an induced CD signal for the metal complex. The extent of change in ellipticity is amongst the largest reported for small-molecule ligand G4 binding. While a promising G4 probe, without modification, the complex is fully water-soluble and readily permeable to live cells.
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11
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Savva L, Fossépré M, Keramidas O, Themistokleous A, Rizeq N, Panagiotou N, Leclercq M, Nicolaidou E, Surin M, Hayes SC, Georgiades SN. Gaining Insights on the Interactions of a Class of Decorated (2-([2,2'-Bipyridin]-6-yl)phenyl)platinum Compounds with c-Myc Oncogene Promoter G-Quadruplex and Other DNA Structures. Chemistry 2022; 28:e202201497. [PMID: 35726630 PMCID: PMC9804160 DOI: 10.1002/chem.202201497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Indexed: 01/05/2023]
Abstract
Organometallic molecules offer some of the most promising scaffolds for interaction with G-quadruplex nucleic acids. We report the efficient synthesis of a family of organoplatinum(II) complexes, featuring a 2-([2,2'-bipyridin]-6-yl)phenyl tridentate (N∧ N∧ C) ligand, that incorporates peripheral side-chains aiming at enhancing and diversifying its interaction capabilities. These include a di-isopropyl carbamoyl amide, a morpholine ethylenamide, two enantiomeric proline imides and an oxazole. The binding affinities of the Pt-complexes were evaluated via UV-vis and fluorescence titrations, against 5 topologically-distinct DNA structures, including c-myc G-quadruplex, two telomeric (22AG) G-quadruplexes, a duplex (ds26) and a single-stranded (polyT) DNA. All compounds exhibited binding selectivity in favour of c-myc, with association constants (Ka ) in the range of 2-5×105 M-1 , lower affinity for both folds of 22AG and for ds26 and negligible affinity for polyT. Remarkable emission enhancements (up to 200-fold) upon addition of excess DNA were demonstrated by a subset of the compounds with c-myc, providing a basis for optical selectivity, since optical response to all other tested DNAs was low. A c-myc DNA-melting experiment showed significant stabilizing abilities for all compounds, with the most potent binder, the morpholine-Pt-complex, exhibiting a ΔTm >30 °C, at 1 : 5 DNA-to-ligand molar ratio. The same study implied contributions of the diverse side-chains to helix stabilization. To gain direct evidence of the nature of the interactions, mixtures of c-myc with the four most promising compounds were studied via UV Resonance Raman (UVRR) spectroscopy, which revealed end-stacking binding mode, combined with interactions of side-chains with loop nucleobase residues. Docking simulations were conducted to provide insights into the binding modes for the same four Pt-compounds, suggesting that the binding preference for two alternative orientations of the c-myc G-quadruplex thymine 'cap' ('open' vs. 'closed'), as well as the relative contributions to affinity from end-stacking and H-bonding, are highly dependent on the nature of the interacting Pt-complex side-chain.
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Affiliation(s)
- Loukiani Savva
- Department of ChemistryUniversity of Cyprus1 Panepistimiou Avenue, Aglandjia2109NicosiaCyprus
| | - Mathieu Fossépré
- Laboratory for Chemistry of Novel MaterialsUniversity of Mons – UMONS20 Place du ParcB-7000MonsBelgium
| | - Odysseas Keramidas
- Department of ChemistryUniversity of Cyprus1 Panepistimiou Avenue, Aglandjia2109NicosiaCyprus
| | | | - Natalia Rizeq
- Department of ChemistryUniversity of Cyprus1 Panepistimiou Avenue, Aglandjia2109NicosiaCyprus
| | - Nikos Panagiotou
- Department of ChemistryUniversity of Cyprus1 Panepistimiou Avenue, Aglandjia2109NicosiaCyprus
| | - Maxime Leclercq
- Laboratory for Chemistry of Novel MaterialsUniversity of Mons – UMONS20 Place du ParcB-7000MonsBelgium
| | - Eliana Nicolaidou
- Department of ChemistryUniversity of Cyprus1 Panepistimiou Avenue, Aglandjia2109NicosiaCyprus
| | - Mathieu Surin
- Laboratory for Chemistry of Novel MaterialsUniversity of Mons – UMONS20 Place du ParcB-7000MonsBelgium
| | - Sophia C. Hayes
- Department of ChemistryUniversity of Cyprus1 Panepistimiou Avenue, Aglandjia2109NicosiaCyprus
| | - Savvas N. Georgiades
- Department of ChemistryUniversity of Cyprus1 Panepistimiou Avenue, Aglandjia2109NicosiaCyprus
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12
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Lizunova SA, Tsvetkov VB, Skvortsov DA, Kamzeeva PN, Ivanova OM, Vasilyeva LA, Chistov AA, Belyaev ES, Khrulev AA, Vedekhina TS, Bogomazova AN, Lagarkova MA, Varizhuk AM, Aralov AV. Anticancer activity of G4-targeting phenoxazine derivatives in vitro. Biochimie 2022; 201:43-54. [PMID: 35817132 DOI: 10.1016/j.biochi.2022.07.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 06/27/2022] [Accepted: 07/01/2022] [Indexed: 11/02/2022]
Abstract
G4-stabilizing ligands are now being considered as anticancer, antiviral and antibacterial agents. Phenoxazine is a promising scaffold for the development of G4 ligands. Here, we profiled two known phenoxazine-based nucleoside analogs and five new nucleoside and non-nucleoside derivatives against G4 targets from telomere repeats and the KIT promoter region. Leading new derivatives exhibited remarkably high G4-stabilizing effects (comparable or superior to the effects of the commonly used selective G4 ligands PDS and NMM) and selectivity toward G4s over duplex (superior to BRACO-19). All phenoxazine-based ligands inhibited cellular metabolic activity. The phenoxazine derivatives were particularly toxic for lung adenocarcinoma cells A549' and human liver cancer cells HepG2 (CC50 of the nucleoside analogues in the nanomolar range), but also affected breast cancer cells MCF7, as well as immortalized fibroblasts VA13 and embryonic kidney cells HEK293t (CC50 in the micromolar range). Importantly, the CC50 values varied mostly in accordance with G4-binding affinities and G4-stabilizing effects, and the phenoxazine derivatives localized in the cell nuclei, which corroborates G4-mediated mechanisms of action.
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Affiliation(s)
- Sofia A Lizunova
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya Str. 1a, Moscow, 119435, Russia
| | - Vladimir B Tsvetkov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya Str. 1a, Moscow, 119435, Russia; I.M. Sechenov First Moscow State Medical University, Trubetskaya Str. 8-2, Moscow, 119991, Russia; A.V. Topchiev Institute of Petrochemical Synthesis RAS, Leninsky Prospect Str. 29, Moscow, 119991, Russia.
| | - Dmitry A Skvortsov
- Lomonosov Moscow State University, Department of Chemistry and Faculty of Bioengineering and Bioinformatics, Moscow, 119991, Russia
| | - Polina N Kamzeeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya Str. 16/10, Moscow, 117997, Russia
| | - Olga M Ivanova
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya Str. 1a, Moscow, 119435, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya Str. 1a, Moscow, 119435, Russia
| | - Lilja A Vasilyeva
- Lomonosov Moscow State University, Department of Chemistry and Faculty of Bioengineering and Bioinformatics, Moscow, 119991, Russia
| | - Alexey A Chistov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya Str. 16/10, Moscow, 117997, Russia
| | - Evgeny S Belyaev
- Frumkin Institute of Physical Chemistry and Electrochemistry of the Russian Academy of Science, Moscow, 119071, Russia
| | - Alexei A Khrulev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya Str. 16/10, Moscow, 117997, Russia
| | - Tatiana S Vedekhina
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya Str. 1a, Moscow, 119435, Russia; G4_Interact, USERN, University of Pavia, 27100 Pavia, Italy
| | - Alexandra N Bogomazova
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya Str. 1a, Moscow, 119435, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya Str. 1a, Moscow, 119435, Russia
| | - Maria A Lagarkova
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya Str. 1a, Moscow, 119435, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya Str. 1a, Moscow, 119435, Russia
| | - Anna M Varizhuk
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya Str. 1a, Moscow, 119435, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya Str. 1a, Moscow, 119435, Russia; Moscow Institute of Physics and Technology, Institutskiy Pereulok 9, Dolgoprudny, 141701, Russia; G4_Interact, USERN, University of Pavia, 27100 Pavia, Italy.
| | - Andrey V Aralov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya Str. 16/10, Moscow, 117997, Russia.
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13
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Mendes E, Bahls B, Aljnadi IM, Paulo A. Indoloquinolines as scaffolds for the design of potent G-quadruplex ligands. Bioorg Med Chem Lett 2022; 72:128862. [PMID: 35716866 DOI: 10.1016/j.bmcl.2022.128862] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/09/2022] [Accepted: 06/13/2022] [Indexed: 11/19/2022]
Abstract
Indoloquinolines are natural alkaloids with known affinity to DNA and antiproliferative activity against bacteria, parasites, and cancer cells. Due to their non-chiral skeleton, their total synthesis is easy to achieve and throughout the years, many derivatives have been studied for their potential as drugs. Herein we review the indoloquinolines and bioisosters that have been designed, synthesised, and evaluated for their selective binding to G-quadruplex nucleic acid structures, as well as the reported effects in cancer cells. The data collected so far strongly suggest that indoloquinolines are good scaffolds for the development of drugs and probes targeting the G-quadruplex structures, but they also show that this scaffold is still underexplored.
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Affiliation(s)
- Eduarda Mendes
- Faculty of Pharmacy, Research Institute for Medicines (iMed.ULisboa), Universidade de Lisboa, Av. Prof. Gama Pinto, Lisbon 1649-003, Portugal
| | - Bárbara Bahls
- Faculty of Pharmacy, Research Institute for Medicines (iMed.ULisboa), Universidade de Lisboa, Av. Prof. Gama Pinto, Lisbon 1649-003, Portugal
| | - Israa M Aljnadi
- Faculty of Pharmacy, Research Institute for Medicines (iMed.ULisboa), Universidade de Lisboa, Av. Prof. Gama Pinto, Lisbon 1649-003, Portugal
| | - Alexandra Paulo
- Faculty of Pharmacy, Research Institute for Medicines (iMed.ULisboa), Universidade de Lisboa, Av. Prof. Gama Pinto, Lisbon 1649-003, Portugal.
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14
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Gratal P, Arias-Pérez MS, Gude L. 1H-imidazo[4,5-f][1,10]phenanthroline carbohydrate conjugates: synthesis, DNA interactions and cytotoxic activity. Bioorg Chem 2022; 125:105851. [DOI: 10.1016/j.bioorg.2022.105851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 04/05/2022] [Accepted: 04/29/2022] [Indexed: 11/02/2022]
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15
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Dong J, Ouyang Y, Wang J, O’Hagan MP, Willner I. Assembly of Dynamic Gated and Cascaded Transient DNAzyme Networks. ACS NANO 2022; 16:6153-6164. [PMID: 35294174 PMCID: PMC9047661 DOI: 10.1021/acsnano.1c11631] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 03/11/2022] [Indexed: 06/14/2023]
Abstract
The dynamic transient formation and depletion of G-quadruplexes regulate gene replication and transcription. This process was found to be related to various diseases such as cancer and premature aging. We report on the engineering of nucleic acid modules revealing dynamic, transient assembly and disassembly of G-quadruplex structures and G-quadruplex-based DNAzymes, gated transient processes, and cascaded dynamic transient reactions that involve G-quadruplex and DNAzyme structures. The dynamic transient processes are driven by functional DNA reaction modules activated by a fuel strand and guided toward dissipative operation by a nicking enzyme (Nt.BbvCI). The dynamic networks were further characterized by computational simulation of the experiments using kinetic models, allowing us to predict the dynamic performance of the networks under different auxiliary conditions applied to the systems. The systems reported herein could provide functional DNA machineries for the spatiotemporal control of G-quadruplex structures perturbing gene expression and thus provide a therapeutic means for related emergent diseases.
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16
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Mendes E, Aljnadi IM, Bahls B, Victor BL, Paulo A. Major Achievements in the Design of Quadruplex-Interactive Small Molecules. Pharmaceuticals (Basel) 2022; 15:ph15030300. [PMID: 35337098 PMCID: PMC8953082 DOI: 10.3390/ph15030300] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 12/17/2022] Open
Abstract
Organic small molecules that can recognize and bind to G-quadruplex and i-Motif nucleic acids have great potential as selective drugs or as tools in drug target discovery programs, or even in the development of nanodevices for medical diagnosis. Hundreds of quadruplex-interactive small molecules have been reported, and the challenges in their design vary with the intended application. Herein, we survey the major achievements on the therapeutic potential of such quadruplex ligands, their mode of binding, effects upon interaction with quadruplexes, and consider the opportunities and challenges for their exploitation in drug discovery.
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Affiliation(s)
- Eduarda Mendes
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal; (E.M.); (I.M.A.); (B.B.)
| | - Israa M. Aljnadi
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal; (E.M.); (I.M.A.); (B.B.)
- Faculty of Sciences, BioISI, Biosystems and Integrative Sciences Institute, Universidade de Lisboa, 1749-016 Lisbon, Portugal;
| | - Bárbara Bahls
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal; (E.M.); (I.M.A.); (B.B.)
- Faculty of Sciences, BioISI, Biosystems and Integrative Sciences Institute, Universidade de Lisboa, 1749-016 Lisbon, Portugal;
| | - Bruno L. Victor
- Faculty of Sciences, BioISI, Biosystems and Integrative Sciences Institute, Universidade de Lisboa, 1749-016 Lisbon, Portugal;
| | - Alexandra Paulo
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal; (E.M.); (I.M.A.); (B.B.)
- Correspondence:
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17
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Duraisamy R, Palanisamy UM, Sheriffa Begum KMM, Dharmar P. Facile induction and stabilization of intramolecular antiparallel G-quadruplex of d(TTAGGG)n on interaction with triazine-2-imidazole ethyl amine compound and its Cu(II), Zn(II) complexes under no-salt conditions. J CHEM SCI 2022. [DOI: 10.1007/s12039-021-01996-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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18
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Miron CE, Chen M, Mergny JL, Petitjean A. Portrait of a Family of Highly Stabilizing and Selective Guanine Quadruplex Platinum(II)-Based Binders. Chemistry 2021; 28:e202103839. [PMID: 34862673 DOI: 10.1002/chem.202103839] [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: 10/25/2021] [Indexed: 11/12/2022]
Abstract
The long-standing history of platinum coordination complexes in nucleic acid recognition attests to the unique suitability of such species for therapeutic applications. Here, we report the synthetic exploration and development of a family of di-imine ligands, and their platinum(II) complexes, elaborated on a 3-(2-pyridyl)-[1,2,4]triazolo[4,3-a]pyridine platform which, in its unsubstituted form, has recently been shown to display exceptional capabilities for guanine quadruplex (G4) targeting. The identification of facile, high-yielding synthetic methods for the derivatization of this platform for the incorporation of additional sites of interactions with guanine quadruplex loops and grooves, along with the optimization of platinum(II) complexation methods, are discussed. Gratifyingly, preliminary biophysical screening of this novel family of binders validates all but one family members as robust G4 binders and highlights enhanced selectivity for quadruplex versus duplex DNA compared to the parent compound. These results bear promise for practical developments based on this platform.
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Affiliation(s)
- Caitlin E Miron
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, ON K7L3N6, Canada.,Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC H3A0B8, Canada
| | - Mickey Chen
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, ON K7L3N6, Canada
| | - Jean-Louis Mergny
- Institut Européen de Chimie et Biologie, 2 rue Escarpit, F-33607, Pessac, France.,Laboratoire d'Optique et Biosciences, École Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128, Palaiseau cedex, France
| | - Anne Petitjean
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, ON K7L3N6, Canada
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19
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Ramos-Soriano J, Galan MC. Photoresponsive Control of G-Quadruplex DNA Systems. JACS AU 2021; 1:1516-1526. [PMID: 34723256 PMCID: PMC8549047 DOI: 10.1021/jacsau.1c00283] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Indexed: 05/14/2023]
Abstract
G-quadruplex (G4) oligonucleotide secondary structures have recently attracted significant attention as therapeutic targets owing to their occurrence in human oncogene promoter sequences and the genome of pathogenic organisms. G4s also demonstrate interesting catalytic activities in their own right, as well as the ability to act as scaffolds for the development of DNA-based materials and nanodevices. Owing to this diverse range of opportunities to exploit G4 in a variety of applications, several strategies to control G4 structure and function have emerged. Interrogating the role of G4s in biology requires the delivery of small-molecule ligands that promote its formation under physiological conditions, while exploiting G4 in the development of responsive nanodevices is normally achieved by the addition and sequestration of the metal ions required for the stabilization of the folded structure. Although these strategies prove successful, neither allows the system in question to be controlled externally. Meanwhile, light has proven to be an attractive means for the control of DNA-based systems as it is noninvasive, can be delivered with high spatiotemporal precision, and is orthogonal to many chemical and biological processes. A plethora of photoresponsive DNA systems have been reported to date; however, the vast majority deploy photoreactive moieties to control the stability and assembly of duplex DNA hybrids. Despite the unique opportunities afforded by the regulation of G-quadruplex formation in biology, catalysis, and nanotechnology, comparatively little attention has been devoted to the design of photoresponsive G4-based systems. In this Perspective, we consider the potential of photoresponsive G4 assemblies and examine the strategies that may be used to engineer these systems toward a variety of applications. Through an overview of the main developments in the field to date, we highlight recent progress made toward this exciting goal and the emerging opportunities that remain ripe for further exploration in the coming years.
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Affiliation(s)
- Javier Ramos-Soriano
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
| | - M Carmen Galan
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
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20
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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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21
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Santos T, Salgado GF, Cabrita EJ, Cruz C. G-Quadruplexes and Their Ligands: Biophysical Methods to Unravel G-Quadruplex/Ligand Interactions. Pharmaceuticals (Basel) 2021; 14:769. [PMID: 34451866 PMCID: PMC8401999 DOI: 10.3390/ph14080769] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 07/31/2021] [Accepted: 08/03/2021] [Indexed: 12/12/2022] Open
Abstract
Progress in the design of G-quadruplex (G4) binding ligands relies on the availability of approaches that assess the binding mode and nature of the interactions between G4 forming sequences and their putative ligands. The experimental approaches used to characterize G4/ligand interactions can be categorized into structure-based methods (circular dichroism (CD), nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography), affinity and apparent affinity-based methods (surface plasmon resonance (SPR), isothermal titration calorimetry (ITC) and mass spectrometry (MS)), and high-throughput methods (fluorescence resonance energy transfer (FRET)-melting, G4-fluorescent intercalator displacement assay (G4-FID), affinity chromatography and microarrays. Each method has unique advantages and drawbacks, which makes it essential to select the ideal strategies for the biological question being addressed. The structural- and affinity and apparent affinity-based methods are in several cases complex and/or time-consuming and can be combined with fast and cheap high-throughput approaches to improve the design and development of new potential G4 ligands. In recent years, the joint use of these techniques permitted the discovery of a huge number of G4 ligands investigated for diagnostic and therapeutic purposes. Overall, this review article highlights in detail the most commonly used approaches to characterize the G4/ligand interactions, as well as the applications and types of information that can be obtained from the use of each technique.
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Affiliation(s)
- Tiago Santos
- CICS-UBI—Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal;
| | - Gilmar F. Salgado
- ARNA Laboratory, Université de Bordeaux, Inserm U1212, CNRS UMR 5320, IECB, 33607 Pessac, France;
| | - Eurico J. Cabrita
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal;
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
| | - Carla Cruz
- CICS-UBI—Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal;
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22
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Mitteaux J, Lejault P, Wojciechowski F, Joubert A, Boudon J, Desbois N, Gros CP, Hudson RHE, Boulé JB, Granzhan A, Monchaud D. Identifying G-Quadruplex-DNA-Disrupting Small Molecules. J Am Chem Soc 2021; 143:12567-12577. [PMID: 34346684 DOI: 10.1021/jacs.1c04426] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The quest for small molecules that strongly bind to G-quadruplex-DNA (G4), so-called G4 ligands, has invigorated the G4 research field from its very inception. Massive efforts have been invested to discover or rationally design G4 ligands, evaluate their G4-interacting properties in vitro through a series of now widely accepted and routinely implemented assays, and use them as innovative chemical biology tools to interrogate cellular networks that might involve G4s. In sharp contrast, only uncoordinated efforts aimed at developing small molecules that destabilize G4s have been invested to date, even though it is now recognized that such molecular tools would have tremendous application in neurobiology as many genetic and age-related diseases are caused by an overrepresentation of G4s. Herein, we report on our efforts to develop in vitro assays to reliably identify molecules able to destabilize G4s. This workflow comprises the newly designed G4-unfold assay, adapted from the G4-helicase assay implemented with Pif1, as well as a series of biophysical and biochemical techniques classically used to study G4/ligand interactions (CD, UV-vis, PAGE, and FRET-melting), and a qPCR stop assay, adapted from a Taq-based protocol recently used to identify G4s in the genomic DNA of Schizosaccharomyces pombe. This unique, multipronged approach leads to the characterization of a phenylpyrrolocytosine (PhpC)-based G-clamp analog as a prototype of G4-disrupting small molecule whose properties are validated through many different and complementary in vitro evaluations.
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Affiliation(s)
- Jérémie Mitteaux
- Institut de Chimie Moléculaire, ICMUB CNRS UMR 6302, UBFC, 21078 Dijon, France
| | - Pauline Lejault
- Institut de Chimie Moléculaire, ICMUB CNRS UMR 6302, UBFC, 21078 Dijon, France
| | - Filip Wojciechowski
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Alexandra Joubert
- Genome Structure and Instability Laboratory, CNRS UMR 7196, INSERM U1154, National Museum of Natural History, Alliance Sorbonne Université, 75005 Paris, France
| | - Julien Boudon
- Laboratoire Interdisciplinaire Carnot de Bourgogne, ICB CNRS UMR 6303, UBFC, 21078 Dijon, France
| | - Nicolas Desbois
- Institut de Chimie Moléculaire, ICMUB CNRS UMR 6302, UBFC, 21078 Dijon, France
| | - Claude P Gros
- Institut de Chimie Moléculaire, ICMUB CNRS UMR 6302, UBFC, 21078 Dijon, France
| | - Robert H E Hudson
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Jean-Baptiste Boulé
- Genome Structure and Instability Laboratory, CNRS UMR 7196, INSERM U1154, National Museum of Natural History, Alliance Sorbonne Université, 75005 Paris, France
| | - Anton Granzhan
- Institut Curie, CNRS UMR 9187, INSERM U1196, PSL Research University, 91405 Orsay, France.,Université Paris Saclay, CNRS UMR 9187, INSERM U1196, 91405 Orsay, France
| | - David Monchaud
- Institut de Chimie Moléculaire, ICMUB CNRS UMR 6302, UBFC, 21078 Dijon, France
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23
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Cadoni E, De Paepe L, Manicardi A, Madder A. Beyond small molecules: targeting G-quadruplex structures with oligonucleotides and their analogues. Nucleic Acids Res 2021; 49:6638-6659. [PMID: 33978760 PMCID: PMC8266634 DOI: 10.1093/nar/gkab334] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 04/15/2021] [Accepted: 04/29/2021] [Indexed: 12/20/2022] Open
Abstract
G-Quadruplexes (G4s) are widely studied secondary DNA/RNA structures, naturally occurring when G-rich sequences are present. The strategic localization of G4s in genome areas of crucial importance, such as proto-oncogenes and telomeres, entails fundamental implications in terms of gene expression regulation and other important biological processes. Although thousands of small molecules capable to induce G4 stabilization have been reported over the past 20 years, approaches based on the hybridization of a synthetic probe, allowing sequence-specific G4-recognition and targeting are still rather limited. In this review, after introducing important general notions about G4s, we aim to list, explain and critically analyse in more detail the principal approaches available to target G4s by using oligonucleotides and synthetic analogues such as Locked Nucleic Acids (LNAs) and Peptide Nucleic Acids (PNAs), reporting on the most relevant examples described in literature to date.
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Affiliation(s)
- Enrico Cadoni
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Lessandro De Paepe
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Alex Manicardi
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
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24
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Revikumar A, Kashyap V, Palollathil A, Aravind A, Raguraman R, Kumar KMK, Vijayakumar M, Prasad TSK, Raju R. Multiple G-quadruplex binding ligand induced transcriptomic map of cancer cell lines. J Cell Commun Signal 2021; 16:129-135. [PMID: 34309794 DOI: 10.1007/s12079-021-00637-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 07/13/2021] [Indexed: 10/20/2022] Open
Abstract
The G-quadruplexes (G4s) are a class of DNA secondary structures with guanine rich DNA sequences that can fold into four stranded non-canonical structures. At the genomic level, their pivotal role is well established in DNA replication, telomerase functions, constitution of topologically associating domains, and the regulation of gene expression. Genome instability mediated by altered G4 formation and assembly has been associated with multiple disorders including cancers and neurodegenerative disorders. Multiple tools have also been developed to predict the potential G4 regions in genomes and the whole genome G4 maps are also being derived through sequencing approaches. Enrichment of G4s in the cis-regulatory elements of genes associated with tumorigenesis has accelerated the quest for identification of G4-DNA binding ligands (G4DBLs) that can selectively bind and regulate the expression of such specific genes. In this context, the analysis of G4DBL responsive transcriptome in diverse cancer cell lines is inevitable for assessment of the specificity of novel G4DBLs. Towards this, we assembled the transcripts differentially regulated by different G4DBLs and have also identified a core set of genes regulated in diverse cancer cell lines in response to 3 or more of these ligands. With the mode of action of G4DBLs towards topology shifts, folding, or disruption of G4 structure being currently visualized, we believe that this dataset will serve as a platform for assembly of G4DBL responsive transcriptome for comparative analysis of G4DBLs in multiple cancer cells based on the expression of specific cis-regulatory G4 associated genes in the future.
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Affiliation(s)
- Amjesh Revikumar
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, India.
| | - Vivek Kashyap
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed To Be University), Mangalore, 575018, India
| | - Akhina Palollathil
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed To Be University), Mangalore, 575018, India
| | - Anjana Aravind
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed To Be University), Mangalore, 575018, India
| | - Rajeswari Raguraman
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, India.,Health Science Centre, University of Oklahoma, Oklahoma City, USA
| | | | - Manavalan Vijayakumar
- Department of Surgical Oncology, Yenepoya Medical College, Yenepoya (Deemed to Be University), Mangalore, 575018, India
| | | | - Rajesh Raju
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, India. .,Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed To Be University), Mangalore, 575018, India.
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25
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Yu Z, Hendricks AL, Cowan JA. G-quadruplex targeting chemical nucleases as a nonperturbative tool for analysis of cellular G-quadruplex DNA. iScience 2021; 24:102661. [PMID: 34189433 PMCID: PMC8215219 DOI: 10.1016/j.isci.2021.102661] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 03/04/2021] [Accepted: 05/26/2021] [Indexed: 11/21/2022] Open
Abstract
G-quadruplex structures are associated with various biological activities, while in vivo evidence is essential to confirm the formation of G-quadruplexes inside cells. Most conventional agents that recognize G-quadruplex, including antibodies and small-molecule G-quadruplex ligands, either stabilize the G-quadruplex or prevent G-quadruplex unfolding by helicase, thereby artificially increasing the G-quadruplex levels in cells. Unambiguous study of G-quadruplexes at natural cellular levels requires agents that do not enhance the stability of G-quadruplex. Herein, we report the first example of nonperturbative chemical nucleases that do not influence the stability of G-quadruplex telomeric DNA but can selectively cleave G-quadruplex DNA over duplex DNA. These chemical nucleases can be readily taken up by cells and promote selective cleavage of telomeric DNA with low levels of nonselective DNA cleavage of other regions of the genome. The cleavage of G-quadruplex telomeric DNA by nonperturbative chemical nucleases confirms the formation of G-quadruplex telomeric DNA in live cells. Novel chemical nucleases exhibit no effect on G-quadruplex telomeric DNA stability Selective nucleases cleave G-quadruplex DNA over duplex DNA Cleavage of G-quadruplex telomeric DNA motifs confirms their existence in cells
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Affiliation(s)
- Zhen Yu
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210, USA
| | - Amber L. Hendricks
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210, USA
| | - James A. Cowan
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210, USA
- Corresponding author
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26
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Street STG, Peñalver P, O'Hagan MP, Hollingworth GJ, Morales JC, Galan MC. Imide Condensation as a Strategy for the Synthesis of Core-Diversified G-Quadruplex Ligands with Anticancer and Antiparasitic Activity*. Chemistry 2021; 27:7712-7721. [PMID: 33780044 PMCID: PMC8251916 DOI: 10.1002/chem.202100040] [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: 02/05/2021] [Indexed: 11/22/2022]
Abstract
A facile imide coupling strategy for the one-step preparation of G-quadruplex ligands with varied core chemistries is described. The G-quadruplex stabilization of a library of nine compounds was examined using FRET melting experiments, and CD, UV-Vis, fluorescence and NMR titrations, identifying several compounds that were capable of stabilizing G-quadruplex DNA with interesting selectivity profiles. The best G4 ligand was identified as compound 3, which was based on a perylene scaffold and exhibited 40-fold selectivity for a telomeric G-quadruplex over duplex DNA. Surprisingly, a tetra-substituted flexible core, compound 11, also exhibited selective stabilization of G4 DNA over duplex DNA. The anticancer and antiparasitic activity of the library was also examined, with the lead compound 3 exhibiting nanomolar inhibition of Trypanosoma brucei with 78-fold selectivity over MRC5 cells. The cellular localization of this compound was also studied via fluorescence microscopy. We found that uptake was time dependant, with localization outside the nucleus and kinetoplast that could be due to strong fluorescence quenching in the presence of small amounts of DNA.
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Affiliation(s)
- Steven T. G. Street
- School of ChemistryUniversity of BristolCantocks CloseBristolBS8 1TSUK
- Department of ChemistryUniversity of VictoriaDr. S. T. G. StreetVictoriaBC V8P 5C2Canada
| | - Pablo Peñalver
- Instituto de Parasitología y Biomedicina López NeyraCSIC, PTS GranadaAvenida del Conocimiento, 1718016Armilla, GranadaSpain
| | | | | | - Juan C. Morales
- Instituto de Parasitología y Biomedicina López NeyraCSIC, PTS GranadaAvenida del Conocimiento, 1718016Armilla, GranadaSpain
| | - M. Carmen Galan
- School of ChemistryUniversity of BristolCantocks CloseBristolBS8 1TSUK
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27
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Lousen B, Pedersen SK, Răsădean DM, Pantoş GD, Pittelkow M. Triggering G-Quadruplex Conformation Switching with [7]Helicenes. Chemistry 2021; 27:6064-6069. [PMID: 33326174 DOI: 10.1002/chem.202004990] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Indexed: 12/14/2022]
Abstract
The dynamic interplay between two types of chiral structures; fully conjugated racemic hetero[7]helicenes and DNA strands prone to fold into G-quadruplex structures is described. Both the [7]helicenes and the G-quadruplex DNA structures exist in more than one conformation in solution. We show that the structures interact with and stabilise each other, mutually amplifying and stabilising certain conformations at increased temperatures. The [7]helicene ligands L1 and L2 stabilise the parallel conformation of k-ras significantly, whereas hybrid (K+ ) and antiparallel (Na+ ) h-telo G-quadruplexes are stabilised upon conformational switching into altered G-quadruplex conformations. Both L1 and L2 induce parallel G-quadruplexes from hybrid structures (K+ ) and L1 induces hybrid G-quadruplexes from antiparallel conformations (Na+ ). Enantioselective binding of one helicene enantiomer is observed for helicene ligand L2, and VTCD melting experiments are used to estimate the racemisation barrier of the helicene.
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Affiliation(s)
- Bodil Lousen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark
| | - Stephan K Pedersen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark
| | - Dora M Răsădean
- Department of Chemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - G Dan Pantoş
- Department of Chemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Michael Pittelkow
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark
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28
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Lejault P, Mitteaux J, Sperti FR, Monchaud D. How to untie G-quadruplex knots and why? Cell Chem Biol 2021; 28:436-455. [PMID: 33596431 DOI: 10.1016/j.chembiol.2021.01.015] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 12/08/2020] [Accepted: 01/20/2021] [Indexed: 12/12/2022]
Abstract
For over two decades, the prime objective of the chemical biology community studying G-quadruplexes (G4s) has been to use chemicals to interact with and stabilize G4s in cells to obtain mechanistic interpretations. This strategy has been undoubtedly successful, as demonstrated by recent advances. However, these insights have also led to a fundamental rethinking of G4-targeting strategies: due to the prevalence of G4s in the human genome, transcriptome, and ncRNAome (collectively referred to as the G4ome), and their involvement in human diseases, should we continue developing G4-stabilizing ligands or should we invest in designing molecular tools to unfold G4s? Here, we first focus on how, when, and where G4s fold in cells; then, we describe the enzymatic systems that have evolved to counteract G4 folding and how they have been used as tools to manipulate G4s in cells; finally, we present strategies currently being implemented to devise new molecular G4 unwinding agents.
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Affiliation(s)
- Pauline Lejault
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon, France
| | - Jérémie Mitteaux
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon, France
| | - Francesco Rota Sperti
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon, France
| | - David Monchaud
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon, France.
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29
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Stadlbauer P, Islam B, Otyepka M, Chen J, Monchaud D, Zhou J, Mergny JL, Šponer J. Insights into G-Quadruplex-Hemin Dynamics Using Atomistic Simulations: Implications for Reactivity and Folding. J Chem Theory Comput 2021; 17:1883-1899. [PMID: 33533244 DOI: 10.1021/acs.jctc.0c01176] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Guanine quadruplex nucleic acids (G4s) are involved in key biological processes such as replication or transcription. Beyond their biological relevance, G4s find applications as biotechnological tools since they readily bind hemin and enhance its peroxidase activity, creating a G4-DNAzyme. The biocatalytic properties of G4-DNAzymes have been thoroughly studied and used for biosensing purposes. Despite hundreds of applications and massive experimental efforts, the atomistic details of the reaction mechanism remain unclear. To help select between the different hypotheses currently under investigation, we use extended explicit-solvent molecular dynamics (MD) simulations to scrutinize the G4/hemin interaction. We find that besides the dominant conformation in which hemin is stacked atop the external G-quartets, hemin can also transiently bind to the loops and be brought to the external G-quartets through diverse delivery mechanisms. The simulations do not support the catalytic mechanism relying on a wobbling guanine. Similarly, the catalytic role of the iron-bound water molecule is not in line with our results; however, given the simulation limitations, this observation should be considered with some caution. The simulations rather suggest tentative mechanisms in which the external G-quartet itself could be responsible for the unique H2O2-promoted biocatalytic properties of the G4/hemin complexes. Once stacked atop a terminal G-quartet, hemin rotates about its vertical axis while readily sampling shifted geometries where the iron transiently contacts oxygen atoms of the adjacent G-quartet. This dynamics is not apparent from the ensemble-averaged structure. We also visualize transient interactions between the stacked hemin and the G4 loops. Finally, we investigated interactions between hemin and on-pathway folding intermediates of the parallel-stranded G4 fold. The simulations suggest that hemin drives the folding of parallel-stranded G4s from slip-stranded intermediates, acting as a G4 chaperone. Limitations of the MD technique are briefly discussed.
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Affiliation(s)
- Petr Stadlbauer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Barira Islam
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Michal Otyepka
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute, Palacký University, Křížkovského 8, 779 00 Olomouc, Czech Republic
| | - Jielin Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - David Monchaud
- Institut de Chimie Moléculaire (ICMUB), CNRS UMR6302, UBFC, Dijon 21078, France
| | - Jun Zhou
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jean-Louis Mergny
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic.,State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China.,Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau cedex, France
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
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30
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Cadoni E, Manicardi A, Fossépré M, Heirwegh K, Surin M, Madder A. Teaching photosensitizers a new trick: red light-triggered G-quadruplex alkylation by ligand co-localization. Chem Commun (Camb) 2021; 57:1010-1013. [PMID: 33404017 DOI: 10.1039/d0cc06030e] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We propose a bimolecular approach for G-quadruplex alkylation, using a pro-reactive furan-containing ligand, activated by red-light irradiation of a proximate G4-binding photosensitizer. G4- over dsDNA alkylation can be achieved selectively and proves high-yielding at low ligand excess. HPLC and modelling studies allowed identifying potential residues involved in the alkylation.
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Affiliation(s)
- Enrico Cadoni
- Organic and Biomimetic Research Group, Faculty of Sciences, University of Ghent Campus Sterre, Krijgslaan 281, Building S4, B-9000 Gent, Belgium.
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31
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Luo Y, Granzhan A, Verga D, Mergny JL. FRET-MC: A fluorescence melting competition assay for studying G4 structures in vitro. Biopolymers 2020; 112:e23415. [PMID: 33368198 DOI: 10.1002/bip.23415] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/10/2020] [Accepted: 12/11/2020] [Indexed: 12/16/2022]
Abstract
G-quadruplexes (G4) play crucial roles in biology, analytical chemistry and nanotechnology. The stability of G4 structures is impacted by the number of G-quartets, the length and positions of loops, flanking motifs, as well as additional structural elements such as bulges, capping base pairs, or triads. Algorithms such as G4Hunter or Quadparser may predict if a given sequence is G4-prone by calculating a quadruplex propensity score; however, experimental validation is still required. We previously demonstrated that this validation is not always straightforward, and that a combination of techniques is often required to unambiguously establish whether a sequence forms a G-quadruplex or not. In this article, we adapted the well-known FRET-melting assay to characterize G4 in batch, where the sequence to be tested is added, as an unlabeled competitor, to a system composed of a dual-labeled probe (F21T) and a specific quadruplex ligand. PhenDC3 was preferred over TMPyP4 because of its better selectivity for G-quadruplexes. In this so-called FRET-MC (melting competition) assay, G4-forming competitors lead to a marked decrease of the ligand-induced stabilization effect (∆Tm ), while non-specific competitors (e.g., single- or double-stranded sequences) have little effect. Sixty-five known sequences with different typical secondary structures were used to validate the assay, which was subsequently employed to assess eight novel sequences that were not previously characterized.
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Affiliation(s)
- Yu Luo
- Université Paris Saclay, CNRS UMR9187, INSERM U1196, Institut Curie, Orsay, France.,Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, Inserm, Institut Polytechnique de Paris, Palaiseau, France
| | - Anton Granzhan
- Université Paris Saclay, CNRS UMR9187, INSERM U1196, Institut Curie, Orsay, France
| | - Daniela Verga
- Université Paris Saclay, CNRS UMR9187, INSERM U1196, Institut Curie, Orsay, France
| | - Jean-Louis Mergny
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, Inserm, Institut Polytechnique de Paris, Palaiseau, France
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32
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Sasaki S, Ma Y, Ishizuka T, Bao HL, Hirokawa T, Xu Y, Tera M, Nagasawa K. Linear consecutive hexaoxazoles as G4 ligands inducing chair-type anti-parallel topology of a telomeric G-quadruplex. RSC Adv 2020; 10:43319-43323. [PMID: 35519695 PMCID: PMC9058415 DOI: 10.1039/d0ra09413g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 11/23/2020] [Indexed: 12/12/2022] Open
Abstract
G-quadruplex structures (G4s) in guanine-rich regions of DNA play critical roles in various biological phenomena, including replication, translation, and gene expression. There are three types of G4 topology, i.e., parallel, anti-parallel, and hybrid, and ligands that selectively interact with or stabilize a specific topology have been extensively explored to enable studies of topology-related functions. Here, we describe the synthesis of a new series of G4 ligands based on 6LCOs (6-linear consecutive oxazoles), i.e., L2H2-2M2EA-6LCO (2), L2A2-2M2EAc-6LCO (3), and L2G2-2M2EG-6LCO (4), which bear four aminoalkyl, acetamidealkyl, and guanidinylalkyl side chains, respectively. Among them, ligand 2 stabilized telomeric G4 and induced anti-parallel topology independently of the presence of cations. The anti-parallel topology induced by 2 was identified as chair-type by means of 19F NMR spectroscopy and fluorescence experiments with 2-aminopurine-labeled DNA.
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Affiliation(s)
- Shogo Sasaki
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology 2-24-16 Naka-cho, Koganei Tokyo 184-8588 Japan
| | - Yue Ma
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology 2-24-16 Naka-cho, Koganei Tokyo 184-8588 Japan
| | - Takumi Ishizuka
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazak 5200 Kihara, Kiyotake Miyazaki 889-1692 Japan
| | - Hong-Liang Bao
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazak 5200 Kihara, Kiyotake Miyazaki 889-1692 Japan
| | - Takatsugu Hirokawa
- Transborder Medical Research Center, University of Tsukuba 1-1-1 Tennodai Tsukuba, 305-8575 Japan
- Division of Biomedical Science, University of Tsukuba 1-1-1 Tennodai Tsukuba, 305-8575 Japan
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology 2-4-7 Aomi, Koto-ward Tokyo 135-0064 Japan
| | - Yan Xu
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazak 5200 Kihara, Kiyotake Miyazaki 889-1692 Japan
| | - Masayuki Tera
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology 2-24-16 Naka-cho, Koganei Tokyo 184-8588 Japan
| | - Kazuo Nagasawa
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology 2-24-16 Naka-cho, Koganei Tokyo 184-8588 Japan
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33
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O'Hagan MP, Haldar S, Morales JC, Mulholland AJ, Galan MC. Enhanced sampling molecular dynamics simulations correctly predict the diverse activities of a series of stiff-stilbene G-quadruplex DNA ligands. Chem Sci 2020; 12:1415-1426. [PMID: 34163904 PMCID: PMC8179204 DOI: 10.1039/d0sc05223j] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Ligands with the capability to bind G-quadruplexes (G4s) specifically, and to control G4 structure and behaviour, offer great potential in the development of novel therapies, technologies and functional materials. Most known ligands bind to a pre-formed topology, but G4s are highly dynamic and a small number of ligands have been discovered that influence these folding equilibria. Such ligands may be useful as probes to understand the dynamic nature of G4 in vivo, or to exploit the polymorphism of G4 in the development of molecular devices. To date, these fascinating molecules have been discovered serendipitously. There is a need for tools to predict such effects to drive ligand design and development, and for molecular-level understanding of ligand binding mechanisms and associated topological perturbation of G4 structures. Here we study the G4 binding mechanisms of a family of stiff-stilbene G4 ligands to human telomeric DNA using molecular dynamics (MD) and enhanced sampling (metadynamics) MD simulations. The simulations predict a variety of binding mechanisms and effects on G4 structure for the different ligands in the series. In parallel, we characterize the binding of the ligands to the G4 target experimentally using NMR and CD spectroscopy. The results show good agreement between the simulated and experimentally observed binding modes, binding affinities and ligand-induced perturbation of the G4 structure. The simulations correctly predict ligands that perturb G4 topology. Metadynamics simulations are shown to be a powerful tool to aid development of molecules to influence G4 structure, both in interpreting experiments and to help in the design of these chemotypes.
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Affiliation(s)
- Michael P O'Hagan
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Susanta Haldar
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
- Centre for Computational Chemistry, School of Chemistry, University of Bristol Bristol BS8 1TS UK
| | - Juan C Morales
- Instituto de Parasitología y Biomedicina "López Neyra" Consejo Superior de Investigaciones Científicas (CSIC), PTS Granada Avenida del Conocimiento 17, 18016 Armilla Granada Spain
| | - Adrian J Mulholland
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
- Centre for Computational Chemistry, School of Chemistry, University of Bristol Bristol BS8 1TS UK
| | - M Carmen Galan
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
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34
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Becher J, Berdnikova DV, Ihmels H, Stremmel C. Synthesis and investigation of quadruplex-DNA-binding, 9- O-substituted berberine derivatives. Beilstein J Org Chem 2020; 16:2795-2806. [PMID: 33281983 PMCID: PMC7684686 DOI: 10.3762/bjoc.16.230] [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: 09/20/2020] [Accepted: 11/02/2020] [Indexed: 12/20/2022] Open
Abstract
A small series of five novel berberine derivatives was synthesized by the Cu-catalyzed click reaction of 9-propargyladenine with 9-O-(azidoalkyl)berberine derivatives. The association of the resulting berberine-adenine conjugates with representative quadruplex-forming oligonucleotides 22AG dA(G3TTA)3G3 and a2 d(ACAG4TGTG4)2 was examined with photometric and fluorimetric titrations, thermal DNA denaturation analysis, and CD spectroscopy. The results from the spectrometric titrations indicated the formation of 2:1 or 1:1 complexes (ligand:G4-DNA) with log K b values of 10-11 (2:1) and 5-6 (1:1), which are typical for berberine derivatives. Notably, a clear relationship between the binding affinity of the ligands with the length of the alkyl linker chain, n, was not observed. However, depending on the structure, the ligands exhibited different effects when bound to the G4-DNA, such as fluorescent light-up effects and formation of ICD bands, which are mostly pronounced with a linker length of n = 4 (with a2) and n = 5 (with 22AG), thus indicating that each ligand-G4-DNA complex has a specific structure with respect to relative alignment and conformational flexibility of the ligand in the binding site. It was shown exemplarily with one representative ligand from the series that such berberine-adenine conjugates exhibit a selective binding, specifically a selectivity to quadruplex DNA in competition with duplex DNA, and a preferential thermal stabilization of the G4-DNA forms 22AG and KRAS. Notably, the experimental data do not provide evidence for a significant effect of the adenine unit on the binding affinity of the ligands, for example, by additional association with the loops, presumably because the adenine residue is sterically shielded by the neighboring triazole unit.
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Affiliation(s)
- Jonas Becher
- Department of Chemistry and Biology, University of Siegen and Center of Micro- and Nanochemistry and Engineering (Cμ); Adolf-Reichwein-Str. 2, 57068 Siegen, Germany
| | - Daria V Berdnikova
- Department of Chemistry and Biology, University of Siegen and Center of Micro- and Nanochemistry and Engineering (Cμ); Adolf-Reichwein-Str. 2, 57068 Siegen, Germany
| | - Heiko Ihmels
- Department of Chemistry and Biology, University of Siegen and Center of Micro- and Nanochemistry and Engineering (Cμ); Adolf-Reichwein-Str. 2, 57068 Siegen, Germany
| | - Christopher Stremmel
- Department of Chemistry and Biology, University of Siegen and Center of Micro- and Nanochemistry and Engineering (Cμ); Adolf-Reichwein-Str. 2, 57068 Siegen, Germany
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35
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36
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Wise DE, Gamble AJ, Arkawazi SW, Walton PH, Galan MC, O'Hagan MP, Hogg KG, Marrison JL, O'Toole PJ, Sparkes HA, Lynam JM, Pringle PG. Cytotoxic ( cis, cis-1,3,5-triaminocyclohexane)ruthenium(II)-diphosphine complexes; evidence for covalent binding and intercalation with DNA. Dalton Trans 2020; 49:15219-15230. [PMID: 33021299 DOI: 10.1039/d0dt02612c] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
We report cytotoxic ruthenium(ii) complexes of the general formula [RuCl(cis-tach)(diphosphine)]+ (cis-tach = cis-cis-1,3,5-triaminocyclohexane) that have been characterised by 1H, 13C and 31P{1H} NMR spectroscopy, mass spectrometry, X-ray crystallography and elemental analysis. The kinetics of aquation and stability of the active species have been studied, showing that the chlorido ligand is substituted by water at 298 K with first order rate constants of 10-2-10-3 s-1, ideal for potential clinical use as anti-tumour agents. Strong interactions with biologically relevant duplex and quadruplex DNA models correlate with the activity observed with A549, A2780 and 293T cell lines, and the degree of activity was found to be sensitive to the chelating diphosphine ligand. A label-free ptychographic cell imaging technique recorded cell death processes over 4 days. The Ru(ii) cis-tach diphosphine complexes exhibit anti-proliferative effects, in some cases outperforming cisplatin and other cytotoxic ruthenium complexes.
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Affiliation(s)
- Dan E Wise
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | - Aimee J Gamble
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK.
| | - Sham W Arkawazi
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK.
| | - Paul H Walton
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK.
| | - M Carmen Galan
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | - Michael P O'Hagan
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | - Karen G Hogg
- Imaging and Cytometry Laboratory, Bioscience Technology Facility, Department of Biology, University of York, UK
| | - Joanne L Marrison
- Imaging and Cytometry Laboratory, Bioscience Technology Facility, Department of Biology, University of York, UK
| | - Peter J O'Toole
- Imaging and Cytometry Laboratory, Bioscience Technology Facility, Department of Biology, University of York, UK
| | - Hazel A Sparkes
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | - Jason M Lynam
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK.
| | - Paul G Pringle
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
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Rodriguez J, Mosquera J, Learte-Aymamı́ S, Vázquez ME, Mascareñas JL. Stimuli-Responsive DNA Binding by Synthetic Systems. Acc Chem Res 2020; 53:2286-2298. [PMID: 32997936 DOI: 10.1021/acs.accounts.0c00415] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA is the molecule responsible for the storage and transmission of the genetic information in living organisms. The expression of this information is highly regulated. In eukaryotes, it is achieved mainly at the transcription level thanks to specialized proteins called transcription factors (TFs) that recognize specific DNA sequences, thereby promoting or inhibiting the transcription of particular genes. In many cases, TFs are present in the cell in an inactive form but become active in response to an external signal, which might modify their localization and DNA binding properties or modulate their interactions with the rest of the transcriptional machinery. As a result of the crucial role of TFs, the design of synthetic peptides or miniproteins that can emulate their DNA binding properties and eventually respond to external stimuli is of obvious interest. On the other hand, although the B-form double helix is the most common DNA secondary structure, it is not the only one with an essential biological function. Guanine quadruplexes (GQs) have received considerable attention due to their critical role in the regulation of gene expression, which is usually associated with a change in the GQ conformation. Thus, the development of GQ probes whose properties can be controlled using external signals is also of significant relevance.In this Account, we present a summary of the recent efforts toward the development of stimuli-responsive synthetic DNA binders with a particular emphasis on our own contributions. We first introduce the structure of B and GQ DNAs, and some of the main factors underlying their selective recognition. We then discuss some of the different approaches used for the design of stimulus-mediated DNA binders. We have organized our discussion according to whether the interaction takes place with duplex or guanine quadruplex DNAs, and each section is divided according to the nature of the stimulus (i.e., physical or chemical). Regarding physical stimuli, light (through the incorporation of photolabile protecting groups or photoisomerizable agents) is the most common input for the activation/deactivation of DNA binding events. With respect to chemical signals, the use of metals (through the incorporation of metal-coordinating groups in the DNA binding agent) has allowed the development of a wide range of stimuli-responsive DNA binders. More recently, redox-based systems have also been used to control DNA interactions.This Account ends with a "Conclusions and Outlook" section highlighting some of the general lessons that have been learned and future directions toward further advancing the field.
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Affiliation(s)
- Jessica Rodriguez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS) and Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Jesús Mosquera
- Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow G1 1XQ, United Kingdom
| | - Soraya Learte-Aymamı́
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS) and Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - M. Eugenio Vázquez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS) and Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - José Luis Mascareñas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS) and Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
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Avagliano D, Sánchez‐Murcia PA, González L. Spiropyran Meets Guanine Quadruplexes: Isomerization Mechanism and DNA Binding Modes of Quinolizidine-Substituted Spiropyran Probes. Chemistry 2020; 26:13039-13045. [PMID: 32368812 PMCID: PMC7589282 DOI: 10.1002/chem.202001586] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/04/2020] [Indexed: 12/17/2022]
Abstract
The recent delivery of a fluorescent quinolizidine-substituted spiropyran, which is able to switch in vivo and bind to guanine quadruplexes (G4) at physiological pH values, urged us to elucidate its molecular switching and binding mechanism. Combining multiscale dynamical studies and accurate quantum chemical calculations, we show that, both in water and in the G4 environment, the switching of the spiropyran ring is not promoted by an initial protonation event-as expected by the effect of low pH solutions-but that the deprotonated merocyanine form is an intermediate of the reaction leading to the protonated open species. Additionally, we investigate the binding of both deprotonated and protonated open forms of merocyanine to c-MYC G4s. Both species bind to G4s albeit with different hydrogen-bond patterns and provide distinct rotamers around the exocyclic double bond of the merocyanine forms. Altogether, our study sheds light on the pharmacophoric points for the binding of these probes to DNA, and thereby, contributes to future developments of new G4 binders of the remarkable family of quinolizidine-substituted spiropyrans.
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Affiliation(s)
- Davide Avagliano
- Institute of Theoretical ChemistryFaculty of ChemistryUniversity of ViennaWähringer Straße 171090ViennaAustria
| | - Pedro A. Sánchez‐Murcia
- Institute of Theoretical ChemistryFaculty of ChemistryUniversity of ViennaWähringer Straße 171090ViennaAustria
| | - Leticia González
- Institute of Theoretical ChemistryFaculty of ChemistryUniversity of ViennaWähringer Straße 171090ViennaAustria
- Vienna Research Platform on Accelerating Photoreaction DiscoveryUniversity of ViennaWähringer Straße 17-A1090ViennaAustria
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Gillard M, Weynand J, Bonnet H, Loiseau F, Decottignies A, Dejeu J, Defrancq E, Elias B. Flexible Ru
II
Schiff Base Complexes: G‐Quadruplex DNA Binding and Photo‐Induced Cancer Cell Death. Chemistry 2020; 26:13849-13860. [DOI: 10.1002/chem.202001409] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 05/28/2020] [Indexed: 12/20/2022]
Affiliation(s)
- Martin Gillard
- Institut de la Matière Condensée et des Nanosciences (IMCN) Molecular Chemistry, Materials and Catalysis (MOST) Université catholique de Louvain (UCLouvain) Place Louis Pasteur 1, bte L4.01.02 1348 Louvain-la-Neuve Belgium
| | - Justin Weynand
- Institut de la Matière Condensée et des Nanosciences (IMCN) Molecular Chemistry, Materials and Catalysis (MOST) Université catholique de Louvain (UCLouvain) Place Louis Pasteur 1, bte L4.01.02 1348 Louvain-la-Neuve Belgium
- Département de Chimie Moléculaire UMR CNRS 5250 Université Grenoble Alpes (UGA) CS 40700-38058 Grenoble France
| | - Hugues Bonnet
- Département de Chimie Moléculaire UMR CNRS 5250 Université Grenoble Alpes (UGA) CS 40700-38058 Grenoble France
| | - Frédérique Loiseau
- Département de Chimie Moléculaire UMR CNRS 5250 Université Grenoble Alpes (UGA) CS 40700-38058 Grenoble France
| | - Anabelle Decottignies
- Université catholique de Louvain (UCLouvain) de Duve Institute Avenue Hippocrate 75 1200 Brussels Belgium
| | - Jérôme Dejeu
- Département de Chimie Moléculaire UMR CNRS 5250 Université Grenoble Alpes (UGA) CS 40700-38058 Grenoble France
| | - Eric Defrancq
- Département de Chimie Moléculaire UMR CNRS 5250 Université Grenoble Alpes (UGA) CS 40700-38058 Grenoble France
| | - Benjamin Elias
- Institut de la Matière Condensée et des Nanosciences (IMCN) Molecular Chemistry, Materials and Catalysis (MOST) Université catholique de Louvain (UCLouvain) Place Louis Pasteur 1, bte L4.01.02 1348 Louvain-la-Neuve Belgium
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41
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Recagni M, Tassinari M, Doria F, Cimino-Reale G, Zaffaroni N, Freccero M, Folini M, Richter SN. The Oncogenic Signaling Pathways in BRAF-Mutant Melanoma Cells are Modulated by Naphthalene Diimide-Like G-Quadruplex Ligands. Cells 2019; 8:cells8101274. [PMID: 31635389 PMCID: PMC6830342 DOI: 10.3390/cells8101274] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 09/27/2019] [Accepted: 10/16/2019] [Indexed: 01/12/2023] Open
Abstract
Melanoma is the most aggressive and deadly type of skin cancer. Despite the advent of targeted therapies directed against specific oncogene mutations, melanoma remains a tumor that is very difficult to treat, and ultimately remains incurable. In the past two decades, stabilization of the non-canonical nucleic acid G-quadruplex structures within oncogene promoters has stood out as a promising approach to interfere with oncogenic signaling pathways in cancer cells, paving the way toward the development of G-quadruplex ligands as antitumor drugs. Here, we present the synthesis and screening of a library of differently functionalized core-extended naphthalene diimides for their activity against the BRAFV600E-mutant melanoma cell line. The most promising compound was able to stabilize G-quadruplexes that formed in the promoter regions of two target genes relevant to melanoma, KIT and BCL-2. This activity led to the suppression of protein expression and thus to interference with oncogenic signaling pathways involved in BRAF-mutant melanoma cell survival, apoptosis, and resistance to drugs. This G-quadruplex ligand thus represents a suitable candidate for the development of melanoma treatment options based on a new mechanism of action and could reveal particular significance in the context of resistance to targeted therapies of BRAF-mutant melanoma cells.
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Affiliation(s)
- Marta Recagni
- Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Via G.A. Amadeo 42, 20133 Milan, Italy.
| | - Martina Tassinari
- Department of Molecular Medicine, University of Padua, via A. Gabelli 63, 35121 Padua, Italy.
| | - Filippo Doria
- Department of Chemistry, University of Pavia, v. le Taramelli 10, 27100 Pavia, Italy.
| | - Graziella Cimino-Reale
- Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Via G.A. Amadeo 42, 20133 Milan, Italy.
| | - Nadia Zaffaroni
- Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Via G.A. Amadeo 42, 20133 Milan, Italy.
| | - Mauro Freccero
- Department of Chemistry, University of Pavia, v. le Taramelli 10, 27100 Pavia, Italy.
| | - Marco Folini
- Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Via G.A. Amadeo 42, 20133 Milan, Italy.
| | - Sara N Richter
- Department of Molecular Medicine, University of Padua, via A. Gabelli 63, 35121 Padua, Italy.
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