1
|
Brown A, Brill J, Amini R, Nurmi C, Li Y. Development of Better Aptamers: Structured Library Approaches, Selection Methods, and Chemical Modifications. Angew Chem Int Ed Engl 2024; 63:e202318665. [PMID: 38253971 DOI: 10.1002/anie.202318665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/22/2024] [Accepted: 01/22/2024] [Indexed: 01/24/2024]
Abstract
Systematic evolution of ligands by exponential enrichment (SELEX) has been used to discover thousands of aptamers since its development in 1990. Aptamers are short single-stranded oligonucleotides capable of binding to targets with high specificity and selectivity through structural recognition. While aptamers offer advantages over other molecular recognition elements such as their ease of production, smaller size, extended shelf-life, and lower immunogenicity, they have yet to show significant success in real-world applications. By analyzing the importance of structured library designs, reviewing different SELEX methodologies, and the effects of chemical modifications, we provide a comprehensive overview on the production of aptamers for applications in drug delivery systems, therapeutics, diagnostics, and molecular imaging.
Collapse
Affiliation(s)
- Alex Brown
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4 K1, Canada
| | - Jake Brill
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4 K1, Canada
| | - Ryan Amini
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4 K1, Canada
| | - Connor Nurmi
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4 K1, Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4 K1, Canada
| |
Collapse
|
2
|
Figueiredo J, Mergny JL, Cruz C. G-quadruplex ligands in cancer therapy: Progress, challenges, and clinical perspectives. Life Sci 2024; 340:122481. [PMID: 38301873 DOI: 10.1016/j.lfs.2024.122481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 01/20/2024] [Accepted: 01/29/2024] [Indexed: 02/03/2024]
Abstract
Guanine-rich sequences can form G-quadruplexes (G4) in living cells, making these structures promising anti-cancer targets. Compounds able to recognize these structures have been investigated as potential anticancer drugs; however, no G4 binder has yet been approved in the clinic. Here, we describe G4 ligands structure-activity relationships, in vivo effects as well as clinical trials. Addressing G4 ligand characteristics, targeting challenges, and structure-activity relationships, this review provides insights into the development of potent and selective G4-targeting molecules for therapeutic applications.
Collapse
Affiliation(s)
- Joana Figueiredo
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal
| | - Jean-Louis Mergny
- Laboratoire d'Optique et Biosciences, Institut Polytechnique de Paris, CNRS, INSERM, Université Paris-Saclay, 91128 Palaiseau cedex, France; Institute of Biophysics of the CAS, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic.
| | - Carla Cruz
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal; Departamento de Química, Faculdade de Ciências, Universidade da Beira Interior, Rua Marquês de Ávila e Bolama, 6201-001 Covilhã, Portugal.
| |
Collapse
|
3
|
Nannan L, Decombis S, Terryn C, Audonnet S, Michel J, Brassart‐Pasco S, Gsell W, Himmelreich U, Brassart B. Dysregulation of intercellular communication in vitro and in vivo via extracellular vesicles secreted by pancreatic duct adenocarcinoma cells and generated under the influence of the AG9 elastin peptide-conditioned microenvironment. JOURNAL OF EXTRACELLULAR BIOLOGY 2024; 3:e145. [PMID: 38939412 PMCID: PMC11080898 DOI: 10.1002/jex2.145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 01/24/2024] [Accepted: 02/22/2024] [Indexed: 06/29/2024]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is an aggressive malignancy with poor prognosis due to its highly metastatic profile. Intercellular communication between cancer and stromal cells via extracellular vesicles (EVs) is crucial for the premetastatic microenvironment preparation leading to tumour metastasis. This study shows that under the influence of bioactive peptides derived from the extracellular matrix microenvironment, illustrated here by the AG-9 elastin-derived peptide (EDP), PDAC cells secrete more tumour-derived EVs. Compared to PDAC-derived EVs, tumour-derived EVs resulting from AG-9 treatment (PDAC AG-9-derived EVs) significantly stimulated cell proliferation. At constant amount, tumour-derived EVs were similarly taken up by PDAC and HMEC-1 cells. Tumour-derived EVs stimulated cell proliferation, migration, proteinase secretion, and angiogenesis. Bioluminescence imaging allowed tumour-derived EV/FLuc+ tracking in vivo in a PDAC mouse model. The biodistribution of PDAC AG-9-derived EVs was different to PDAC-derived EVs. Our results demonstrate that the microenvironment, through EDP release, may not only influence the genesis of EVs but may also affect tumour progression (tumour growth and angiogenesis), and metastatic homing by modifying the in vivo biodistribution of tumour-derived EVs. They are potential candidates for targeted drug delivery and modulation of tumour progression, and they constitute a new generation of therapeutic tools, merging oncology and genic therapy.
Collapse
Affiliation(s)
- Lise Nannan
- Université de Reims Champagne‐ArdenneLaboratoire de Biochimie Médicale et Biologie Moléculaire, UFR MédecineReimsFrance
- CNRS UMR 7369 Matrice Extracellulaire et Dynamique CellulaireReimsFrance
- KU Leuven, Department of Imaging and PathologyBiomedical MRILeuvenBelgium
| | - Salomé Decombis
- Université de Reims Champagne‐ArdenneLaboratoire de Biochimie Médicale et Biologie Moléculaire, UFR MédecineReimsFrance
- CNRS UMR 7369 Matrice Extracellulaire et Dynamique CellulaireReimsFrance
| | | | - Sandra Audonnet
- URCACyt PlatformUniversity of Reims Champagne‐ArdenneReimsFrance
| | - Jean Michel
- Inserm, Université de Reims Champagne‐Ardenne, P3Cell UMR‐S1250, SFR CAP‐SANTEReimsFrance
| | - Sylvie Brassart‐Pasco
- Université de Reims Champagne‐ArdenneLaboratoire de Biochimie Médicale et Biologie Moléculaire, UFR MédecineReimsFrance
- CNRS UMR 7369 Matrice Extracellulaire et Dynamique CellulaireReimsFrance
| | - Willy Gsell
- KU Leuven, Department of Imaging and PathologyBiomedical MRILeuvenBelgium
| | - Uwe Himmelreich
- KU Leuven, Department of Imaging and PathologyBiomedical MRILeuvenBelgium
| | - Bertrand Brassart
- Université de Reims Champagne‐ArdenneLaboratoire de Biochimie Médicale et Biologie Moléculaire, UFR MédecineReimsFrance
- CNRS UMR 7369 Matrice Extracellulaire et Dynamique CellulaireReimsFrance
| |
Collapse
|
4
|
Kumar S, Biswas A, Sudhakar S, Kumari D, Pradeepkumar PI. Estrone-Based Derivatives Stabilize the c-MYC and c-KIT G-Quadruplex DNA Structures. ACS OMEGA 2024; 9:6616-6626. [PMID: 38371752 PMCID: PMC10870291 DOI: 10.1021/acsomega.3c07574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 11/20/2023] [Accepted: 11/28/2023] [Indexed: 02/20/2024]
Abstract
G-rich sequences are present across the genome and can fold to form dynamic secondary structures, namely, G-quadruplexes (G4). These structures play a pivotal role in regulating numerous biological processes including replication, transcription, and translation. Therefore, targeting these structures using molecular scaffolds is an attractive approach to modulating their functions. Herein, we report the synthesis of three estrone-based derivatives (Est-1, Est-2, and Est-3) with a nonplanar core and a cationic alkyl side chain as G4 stabilizers. CD melting and polymerase stop assay results indicate that these ligands preferentially stabilize parallel c-MYC and c-KIT1 G4s over the other G4s and duplex DNAs. The ligand Est-3 shows cytotoxicity against cancer cell lines and effectively downregulates the c-KIT gene in HepG2 cell lines. Molecular modeling and dynamics studies showed that the ligand prefers stacking over the 5'-quartet of c-MYC G4 using the aromatic ring of the ligand. Overall, the findings of this study demonstrate that even G4 ligands can accommodate nonplanar scaffolds, which opens up new avenues for ligand design.
Collapse
Affiliation(s)
- Satendra Kumar
- Department of Chemistry, Indian
Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Annyesha Biswas
- Department of Chemistry, Indian
Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Sruthi Sudhakar
- Department of Chemistry, Indian
Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Divya Kumari
- Department of Chemistry, Indian
Institute of Technology Bombay, Powai, Mumbai 400076, India
| | | |
Collapse
|
5
|
Nicolás Á, Quero JG, Barroso M, Gándara Z, Gude L. DNA Interactions and Biological Activity of 2,9-Disubstituted 1,10-Phenanthroline Thiosemicarbazone-Based Ligands and a 4-Phenylthiazole Derivative. BIOLOGY 2024; 13:60. [PMID: 38275736 PMCID: PMC10813753 DOI: 10.3390/biology13010060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024]
Abstract
Four 1,10-phenanthroline derivatives (1-4) were synthesized as potential telomeric DNA binders, three substituted in their chains with thiosemicarbazones (TSCs) and one 4-phenylthiazole derivative. The compounds were characterized using NMR, HRMS, FTIR-spectroscopy and combustion elemental analysis. Quadruplex and dsDNA interactions were preliminarily studied, especially for neutral derivative 1, using FRET-based DNA melting assays, equilibrium dialysis (both competitive and non-competitive), circular dichroism and viscosity titrations. The TSC derivatives bind and stabilize the telomeric Tel22 quadruplex more efficiently than dsDNA, with an estimated 24-fold selectivity determined through equilibrium dialysis for compound 1. In addition, cytotoxic activity against various tumor cells (PC-3, DU145, HeLa, MCF-7 and HT29) and two normal cell lines (HFF-1 and RWPE-1) was evaluated. Except for the 4-phenylthiazole derivative, which was inactive, the compounds showed moderate cytotoxic properties, with the salts displaying lower IC50 values (30-80 μM), compared to the neutral TSC, except in PC-3 cells (IC50 (1) = 18 μM). However, the neutral derivative was the only compound that exhibited a modest selectivity in the case of prostate cells (tumor PC-3 versus healthy RWPE-1). Cell cycle analysis and Annexin V/PI assays revealed that the compounds can produce cell death by apoptosis, an effect that has proven to be similar to that demonstrated by other known 1,10-phenanthroline G4 ligands endowed with antitumor properties, such as PhenDC3 and PhenQE8.
Collapse
Affiliation(s)
- Álvaro Nicolás
- Universidad de Alcalá, Departamento de Química Orgánica y Química Inorgánica, Instituto de Investigación Química “Andrés M. del Río” (IQAR), 28805 Madrid, Spain; (Á.N.)
- Grupo DISCOBAC, Instituto de Investigación Sanitaria de Castilla-La Mancha (IDISCAM), 45071 Toledo, Spain
| | - Julia G. Quero
- Universidad de Alcalá, Departamento de Química Orgánica y Química Inorgánica, Instituto de Investigación Química “Andrés M. del Río” (IQAR), 28805 Madrid, Spain; (Á.N.)
| | - Marta Barroso
- Universidad de Alcalá, Departamento de Química Orgánica y Química Inorgánica, Instituto de Investigación Química “Andrés M. del Río” (IQAR), 28805 Madrid, Spain; (Á.N.)
| | - Zoila Gándara
- Universidad de Alcalá, Departamento de Química Orgánica y Química Inorgánica, Instituto de Investigación Química “Andrés M. del Río” (IQAR), 28805 Madrid, Spain; (Á.N.)
- Grupo DISCOBAC, Instituto de Investigación Sanitaria de Castilla-La Mancha (IDISCAM), 45071 Toledo, Spain
| | - Lourdes Gude
- Universidad de Alcalá, Departamento de Química Orgánica y Química Inorgánica, Instituto de Investigación Química “Andrés M. del Río” (IQAR), 28805 Madrid, Spain; (Á.N.)
- Grupo DISCOBAC, Instituto de Investigación Sanitaria de Castilla-La Mancha (IDISCAM), 45071 Toledo, Spain
| |
Collapse
|
6
|
Ferret L, Alvarez-Valadez K, Rivière J, Muller A, Bohálová N, Yu L, Guittat L, Brázda V, Kroemer G, Mergny JL, Djavaheri-Mergny M. G-quadruplex ligands as potent regulators of lysosomes. Autophagy 2023; 19:1901-1915. [PMID: 36740766 PMCID: PMC10283436 DOI: 10.1080/15548627.2023.2170071] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 12/03/2022] [Accepted: 12/05/2022] [Indexed: 02/07/2023] Open
Abstract
Guanine-quadruplex structures (G4) are unusual nucleic acid conformations formed by guanine-rich DNA and RNA sequences and known to control gene expression mechanisms, from transcription to protein synthesis. So far, a number of molecules that recognize G4 have been developed for potential therapeutic applications in human pathologies, including cancer and infectious diseases. These molecules are called G4 ligands. When the biological effects of G4 ligands are studied, the analysis is often limited to nucleic acid targets. However, recent evidence indicates that G4 ligands may target other cellular components and compartments such as lysosomes and mitochondria. Here, we summarize our current knowledge of the regulation of lysosome by G4 ligands, underlying their potential functional impact on lysosome biology and autophagic flux, as well as on the transcriptional regulation of lysosomal genes. We outline the consequences of these effects on cell fate decisions and we systematically analyzed G4-prone sequences within the promoter of 435 lysosome-related genes. Finally, we propose some hypotheses about the mechanisms involved in the regulation of lysosomes by G4 ligands.
Collapse
Affiliation(s)
- Lucille Ferret
- Centre de Recherche des Cordeliers, INSERM UMRS 1138, Sorbonne Université, Université Paris Cité, Equipe labellisée par la Ligue contre le Cancer, Institut universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, Villejuif, France
| | - Karla Alvarez-Valadez
- Centre de Recherche des Cordeliers, INSERM UMRS 1138, Sorbonne Université, Université Paris Cité, Equipe labellisée par la Ligue contre le Cancer, Institut universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, Villejuif, France
| | - Jennifer Rivière
- Department of Medicine III, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
| | - Alexandra Muller
- Centre de Recherche des Cordeliers, INSERM UMRS 1138, Sorbonne Université, Université Paris Cité, Equipe labellisée par la Ligue contre le Cancer, Institut universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, Villejuif, France
| | - Natalia Bohálová
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics, The Czech Academy of Sciences, Brno, Czech Republic
| | - Luo Yu
- Laboratoire d’Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128Palaiseau, France
- CNRS UMR9187, INSERM U1196, Université Paris-Saclay, Orsay, France
| | - Lionel Guittat
- Laboratoire d’Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128Palaiseau, France
- UFR SMBH, Université Sorbonne Paris Nord, Bobigny, France
| | - Vaclav Brázda
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics, The Czech Academy of Sciences, Brno, Czech Republic
| | - Guido Kroemer
- Centre de Recherche des Cordeliers, INSERM UMRS 1138, Sorbonne Université, Université Paris Cité, Equipe labellisée par la Ligue contre le Cancer, Institut universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, Villejuif, France
- Institut du Cancer Paris CARPEM, Department of Biology, Hôpital Européen Georges Pompidou, AP-HP, Paris, France
| | - Jean-Louis Mergny
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics, The Czech Academy of Sciences, Brno, Czech Republic
- Laboratoire d’Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128Palaiseau, France
| | - Mojgan Djavaheri-Mergny
- Centre de Recherche des Cordeliers, INSERM UMRS 1138, Sorbonne Université, Université Paris Cité, Equipe labellisée par la Ligue contre le Cancer, Institut universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, Villejuif, France
| |
Collapse
|
7
|
Telomerase: A prominent oncological target for development of chemotherapeutic agents. Eur J Med Chem 2023; 249:115121. [PMID: 36669398 DOI: 10.1016/j.ejmech.2023.115121] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 12/26/2022] [Accepted: 01/11/2023] [Indexed: 01/15/2023]
Abstract
Telomerase is a ribonucleoprotein (RNP) responsible for the maintenance of chromosomal integrity by stabilizing telomere length. Telomerase is a widely expressed hallmark responsible for replicative immortality in 80-90% of malignant tumors. Cancer cells produce telomerase which prevents telomere shortening by adding telomeres sequences beyond Hayflick's limit; which enables them to divide uncontrollably. The activity of telomerase is relatively low in somatic cells and absent in normal cells, but the re-activation of this RNP in normal cells suppresses p53 activity which leads to the avoidance of senescence causing malignancy. Here, we have focused explicitly on various anti-telomerase therapies and telomerase-inhibiting molecules for the treatment of cancer. We have covered molecules that are reported in developmental, preclinical, and clinical trial stages as potent telomerase inhibitors. Apart from chemotherapy, we have also included details of immunotherapy, gene therapy, G-quadruplex stabilizers, and HSP-90 inhibitors. The purpose of this work is to discuss the challenges behind the development of novel telomerase inhibitors and to identify various perspectives for designing anti-telomerase compounds.
Collapse
|
8
|
Cyclic Triimidazoles as Stabilizers for Gene Promoter and Human Telomeric DNA G‐Quadruplexes. European J Org Chem 2022. [DOI: 10.1002/ejoc.202200718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
9
|
Hu XX, Wang SQ, Gan SQ, Liu L, Zhong MQ, Jia MH, Jiang F, Xu Y, Xiao CD, Shen XC. A Small Ligand That Selectively Binds to the G-quadruplex at the Human Vascular Endothelial Growth Factor Internal Ribosomal Entry Site and Represses the Translation. Front Chem 2021; 9:781198. [PMID: 34858949 PMCID: PMC8630693 DOI: 10.3389/fchem.2021.781198] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 10/19/2021] [Indexed: 11/13/2022] Open
Abstract
G-quadruplexes are believed to have important biological functions, so many small molecules have been screened or developed for targeting G-quadruplexes. However, it is still a major challenge to find molecules that recognize specific G-quadruplexes. Here, by using a combination of surface plasmon resonance, electrospray ionization mass spectrometry, circular dichroism, Western blot, luciferase assay, and reverse transcriptase stop assay, we observed a small molecule, namely, oxymatrine (OMT) that could selectively bind to the RNA G-quadruplex in 5′-untranslated regions (UTRs) of human vascular endothelial growth factor (hVEGF), but could not bind to other G-quadruplexes. OMT could selectively repress the translation of VEGF in cervical cancer cells. Furthermore, it could recognize VEGF RNA G-quadruplexes in special conformations. The results indicate that OMT may serve as a potentially special tool for studying the VEGF RNA G-quadruplex in cells and as a valuable scaffold for the design of ligands that recognize different G-quadruplexes.
Collapse
Affiliation(s)
- Xiao-Xia Hu
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, China.,Department of Physiology, College of Basic Medical Sciences, Guizhou Medical University, Guiyang, China
| | - Sheng-Quan Wang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, China
| | - Shi-Quan Gan
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, China
| | - Lei Liu
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, China
| | - Ming-Qing Zhong
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, China
| | - Meng-Hao Jia
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, China
| | - Fei Jiang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, China
| | - Yan Xu
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Chao-Da Xiao
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, China.,The Key Laboratory of Optimal Utilization of Natural Medicine Resources, Guizhou Medical University, Guiyang, China
| | - Xiang-Chun Shen
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, China.,The Key Laboratory of Optimal Utilization of Natural Medicine Resources, Guizhou Medical University, Guiyang, China
| |
Collapse
|
10
|
Ali S, Lombardi EP, Ghosh D, Jia T, Vitry G, Saker L, Poupon J, Teulade-Fichou MP, Nicolas A, Londono-Vallejo A, Bombard S. Pt-ttpy, a G-quadruplex binding platinum complex, induces telomere dysfunction and G-rich regions DNA damage. Metallomics 2021; 13:6280987. [PMID: 34021581 DOI: 10.1093/mtomcs/mfab029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 11/14/2022]
Abstract
Pt-ttpy (tolyl terpyridin-Pt complex) covalently binds to G-quadruplex (G4) structures in vitro and to telomeres in cellulo via its Pt moiety. Here, we identified its targets in the human genome, in comparison to Pt-tpy, its derivative without G4 affinity, and cisplatin. Pt-ttpy, but not Pt-tpy, induces the release of the shelterin protein TRF2 from telomeres concomitantly to the formation of DNA damage foci at telomeres but also at other chromosomal locations. γ-H2AX chromatin immunoprecipitation (ChIP-seq) after treatment with Pt-ttpy or cisplatin revealed accumulation in G- and A-rich tandemly repeated sequences, but not particularly in potential G4 forming sequences. Collectively, Pt-ttpy presents dual targeting efficiency on DNA, by inducing telomere dysfunction and genomic DNA damage at specific loci.
Collapse
Affiliation(s)
- Samar Ali
- INSERM UMRS 1007, Université de Paris, 75006 Paris, France
| | - Emilia Puig Lombardi
- Institut Curie, PSL Research University, CNRS UMR3244, Sorbonne Université, Telomeres and Cancer lab, 75005 Paris, France
| | - Deepanjan Ghosh
- Institut Curie, CNRS UMR9187-INSERMU1196, CMBC, 91405 Orsay, France.,Institut Curie, CNRS UMR9187-INSERMU1196, Université Paris-Saclay, 91405 Orsay, France
| | - Tao Jia
- Institut Curie, CNRS UMR9187-INSERMU1196, CMBC, 91405 Orsay, France.,Institut Curie, CNRS UMR9187-INSERMU1196, Université Paris-Saclay, 91405 Orsay, France
| | | | - Lina Saker
- INSERM UMRS 1007, Université de Paris, 75006 Paris, France
| | - Joël Poupon
- Hôpital Lariboisière, Laboratoire de Toxicologie Biologique, 2 rue Ambroise Paré, 75475 Paris, France
| | - Marie-Paule Teulade-Fichou
- Institut Curie, CNRS UMR9187-INSERMU1196, CMBC, 91405 Orsay, France.,Institut Curie, CNRS UMR9187-INSERMU1196, Université Paris-Saclay, 91405 Orsay, France
| | - Alain Nicolas
- Institut Curie, PSL Research University, CNRS UMR3244, Sorbonne Université, Telomeres and Cancer lab, 75005 Paris, France
| | - Arturo Londono-Vallejo
- Institut Curie, PSL Research University, CNRS UMR3244, Sorbonne Université, Telomeres and Cancer lab, 75005 Paris, France
| | - Sophie Bombard
- Institut Curie, CNRS UMR9187-INSERMU1196, CMBC, 91405 Orsay, France.,Institut Curie, CNRS UMR9187-INSERMU1196, Université Paris-Saclay, 91405 Orsay, France
| |
Collapse
|
11
|
Gratal PB, Quero JG, Pérez-Redondo A, Gándara Z, Gude L. PhenQE8, a Novel Ligand of the Human Telomeric Quadruplex. Int J Mol Sci 2021; 22:E749. [PMID: 33451070 PMCID: PMC7828518 DOI: 10.3390/ijms22020749] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/30/2020] [Accepted: 01/10/2021] [Indexed: 01/02/2023] Open
Abstract
A novel quadruplex ligand based on 1,10-phenanthroline and incorporating two guanyl hydrazone functionalities, PhenQE8, is reported herein. Synthetic access was gained in a two-step procedure with an overall yield of 61%. X-ray diffraction studies revealed that PhenQE8 can adopt an extended conformation that may be optimal to favor recognition of quadruplex DNA. DNA interactions with polymorphic G-quadruplex telomeric structures were studied by different techniques, such as Fluorescence resonance energy transfer (FRET) DNA melting assays, circular dichroism and equilibrium dialysis. Our results reveal that the novel ligand PhenQE8 can efficiently recognize the hybrid quadruplex structures of the human telomeric DNA, with high binding affinity and quadruplex/duplex selectivity. Moreover, the compound shows significant cytotoxic activity against a selected panel of cultured tumor cells (PC-3, HeLa and MCF-7), whereas its cytotoxicity is considerably lower in healthy human cells (HFF-1 and RPWE-1).
Collapse
Affiliation(s)
| | | | | | - Zoila Gándara
- Departamento de Química Orgánica y Química Inorgánica, Instituto de Investigación Química “Andrés M. del Río” (IQAR), Universidad de Alcalá, 28805 Alcalá de Henares, Madrid, Spain; (P.B.G.); (J.G.Q.); (A.P.-R.)
| | - Lourdes Gude
- Departamento de Química Orgánica y Química Inorgánica, Instituto de Investigación Química “Andrés M. del Río” (IQAR), Universidad de Alcalá, 28805 Alcalá de Henares, Madrid, Spain; (P.B.G.); (J.G.Q.); (A.P.-R.)
| |
Collapse
|
12
|
Bryan TM. G-Quadruplexes at Telomeres: Friend or Foe? Molecules 2020; 25:molecules25163686. [PMID: 32823549 PMCID: PMC7464828 DOI: 10.3390/molecules25163686] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/09/2020] [Accepted: 08/10/2020] [Indexed: 12/28/2022] Open
Abstract
Telomeres are DNA-protein complexes that cap and protect the ends of linear chromosomes. In almost all species, telomeric DNA has a G/C strand bias, and the short tandem repeats of the G-rich strand have the capacity to form into secondary structures in vitro, such as four-stranded G-quadruplexes. This has long prompted speculation that G-quadruplexes play a positive role in telomere biology, resulting in selection for G-rich tandem telomere repeats during evolution. There is some evidence that G-quadruplexes at telomeres may play a protective capping role, at least in yeast, and that they may positively affect telomere maintenance by either the enzyme telomerase or by recombination-based mechanisms. On the other hand, G-quadruplex formation in telomeric DNA, as elsewhere in the genome, can form an impediment to DNA replication and a source of genome instability. This review summarizes recent evidence for the in vivo existence of G-quadruplexes at telomeres, with a focus on human telomeres, and highlights some of the many unanswered questions regarding the location, form, and functions of these structures.
Collapse
Affiliation(s)
- Tracy M Bryan
- Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW 2145, Australia
| |
Collapse
|
13
|
Chen X, Tang WJ, Shi JB, Liu MM, Liu XH. Therapeutic strategies for targeting telomerase in cancer. Med Res Rev 2019; 40:532-585. [PMID: 31361345 DOI: 10.1002/med.21626] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 07/12/2019] [Accepted: 07/16/2019] [Indexed: 12/13/2022]
Abstract
Telomere and telomerase play important roles in abnormal cell proliferation, metastasis, stem cell maintenance, and immortalization in various cancers. Therefore, designing of drugs targeting telomerase and telomere is of great significance. Over the past two decades, considerable knowledge regarding telomere and telomerase has been accumulated, which provides theoretical support for the design of therapeutic strategies such as telomere elongation. Therefore, the development of telomere-based therapies such as nucleoside analogs, non-nucleoside small molecules, antisense technology, ribozymes, and dominant negative human telomerase reverse transcriptase are being prioritized for eradicating a majority of tumors. While the benefits of telomere-based therapies are obvious, there is a need to address the limitations of various therapeutic strategies to improve the possibility of clinical applications. In this study, current knowledge of telomere and telomerase is discussed, and therapeutic strategies based on recent research are reviewed.
Collapse
Affiliation(s)
- Xing Chen
- School of Pharmacy, Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, Hefei, People's Republic of China
| | - Wen-Jian Tang
- School of Pharmacy, Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, Hefei, People's Republic of China
| | - Jing Bo Shi
- School of Pharmacy, Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, Hefei, People's Republic of China
| | - Ming Ming Liu
- School of Pharmacy, Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, Hefei, People's Republic of China
| | - Xin-Hua Liu
- School of Pharmacy, Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, Hefei, People's Republic of China
| |
Collapse
|
14
|
Badmus JA, Ekpo OE, Hussein AA, Meyer M, Hiss DC. Cytotoxic and cell cycle arrest properties of two steroidal alkaloids isolated from Holarrhena floribunda (G. Don) T. Durand & Schinz leaves. BMC COMPLEMENTARY AND ALTERNATIVE MEDICINE 2019; 19:112. [PMID: 31151442 PMCID: PMC6545003 DOI: 10.1186/s12906-019-2521-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 05/10/2019] [Indexed: 02/06/2023]
Abstract
Background The plant Holarrhena floribunda (H. floribunda; G. Don) is indigenous to sub-Saharan Africa and is traditionally used to treat several ailments. The present study was carried out to isolate and characterize bioactive compounds with anti-proliferative activity present in H. floribunda extracts. Methods Compounds were isolated from H. floribunda using the bioassay-guided fractionation technique of repeated column chromatography and the step-wise application of the MTT reduction assay to assess antiproliferative bioactivity. The structures of the compounds were identified mainly using NMR. The effects of the isolated compounds on the viability, cell cycle and proliferation of human cancer cell lines (MCF-7, HeLa and HT-29) as well as the non-cancerous human fibroblast cell line (KMST-6) were investigated. Results Bioassay-guided fractionation yielded two steroidal alkaloids: holamine (1) and funtumine (2). The MTT reduction assay shows that both compounds exhibited selective dose-dependent cytotoxicity against the cancer cell lines studied. The isolated compounds induced cell cycle arrest at the G0/G1 and G2/M phases in the cancer cell lines with significant reduction in DNA synthesis. The results obtained show that the cancer cells (MCF-7, HeLa and HT-29) used in this study were more sensitive to the isolated compounds compared to the noncancerous fibroblast cells (KMST-6). Conclusion The ability of the isolated compounds to cause cell cycle arrest and reduce DNA synthesis raises hopes for their possible development and use as potent anticancer drugs. However, more mechanistic studies need to be done for complete validation of the efficacy of the two compounds.
Collapse
|
15
|
Zhang R, Cheng M, Zhang LM, Zhu LN, Kong DM. Asymmetric Cationic Porphyrin as a New G-Quadruplex Probe with Wash-Free Cancer-Targeted Imaging Ability Under Acidic Microenvironments. ACS APPLIED MATERIALS & INTERFACES 2018; 10:13350-13360. [PMID: 29619818 DOI: 10.1021/acsami.8b01901] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Porphyrins are promising candidates for nucleic acid G-quadruplex-specific optical recognition. We previously demonstrated that G-quadruplex recognition specificity of porphyrins could be improved by introducing bulky side arm substituents, but the enhanced protonation tendency limits their applications in some cases, such as under acidic conditions. Here, we demonstrated that the protonation tendency of porphyrin derivatives could be efficiently overcome by increasing molecular asymmetry. To validate this, an asymmetric, water-soluble, cationic porphyrin FA-TMPipEOPP (5-{4-[2-[[(2 E)-3-[3-methoxy-4-[2-(1-methyl-1-piperidinyl)ethoxy]phenyl]-1-oxo-2-propenyl]oxy]ethoxy]phenyl},10,15,20-tri{4-[2-(1-methyl-1-piperidinyl)ethoxy]-phenyl}porphyrin) was synthesized by introducing a ferulic acid (FA) unit at one side arm, and its structure was well-characterized. Unlike its symmetric counterpart TMPipEOPP that has a tendency to protonate under acidic conditions, FA-TMPipEOPP remained in the unprotonated monomeric form under the pH range of 2.0-8.0. Correspondingly, FA-TMPipEOPP showed better G-quadruplex recognition specificity than TMPipEOPP and thus might be used as a specific optical probe for colorimetric and fluorescent recognition of G-quadruplexes under acidic conditions. The feasibility was demonstrated by two proof-of-concept studies: probing structural competition between G-quadruplexes and duplexes and label-free and wash-free cancer cell-targeted bioimaging under an acidic tumor microenvironment. As G-quadruplex optical probes, FA-TMPipEOPP works well under acidic conditions, whereas TMPipEOPP works well under neutral conditions. This finding provides useful information for G-quadruplex probe research. That is, porphyrin-based G-quadruplex probes suitable for different pH conditions might be obtained by adjusting the molecular symmetry.
Collapse
Affiliation(s)
- Ran Zhang
- Department of Chemistry, School of Science , Tianjin University , Tianjin 300072 , P R China
- Collaborative Innovation Center of Chemical Science and Engineering , Tianjin 30072 , P R China
| | - Meng Cheng
- Department of Chemistry, School of Science , Tianjin University , Tianjin 300072 , P R China
- Collaborative Innovation Center of Chemical Science and Engineering , Tianjin 30072 , P R China
| | - Li-Ming Zhang
- Department of Chemistry, School of Science , Tianjin University , Tianjin 300072 , P R China
- Collaborative Innovation Center of Chemical Science and Engineering , Tianjin 30072 , P R China
| | - Li-Na Zhu
- Department of Chemistry, School of Science , Tianjin University , Tianjin 300072 , P R China
- Collaborative Innovation Center of Chemical Science and Engineering , Tianjin 30072 , P R China
| | - De-Ming Kong
- Collaborative Innovation Center of Chemical Science and Engineering , Tianjin 30072 , P R China
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry , Nankai University , Tianjin 300071 , P R China
| |
Collapse
|
16
|
Yang KA, Chun H, Zhang Y, Pecic S, Nakatsuka N, Andrews AM, Worgall TS, Stojanovic MN. High-Affinity Nucleic-Acid-Based Receptors for Steroids. ACS Chem Biol 2017; 12:3103-3112. [PMID: 29083858 DOI: 10.1021/acschembio.7b00634] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Artificial receptors for hydrophobic molecules usually have moderate affinities and limited selectivities. We describe three new classes of high affinity hydrophobic receptors for nonaromatic steroids based on deoxyribonucleotides, obtained through five high stringency selections coupled with tailored counter-selections. The isolation of multiple classes of high affinity steroid receptors demonstrates the surprising breadth of moderately sized hydrophobic binding motifs (<40 nucleotides) available to natural nucleic acids. Studies of interactions with analogs indicate that two classes, four-way junctions and 4XGN motifs, comprise receptors with shapes that prevent binding of specific steroid conjugates used in counter-selections. Furthermore, they strongly prefer nonhydroxylated steroid cores, which is typical for hydrophobic receptors. The third new class accommodates hydroxyl groups in high-affinity, high-selectivity binding pockets, thus reversing the preferences of the first two classes. The high-affinity binding of aptamers to targets efficiently inhibits double-helix formation in the presence of the complementary oligonucleotides. The high affinity of some of these receptors and tailored elimination of binding through counter-selections ensures that these new aptamers will enable clinical chemistry applications.
Collapse
Affiliation(s)
| | - Hyosun Chun
- School
of Computer Science and Engineering, Seoul National University, Seoul 08826, Korea
| | | | | | - Nako Nakatsuka
- California
NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department
of Chemistry and Biochemistry, University of California, Los Angeles, Los
Angeles, California 90095, United States
| | - Anne M. Andrews
- California
NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department
of Chemistry and Biochemistry, University of California, Los Angeles, Los
Angeles, California 90095, United States
- Department
of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience
and Human Behavior, and Hatos Center for Neuropharmacology, University of California, Los Angeles, Los Angeles, California 90095, United States
| | | | | |
Collapse
|
17
|
Sillapapongwarakorn S, Yanarojana S, Pinthong D, Thithapandha A, Ungwitayatorn J, Supavilai P. Molecular docking based screening of triterpenoids as potential G-quadruplex stabilizing ligands with anti-cancer activity. Bioinformation 2017; 13:284-292. [PMID: 29081607 PMCID: PMC5651221 DOI: 10.6026/97320630013284] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 08/30/2017] [Accepted: 09/02/2017] [Indexed: 01/13/2023] Open
Abstract
Triterpenoids isolated from Ganoderma lucidum (GLTs) exhibit a broad spectrum of anti-cancer properties, including anti-proliferative, anti-metastatic and anti-angiogenic activities. Current research studies revealed the role by GLTs in inducing apoptosis and suppression of telomerase activity of cancer cells with much lower toxicity to healthy cells. Compounds selectively binding and stabilizing G-quadruplex structures could inhibit the telomerase or downregulate the oncogenes and may act as anti-cancer agents. Targeting human telomeric G-quadruplex DNA could be one of the mechanisms by which these GLTs exert anti-cancer activity. In this study, 208 GLTs were screened for ligands with high binding affinity and selectively to stabilize the pG4DNA by using the docking tool AutoDock4. The results showed that ganoderic acid A and ganoderic acid Df exhibit high binding affinity and selectively bind to the lateral groove of pG4DNA. Based on our findings, we suggest that the triterpenoid represents a new class of G-quadruplex groove binding ligands and thus act as potential anti-cancer agents.
Collapse
Affiliation(s)
| | - Somchai Yanarojana
- Department of Pharmacology, Faculty of Science, Mahidol University, 272 Rama 6 Road, Bangkok 10400, Thailand
| | - Darawan Pinthong
- Department of Pharmacology, Faculty of Science, Mahidol University, 272 Rama 6 Road, Bangkok 10400, Thailand
| | - Amnuay Thithapandha
- Department of Pharmacology, Faculty of Science, Mahidol University, 272 Rama 6 Road, Bangkok 10400, Thailand
| | - Jiraporn Ungwitayatorn
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Mahidol University, 447 Sri-Ayudhaya Road, Bangkok 10400, Thailand
| | - Porntip Supavilai
- Department of Pharmacology, Faculty of Science, Mahidol University, 272 Rama 6 Road, Bangkok 10400, Thailand
| |
Collapse
|
18
|
Charif R, Granotier-Beckers C, Bertrand HC, Poupon J, Ségal-Bendirdjian E, Teulade-Fichou MP, Boussin FD, Bombard S. Association of a Platinum Complex to a G-Quadruplex Ligand Enhances Telomere Disruption. Chem Res Toxicol 2017; 30:1629-1640. [DOI: 10.1021/acs.chemrestox.7b00131] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Razan Charif
- Université
Paris Descartes, INSERM UMR-S-1007, 45 rue des Saints-Pères, 75006 Paris, France
| | - Christine Granotier-Beckers
- CEA/DRF/IRCM,
Laboratoire de RadioPathologie, INSERM U967, Université Paris
VII, Université Paris XI, 18
route du Panorama, 92265 Fontenay-aux-Roses Cedex, France
| | - Hélène Charlotte Bertrand
- Institut
Curie,
Centre Universitaire Paris Saclay, CNRS UMR9187/INSERM U1196, Bâtiments 110-112, 91405 Orsay, France
- Département
de Chimie, Ecole Normale Supérieure, PSL Research University,
UPMC Univ Paris 06, CNRS, Laboratoire des Biomolécules (LBM), 24 rue Lhomond, 75005 Paris, France
- Sorbonne Universités,
UPMC Univ Paris 06, Ecole Normale Supérieure, CNRS, Laboratoire
des Biomolécules (LBM), 24 rue
Lhomond, 75005 Paris, France
| | - Joël Poupon
- Laboratoire
de Toxicologie-Biologique, Hôpital Lariboisière, 2 rue Ambroise Paré, 75475 Paris, France
| | | | - Marie-Paule Teulade-Fichou
- Institut
Curie,
Centre Universitaire Paris Saclay, CNRS UMR9187/INSERM U1196, Bâtiments 110-112, 91405 Orsay, France
| | - François D. Boussin
- CEA/DRF/IRCM,
Laboratoire de RadioPathologie, INSERM U967, Université Paris
VII, Université Paris XI, 18
route du Panorama, 92265 Fontenay-aux-Roses Cedex, France
| | - Sophie Bombard
- Université
Paris Descartes, INSERM UMR-S-1007, 45 rue des Saints-Pères, 75006 Paris, France
- Institut
Curie,
Centre Universitaire Paris Saclay, CNRS UMR9187/INSERM U1196, Bâtiments 110-112, 91405 Orsay, France
| |
Collapse
|
19
|
Beauvineau C, Guetta C, Teulade-Fichou MP, Mahuteau-Betzer F. PhenDV, a turn-off fluorescent quadruplex DNA probe for improving the sensitivity of drug screening assays. Org Biomol Chem 2017; 15:7117-7121. [DOI: 10.1039/c7ob01705g] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
PhenDV is a light-up probe for G4-fluorescent intercalator displacement. This potent G4-DNA binder discriminates between medium and high-affinity ligands.
Collapse
Affiliation(s)
| | - Corinne Guetta
- Institut Curie
- PSL Research University
- CNRS
- INSERM
- UMR9187/U1196
| | | | | |
Collapse
|
20
|
Xiong YX, Su HF, Lv P, Ma Y, Wang SK, Miao H, Liu HY, Tan JH, Ou TM, Gu LQ, Huang ZS. A newly identified berberine derivative induces cancer cell senescence by stabilizing endogenous G-quadruplexes and sparking a DNA damage response at the telomere region. Oncotarget 2016; 6:35625-35. [PMID: 26462146 PMCID: PMC4742130 DOI: 10.18632/oncotarget.5521] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 09/28/2015] [Indexed: 12/16/2022] Open
Abstract
The guanine-rich sequences are able to fold into G-quadruplexes in living cells, making these structures promising anti-cancer drug targets. In the current study, we identified a small molecule, Ber8, from a series of 9-substituted berberine derivatives and found that it could induce acute cell growth arrest and senescence in cancer cells, but not in normal fibroblasts. Further analysis revealed that the cell growth arrest was directly associated with apparent cell cycle arrest, cell senescence, and profound DNA damage at the telomere region. Significantly, our studies also provided evidence that Ber8 could stabilize endogenous telomeric G-quadruplexes structures in cells. Ber8 could then induce the delocalization of TRF1 and POT1 from the telomere accompanied by a rapid telomere uncapping. These results provide compelling insights into direct binding of telomeric G-quadruplexes and might contribute to the development of more selective, effective anticancer drugs.
Collapse
Affiliation(s)
- Yun-Xia Xiong
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P.R.China
| | - Hua-Fei Su
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P.R.China
| | - Peng Lv
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P.R.China
| | - Yan Ma
- Department of Medical Science, Shunde Polytechnic, Foshan 528333, P.R.China
| | - Shi-Ke Wang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P.R.China
| | - Hui Miao
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P.R.China
| | - Hui-Yun Liu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P.R.China
| | - Jia-Heng Tan
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P.R.China
| | - Tian-Miao Ou
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P.R.China
| | - Lian-Quan Gu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P.R.China
| | - Zhi-Shu Huang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P.R.China
| |
Collapse
|
21
|
Pinhatti VR, da Silva J, Martins TLC, Moura DJ, Rosa RM, Villela I, Stopiglia CDO, da Silva Santos S, Scroferneker ML, Machado CR, Saffi J, Henriques JAP. Cytotoxic, mutagenicity, and genotoxicity effects of guanylhydrazone derivatives. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2016; 806:1-10. [DOI: 10.1016/j.mrgentox.2016.06.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 05/19/2016] [Accepted: 06/06/2016] [Indexed: 11/16/2022]
|
22
|
Alkyne-substituted diminazene as G-quadruplex binders with anticancer activities. Eur J Med Chem 2016; 118:266-75. [DOI: 10.1016/j.ejmech.2016.04.030] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 04/11/2016] [Accepted: 04/11/2016] [Indexed: 01/18/2023]
|
23
|
Zheng XH, Mu G, Zhong YF, Zhang TP, Cao Q, Ji LN, Zhao Y, Mao ZW. Trigeminal star-like platinum complexes induce cancer cell senescence through quadruplex-mediated telomere dysfunction. Chem Commun (Camb) 2016; 52:14101-14104. [DOI: 10.1039/c6cc08254h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Trigeminal star-like platinum complexes induce cancer cell senescence through quadruplex-mediated telomeric DNA damage and telomere end-loss.
Collapse
Affiliation(s)
- Xiao-Hui Zheng
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry
- School of Chemistry
- Sun Yat-Sen University
- Guangzhou 510275
- China
| | - Ge Mu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry
- School of Chemistry
- Sun Yat-Sen University
- Guangzhou 510275
- China
| | - Yi-Fang Zhong
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry
- School of Chemistry
- Sun Yat-Sen University
- Guangzhou 510275
- China
| | - Tian-Peng Zhang
- School of Life Sciences
- SunYat-Sen University
- Guangzhou 510006
- China
| | - Qian Cao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry
- School of Chemistry
- Sun Yat-Sen University
- Guangzhou 510275
- China
| | - Liang-Nian Ji
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry
- School of Chemistry
- Sun Yat-Sen University
- Guangzhou 510275
- China
| | - Yong Zhao
- School of Life Sciences
- SunYat-Sen University
- Guangzhou 510006
- China
| | - Zong-Wan Mao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry
- School of Chemistry
- Sun Yat-Sen University
- Guangzhou 510275
- China
| |
Collapse
|
24
|
Highly efficient radiosensitization of human glioblastoma and lung cancer cells by a G-quadruplex DNA binding compound. Sci Rep 2015; 5:16255. [PMID: 26542881 PMCID: PMC4635363 DOI: 10.1038/srep16255] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 10/12/2015] [Indexed: 12/24/2022] Open
Abstract
Telomeres are nucleoprotein structures at the end of chromosomes which stabilize and protect them from nucleotidic degradation and end-to-end fusions. The G-rich telomeric single-stranded DNA overhang can adopt a four-stranded G-quadruplex DNA structure (G4). Stabilization of the G4 structure by binding of small molecule ligands enhances radiosensitivity of tumor cells, and this combined treatment represents a novel anticancer approach. We studied the effect of the platinum-derived G4-ligand, Pt-ctpy, in association with radiation on human glioblastoma (SF763 and SF767) and non-small cell lung cancer (A549 and H1299) cells in vitro and in vivo. Treatments with submicromolar concentrations of Pt-ctpy inhibited tumor proliferation in vitro with cell cycle alterations and induction of apoptosis. Non-toxic concentrations of the ligand were then combined with ionizing radiation. Pt-ctpy radiosensitized all cell lines with dose-enhancement factors between 1.32 and 1.77. The combined treatment led to increased DNA breaks. Furthermore, a significant radiosensitizing effect of Pt-ctpy in mice xenografted with glioblastoma SF763 cells was shown by delayed tumor growth and improved survival. Pt-ctpy can act in synergy with radiation for efficient killing of cancer cells at concentrations at which it has no obvious toxicity per se, opening perspectives for future therapeutic applications.
Collapse
|
25
|
Non-Flat Bisbenzylisoquinoline Alkaloid Fangchinoline As a Class of Potent G-Quadruplex Stabilizer with Anti-cancer Activity. CHINESE J CHEM 2015. [DOI: 10.1002/cjoc.201400841] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
26
|
Chen ZF, Qin QP, Qin JL, Liu YC, Huang KB, Li YL, Meng T, Zhang GH, Peng Y, Luo XJ, Liang H. Stabilization of G-quadruplex DNA, inhibition of telomerase activity, and tumor cell apoptosis by organoplatinum(II) complexes with oxoisoaporphine. J Med Chem 2015; 58:2159-79. [PMID: 25650792 DOI: 10.1021/jm5012484] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Two G-quadruplex ligands [Pt(L(a))(DMSO)Cl] (Pt1) and [Pt(L(b))(DMSO)Cl] (Pt2) have been synthesized and fully characterized. The two complexes are more selective for SK-OV-3/DDP tumor cells versus normal cells (HL-7702). It was found that both Pt1 and Pt2 could be a telomerase inhibitor targeting G-quadruplex DNA. This is the first report demonstrating that telomeric, c-myc, and bcl-2 G-quadruplexes and caspase-3/9 preferred to bind with Pt2 rather than Pt1, which also can induce senescence and apoptosis. The different biological behavior of Pt1 and Pt2 may correlate with the presence of a 6-hydroxyl group in L(b). Importantly, Pt1 and Pt2 exhibited higher safety in vivo and more effective inhibitory effects on tumor growth in the HCT-8 and NCI-H460 xenograft mouse model, compared with cisplatin. Taken together, these mechanistic insights indicate that both Pt1 and Pt2 display low toxicity and could be novel anticancer drug candidates.
Collapse
Affiliation(s)
- Zhen-Feng Chen
- State Key Laboratory Cultivation Base for the Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmacy, Guangxi Normal University , Yucai Road 15, Guilin 541004, P. R. China
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Targeting G-quadruplex nucleic acids with heterocyclic alkaloids and their derivatives. Eur J Med Chem 2014; 97:538-51. [PMID: 25466923 DOI: 10.1016/j.ejmech.2014.11.021] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Revised: 11/05/2014] [Accepted: 11/11/2014] [Indexed: 01/25/2023]
Abstract
G-Quadruplex nucleic acids or G-quadruplexes (G4s) are four-stranded DNA or RNA secondary structures that are formed in guanine-rich sequences. They are widely distributed in functional regions of the human genome, such as telomeres, ribosomal DNA (rDNA), transcription start sites, promoter regions and untranslated regions of mRNA, suggesting that G-quadruplex structures may play a pivotal role in the control of a variety of cellular processes. G-Quadruplexes are viewed as valid therapeutic targets in human cancer diseases. Small molecules, from naturally occurring to synthetic, are exploited to specifically target G-quadruplexes and have proven to be a new class of anticancer agents. Notably, alkaloids are an important source of G-quadruplex ligands and have significant bioactivities in anticancer therapy. In this review, the authors provide a brief, up-to-date summary of heterocyclic alkaloids and their derivatives targeting G-quadruplexes.
Collapse
|
28
|
Small-molecule quadruplex-targeted drug discovery. Bioorg Med Chem Lett 2014; 24:2602-12. [DOI: 10.1016/j.bmcl.2014.04.029] [Citation(s) in RCA: 149] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 04/06/2014] [Accepted: 04/08/2014] [Indexed: 01/24/2023]
|
29
|
|
30
|
Radwan AA, Alanazi FK. Targeting cancer using cholesterol conjugates. Saudi Pharm J 2014; 22:3-16. [PMID: 24493968 PMCID: PMC3909757 DOI: 10.1016/j.jsps.2013.01.003] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Accepted: 01/10/2013] [Indexed: 11/28/2022] Open
Abstract
Conjugation of cholesterol moiety to active compounds for either cancer treatment or diagnosis is an attractive approach. Cholesterol derivatives are widely studied as cancer diagnostic agents and as anticancer derivatives either in vitro or in vivo using animal models. In largely growing studies, anticancer agents have been chemically conjugated to cholesterol molecules, to enhance their pharmacokinetic behavior, cellular uptake, target specificity, and safety. To efficiently deliver anticancer agents to the target cells and tissues, many different cholesterol-anticancer conjugates were synthesized and characterized, and their anticancer efficiencies were tested in vitro and in vivo.
Collapse
Affiliation(s)
- Awwad A. Radwan
- Kayyali Chair for Pharmaceutical Industries, Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt
| | - Fares K. Alanazi
- Kayyali Chair for Pharmaceutical Industries, Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| |
Collapse
|
31
|
Chen X, Wu JH, Lai YW, Zhao R, Chao H, Ji LN. Targeting telomeric G-quadruplexes with the ruthenium(II) complexes [Ru(bpy)(2)(ptpn)](2+) and [Ru(phen)(2)(ptpn)](2+). Dalton Trans 2013; 42:4386-97. [PMID: 23400220 DOI: 10.1039/c3dt32921f] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two ruthenium(II) polypyridyl complexes, [Ru(bpy)(2)(ptpn)](2+) (1) (bpy = 2,2'-bipyridine, ptpn = 3-(1,10-phenanthroline-2-yl)-as-triazino[5,6-f]1,10-phenanthroline) and [Ru(phen)(2)(ptpn)](2+) (2) (phen = 1,10-phenanthroline), were synthesized and characterized. Crystal structure analysis shows that complex 1 has a large planar aromatic area and possesses the potential to fit the geometric structure of G-quadruplex. The interaction of the G-quadruplex DNA with Ru(ii) complexes was explored by means of circular dichroism (CD), fluorescence resonance energy transfer (FRET) melting assay, competitive FRET assay and polymerase chain reaction (PCR) stop assay. The results indicated that complexes 1 and 2 both have the ability to promote the formation and stabilization of the human telomeric d[(TTAGGG)(n)] (HTG22) quadruplex and exhibit high G-quadruplex DNA selectivity over duplex DNA. The telomere repeat amplification protocol (TRAP) assay and long-term proliferation experiments further demonstrate that the Ru(II) complexes are potent telomerase inhibitors and HeLa cell proliferation inhibitors.
Collapse
Affiliation(s)
- Xiang Chen
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, State Key Laboratory of Optoelectronic Materials and Technologies, School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, PR China
| | | | | | | | | | | |
Collapse
|
32
|
Shan C, Tan JH, Ou TM, Huang ZS. Natural products and their derivatives as G-quadruplex binding ligands. Sci China Chem 2013. [DOI: 10.1007/s11426-013-4920-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
33
|
Chung WJ, Heddi B, Tera M, Iida K, Nagasawa K, Phan AT. Solution Structure of an Intramolecular (3 + 1) Human Telomeric G-Quadruplex Bound to a Telomestatin Derivative. J Am Chem Soc 2013; 135:13495-501. [DOI: 10.1021/ja405843r] [Citation(s) in RCA: 137] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Wan Jun Chung
- School of Physical and Mathematical
Sciences, Nanyang Technological University, Singapore
| | - Brahim Heddi
- School of Physical and Mathematical
Sciences, Nanyang Technological University, Singapore
| | - Masayuki Tera
- Department
of Biotechnology and Life Science, Faculty of Technology, Tokyo University of Agriculture and Technology, Japan
- Bioorganic Research Institute, Suntory Foundation for Life Science, Japan
| | - Keisuke Iida
- Department
of Biotechnology and Life Science, Faculty of Technology, Tokyo University of Agriculture and Technology, Japan
| | - Kazuo Nagasawa
- Department
of Biotechnology and Life Science, Faculty of Technology, Tokyo University of Agriculture and Technology, Japan
| | - Anh Tuân Phan
- School of Physical and Mathematical
Sciences, Nanyang Technological University, Singapore
| |
Collapse
|
34
|
Larkin J, Carson S, Stoloff DH, Wanunu M. Nanopore-Based Analysis of Chemically Modified DNA and Nucleic Acid Drug Targets. Isr J Chem 2013. [DOI: 10.1002/ijch.201300006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
|
35
|
Li Q, Xiang JF, Yang QF, Sun HX, Guan AJ, Tang YL. G4LDB: a database for discovering and studying G-quadruplex ligands. Nucleic Acids Res 2012; 41:D1115-23. [PMID: 23161677 PMCID: PMC3531060 DOI: 10.1093/nar/gks1101] [Citation(s) in RCA: 111] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The G-quadruplex ligands database (G4LDB, http://www.g4ldb.org) provides a unique collection of reported G-quadruplex ligands to streamline ligand/drug discovery targeting G-quadruplexes. G-quadruplexes are guanine-rich nucleic acid sequences in human telomeres and gene promoter regions. There is a growing recognition for their profound roles in a wide spectrum of diseases, such as cancer, diabetes and cardiovascular disease. Ligands that affect the structure and activity of G-quadruplexes can shed light on the search for G-quadruplex-targeting drugs. Therefore, we built the G4LDB to (i) compile a data set covering various physical properties and 3D structure of G-quadruplex ligands; (ii) provide Web-based tools for G-quadruplex ligand design; and (iii) to facilitate the discovery of novel therapeutic and diagnostic agents targeting G-quadruplexes. G4LDB currently contains >800 G-quadruplex ligands with ∼4000 activity records, which, to our knowledge, is the most extensive collection of its kind. It offers a user friendly interface that can meet a variety of data inquiries from researchers. For example, ligands can be searched for by name, molecular properties, structures, ligand activities and so on. Building on the reported data, the database also provides an online ligand design module that can predict ligand binding affinity in real time.
Collapse
Affiliation(s)
- Qian Li
- Beijing National Laboratory for Molecular Sciences (BNLMS), Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, PR China
| | | | | | | | | | | |
Collapse
|
36
|
Altschuler SE, Croy JE, Wuttke DS. A small molecule inhibitor of Pot1 binding to telomeric DNA. Biochemistry 2012; 51:7833-45. [PMID: 22978652 DOI: 10.1021/bi300365k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Chromosome ends are complex structures, consisting of repetitive DNA sequence terminating in an ssDNA overhang with many associated proteins. Because alteration of the regulation of these ends is a hallmark of cancer, telomeres and telomere maintenance have been prime drug targets. The universally conserved ssDNA overhang is sequence-specifically bound and regulated by Pot1 (protection of telomeres 1), and perturbation of Pot1 function has deleterious effects for proliferating cells. The specificity of the Pot1/ssDNA interaction and the key involvement of this protein in telomere maintenance have suggested directed inhibition of Pot1/ssDNA binding as an efficient means of disrupting telomere function. To explore this idea, we developed a high-throughput time-resolved fluorescence resonance energy transfer (TR-FRET) screen for inhibitors of Pot1/ssDNA interaction. We conducted this screen with the DNA-binding subdomain of Schizosaccharomyces pombe Pot1 (Pot1pN), which confers the vast majority of Pot1 sequence-specificity and is highly similar to the first domain of human Pot1 (hPOT1). Screening a library of ∼20 000 compounds yielded a single inhibitor, which we found interacted tightly with sub-micromolar affinity. Furthermore, this compound, subsequently identified as the bis-azo dye Congo red (CR), was able to competitively inhibit hPOT1 binding to telomeric DNA. Isothermal titration calorimetry and NMR chemical shift analysis suggest that CR interacts specifically with the ssDNA-binding cleft of Pot1, and that alteration of this surface disrupts CR binding. The identification of a specific inhibitor of ssDNA interaction establishes a new pathway for targeted telomere disruption.
Collapse
Affiliation(s)
- Sarah E Altschuler
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215, USA
| | | | | |
Collapse
|
37
|
Sidibe A, Hamon F, Largy E, Gomez D, Teulade-Fichou MP, Trentesaux C, Riou JF. Effects of a halogenated G-quadruplex ligand from the pyridine dicarboxamide series on the terminal sequence of XpYp telomere in HT1080 cells. Biochimie 2012; 94:2559-68. [PMID: 22796264 DOI: 10.1016/j.biochi.2012.07.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Accepted: 07/05/2012] [Indexed: 10/28/2022]
Abstract
Non-canonical four-stranded structures called G-quadruplexes can form among telomere repeats during its replication. Small molecule ligands able to interact and to stabilize G-quadruplexes were shown to disrupt the binding of essential telomeric components, such as POT1 and to trigger a telomeric dysfunction associated with a delayed growth arrest in tumor cells. We describe here the chemical synthesis and the G-quadruplex binding properties of three halogenated analogs of the 360A ligand that belongs to the 2,6 pyridine dicarboxamide series. 360A is now commonly used as a benchmark both for biophysical and cellular assays as this compound was shown to display a potent affinity and selectivity for telomeric G-quadruplex DNA over duplex DNA and to induce delayed growth inhibition in HT1080 tumor cell line. Two biophysical assays indicate that, in most cases, the presence of the halogen atom seems to slightly improve the interaction with the telomeric quadruplex. For stability reasons, the bromo derivative (360A-Br) was selected for the cellular assays. Since POT1 participates to the fine tuning of the C-strand end resection during telomere replication, we investigated the effect of 360A-Br to alter the terminal nucleotide composition of XpYp telomere in HT1080 cells using C-STELA. HT1080 cells treated for up to 24 days with 360A-Br presented some minor but significant variations of C-strand terminal nucleotide composition, also observed with a partial siRNA depletion of POT1. The relevance of these minor modifications of the telomeric C-strand resection induced by 360A-Br in HT1080 cells are discussed.
Collapse
|
38
|
Sun D, Liu Y, Liu D, Zhang R, Yang X, Liu J. Stabilization of G-Quadruplex DNA, Inhibition of Telomerase Activity and Live Cell Imaging Studies of Chiral Ruthenium(II) Complexes. Chemistry 2012; 18:4285-95. [DOI: 10.1002/chem.201103156] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Indexed: 11/11/2022]
|
39
|
A fragment based click chemistry approach towards hybrid G-quadruplex ligands: design, synthesis and biophysical evaluation. Tetrahedron 2012. [DOI: 10.1016/j.tet.2011.10.066] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
|
40
|
He X, Zhang Z, Zhang Q, Yuan G. Selective recognition of G-quadruplex in the vascular endothelial growth factor gene with small-molecule natural products by electrospray ionization (ESI) mass spectrometry and circular dichroism (CD) spectrometry. CAN J CHEM 2012. [DOI: 10.1139/v11-104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In this study, electrospray ionization mass spectrometry (ESI-MS) and circular dichroism (CD) spectroscopy were used to investigate selective recognition of G-quadruplex in the vascular endothelial growth factor (VEGF) gene with 12 small-molecule natural products. We found that kaempferol, a natural flavonol, shows the highest binding affinity among the 12 natural molecules. The results from ESI-MS and CD spectra indicated that kaempferol could enhance the thermal stability of the VEGF–G-quadruplex and showed selective recognition for the G-quadruplex in a solution consisting of the G-quadruplex and the corresponding duplex DNA.
Collapse
Affiliation(s)
- Xiangwei He
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education, Department of Chemical Biology, College of Chemistry, Peking University, Beijing 100871, P. R. China
| | - Zhenjiang Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education, Department of Chemical Biology, College of Chemistry, Peking University, Beijing 100871, P. R. China
| | - Qiang Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education, Department of Chemical Biology, College of Chemistry, Peking University, Beijing 100871, P. R. China
| | - Gu Yuan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education, Department of Chemical Biology, College of Chemistry, Peking University, Beijing 100871, P. R. China
| |
Collapse
|
41
|
D'Ambrosio D, Reichenbach P, Micheli E, Alvino A, Franceschin M, Savino M, Lingner J. Specific binding of telomeric G-quadruplexes by hydrosoluble perylene derivatives inhibits repeat addition processivity of human telomerase. Biochimie 2011; 94:854-63. [PMID: 22182489 DOI: 10.1016/j.biochi.2011.12.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Accepted: 12/05/2011] [Indexed: 12/15/2022]
Abstract
Telomerase is responsible for the immortal phenotype of cancer cells and telomerase inhibition may specifically target cancer cell proliferation. Ligands able to selectively bind to G-quadruplex telomeric DNA have been considered as telomerase inhibitors but their mechanisms of action have often been deduced from a non-quantitative telomerase activity assay (TRAP assay) that involves a PCR step and that does not provide insight on the mechanism of inhibition. Furthermore, quadruplex ligands have also been shown to exert their effects by affecting association of telomere binding proteins with telomeres. Here, we use quantitative direct telomerase activity assays to evaluate the strength and mechanism of action of hydrosoluble perylene diimides (HPDIs). HPDIs contain a perylene moiety and different numbers of positively charged side chains. Side chain features vary with regard to number and distances of the charges. IC(50) values of HPDIs were in the low micromolar (0.5-5 μM) range depending on the number and features of the side chains. HPDIs having four side chains emerged as the best compounds of this series. Analysis of primer elongation products demonstrated that at low HPDI concentrations, telomerase inhibition involved formation of telomeric G-quadruplex structures, which inhibited further elongation by telomerase. At high HPDI concentrations, telomerase inhibition occurred independently of G-quadruplex formation of the substrate. The mechanism of action of HPDIs and their specific binding to G-quadruplex DNA was supported by PAGE analysis, CD spectroscopy and ESI-MS. Finally, competition Telospot experiments with duplex DNA indicated specific binding of HPDIs to the single-stranded telomeric substrates over double stranded DNA, a result supported by competitive ESI-MS. Altogether, our results indicate that HPDIs act by stabilizing G-quadruplex structures in single-stranded telomeric DNA, which in turn prevents repeat addition processivity of telomerase.
Collapse
Affiliation(s)
- Danilo D'Ambrosio
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Frontiers in Genetics National Center of Competence in Research, Ecole Polytechnique Fédérale de Lausanne, Station 19, 1015 Lausanne, Switzerland
| | | | | | | | | | | | | |
Collapse
|
42
|
Li J, Jin X, Hu L, Wang J, Su Z. Identification of nonplanar small molecule for G-quadruplex grooves: Molecular docking and molecular dynamic study. Bioorg Med Chem Lett 2011; 21:6969-72. [DOI: 10.1016/j.bmcl.2011.09.125] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2011] [Revised: 09/14/2011] [Accepted: 09/29/2011] [Indexed: 12/26/2022]
|
43
|
Guan AJ, Zhang EX, Xiang JF, Li Q, Yang QF, Li L, Tang YL, Wang MX. Effects of loops and nucleotides in G-quadruplexes on their interaction with an azacalixarene, methylazacalix[6]pyridine. J Phys Chem B 2011; 115:12584-90. [PMID: 21923138 DOI: 10.1021/jp204154m] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A novel trend in G-quadruplex ligand design is to build a binder that is able to not only discriminate G-quadruplex from duplex-DNA, but also among various G-quadruplex structures. Methylazacalix[6]pyridine (MACP6), a new type of azacalixarene with flexible conformation, exhibits induced circular dichroism signals when interacted with most of G-quadruplexes. The intensities of the induced signals are strongly dependent on the topology of G-quadruplexes. Further evidence has shown that these signals can be ascribed to the preferred binding of MACP6 to the loops of G-quadruplexes, which rely on the nature of nucleotides in the loops.
Collapse
Affiliation(s)
- Ai-Jiao Guan
- Beijing National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Chinese Academy of Sciences, Beijing, P R China
| | | | | | | | | | | | | | | |
Collapse
|
44
|
Lin S, Li S, Chen Z, He X, Zhang Y, Xu X, Xu M, Yuan G. Formation, recognition and bioactivities of a novel G-quadruplex in the STAT3 gene. Bioorg Med Chem Lett 2011; 21:5987-91. [DOI: 10.1016/j.bmcl.2011.07.121] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Revised: 06/14/2011] [Accepted: 07/14/2011] [Indexed: 01/04/2023]
|
45
|
Quantitative Structure Inter-Activity Relationship (QSInAR). Cytotoxicity Study of Some Hemisynthetic and Isolated Natural Steroids and Precursors on Human Fibrosarcoma Cells HT1080. Molecules 2011; 16:6603-20. [PMID: 25134765 PMCID: PMC6264182 DOI: 10.3390/molecules16086603] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Revised: 07/28/2011] [Accepted: 07/29/2011] [Indexed: 01/08/2023] Open
Abstract
Combined experimental and quantitative structure inter-activity relationship (QSIAR) computation methods were advanced in order to establish the structural and mechanistic influences that steroids and triterpenes, either as newly synthesized or naturally isolated products, have on human HT1080 mammalian cancer cells. The main Hansch structural indicators such as hydrophobicity (LogP), polarizability (POL) and total energy (Etot) were considered and both the structure-projected as well as globally computed correlations were reported; while the inter-activity correlation of the global activity with those projected on structural information was revealed as equal to the direct structural-activity one for the trial sets of compounds, the prediction for the testing set of molecules reported even superior performances respecting those characteristic for the calibration set, validating therefore the present QSInAR models; accordingly, it follows that the LogP carries the most part of the cytotoxic signal, while POL has little influence on inhibiting tumor growth—A complementary behavior with their earlier known influence on genotoxic carcinogenesis. Regarding the newly hemisynthetic compounds it was found that stigmasta-4,22-dien-3-one is not adapted for cell membrane diffusion; it is recommended that aminocinnamyl chlorohydrate be further modified in order to acquire better steric influence, while aminocinnamyl-2,3,4,6-O-tétraacétyl-α-D-glucopyranoside was identified as being inhibited in the tumor cell by other molecular mechanisms–here not revealed–although it has a moderate-high anti-cancer structurally predicted activity.
Collapse
|
46
|
Eddy J, Vallur AC, Varma S, Liu H, Reinhold WC, Pommier Y, Maizels N. G4 motifs correlate with promoter-proximal transcriptional pausing in human genes. Nucleic Acids Res 2011; 39:4975-83. [PMID: 21371997 PMCID: PMC3130262 DOI: 10.1093/nar/gkr079] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The RNA Pol II transcription complex pauses just downstream of the promoter in a significant fraction of human genes. The local features of genomic structure that contribute to pausing have not been defined. Here, we show that genes that pause are more G-rich within the region flanking the transcription start site (TSS) than RefSeq genes or non-paused genes. We show that enrichment of binding motifs for common transcription factors, such as SP1, may account for G-richness upstream but not downstream of the TSS. We further show that pausing correlates with the presence of a GrIn1 element, an element bearing one or more G4 motifs at the 5′-end of the first intron, on the non-template DNA strand. These results suggest potential roles for dynamic G4 DNA and G4 RNA structures in cis-regulation of pausing, and thus genome-wide regulation of gene expression, in human cells.
Collapse
Affiliation(s)
- Johanna Eddy
- Molecular and Cellular Biology Graduate Program, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | | | | | | | | | | | | |
Collapse
|
47
|
Campbell NH, Smith DL, Reszka AP, Neidle S, O'Hagan D. Fluorine in medicinal chemistry: β-fluorination of peripheral pyrrolidines attached to acridine ligands affects their interactions with G-quadruplex DNA. Org Biomol Chem 2011; 9:1328-31. [PMID: 21221451 DOI: 10.1039/c0ob00886a] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Comparative X-ray structure studies reveal that C-F bond incorporation into the peripheral pyrrolidine moieties of the G-quadruplex DNA binding ligand BSU6039 leads to a distinct pyrrolidine ring conformation, relative to the non-fluorinated analogue, and with a different binding mode involving reversal of the pyrrolidinium N(+)-H orientation.
Collapse
Affiliation(s)
- Nancy H Campbell
- The School of Pharmacy, University of London, 29-39 Brunswick Square, London, UK WC1N 1AX
| | | | | | | | | |
Collapse
|
48
|
Tetrasubstituted naphthalene diimide ligands with selectivity for telomeric G-quadruplexes and cancer cells. Bioorg Med Chem Lett 2010; 20:6459-63. [DOI: 10.1016/j.bmcl.2010.09.066] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2010] [Revised: 09/10/2010] [Accepted: 09/13/2010] [Indexed: 01/22/2023]
|
49
|
Ranjan N, Andreasen KF, Kumar S, Hyde-Volpe D, Arya DP. Aminoglycoside binding to Oxytricha nova telomeric DNA. Biochemistry 2010; 49:9891-903. [PMID: 20886815 DOI: 10.1021/bi101517e] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Telomeric DNA sequences have been at the center stage of drug design for cancer treatment in recent years. The ability of these DNA structures to form four-stranded nucleic acid structures, called G-quadruplexes, has been perceived as target for inhibiting telomerase activity vital for the longevity of cancer cells. Being highly diverse in structural forms, these G-quadruplexes are subjects of detailed studies of ligand-DNA interactions of different classes, which will pave the way for logical design of more potent ligands in future. The binding of aminoglycosides was investigated with Oxytricha nova quadruplex forming DNA sequence (GGGGTTTTGGGG)(2). Isothermal titration calorimetry (ITC) determined ligand to quadruplex binding ratio shows 1:1 neomycin:quadruplex binding with association constants (K(a)) ∼ 10(5) M(-1) while paromomycin was found to have a 2-fold weaker affinity than neomycin. The CD titration experiments with neomycin resulted in minimal changes in the CD signal. FID assays, performed to determine the minimum concentration required to displace half of the fluorescent probe bound, showed neomycin as the best of the all aminoglycosides studied for quadruplex binding. Initial NMR footprint suggests that ligand-DNA interactions occur in the wide groove of the quadruplex. Computational docking studies also indicate that aminoglycosides bind in the wide groove of the quadruplex.
Collapse
Affiliation(s)
- Nihar Ranjan
- Laboratories of Medicinal Chemistry, Clemson University, Clemson, South Carolina 29634, United States
| | | | | | | | | |
Collapse
|
50
|
Shinohara KI, Sannohe Y, Kaieda S, Tanaka KI, Osuga H, Tahara H, Xu Y, Kawase T, Bando T, Sugiyama H. A Chiral Wedge Molecule Inhibits Telomerase Activity. J Am Chem Soc 2010; 132:3778-82. [DOI: 10.1021/ja908897j] [Citation(s) in RCA: 164] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ken-ichi Shinohara
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku Kyoto 606-8502, Japan, Department of Materials Science and Chemistry, Faculty of Systems Engineering, Wakayama University, 930 Sakaedani Wakayama 640-8510, Japan, Department of Cellular and Molecular Biology, Hiroshima University, Hiroshima 734-8553, Japan, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba Meguro-ku Tokyo 153-8904, Japan, and Institute for Integrated Cell-Material
| | - Yuta Sannohe
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku Kyoto 606-8502, Japan, Department of Materials Science and Chemistry, Faculty of Systems Engineering, Wakayama University, 930 Sakaedani Wakayama 640-8510, Japan, Department of Cellular and Molecular Biology, Hiroshima University, Hiroshima 734-8553, Japan, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba Meguro-ku Tokyo 153-8904, Japan, and Institute for Integrated Cell-Material
| | - Shuji Kaieda
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku Kyoto 606-8502, Japan, Department of Materials Science and Chemistry, Faculty of Systems Engineering, Wakayama University, 930 Sakaedani Wakayama 640-8510, Japan, Department of Cellular and Molecular Biology, Hiroshima University, Hiroshima 734-8553, Japan, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba Meguro-ku Tokyo 153-8904, Japan, and Institute for Integrated Cell-Material
| | - Ken-ichi Tanaka
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku Kyoto 606-8502, Japan, Department of Materials Science and Chemistry, Faculty of Systems Engineering, Wakayama University, 930 Sakaedani Wakayama 640-8510, Japan, Department of Cellular and Molecular Biology, Hiroshima University, Hiroshima 734-8553, Japan, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba Meguro-ku Tokyo 153-8904, Japan, and Institute for Integrated Cell-Material
| | - Hideji Osuga
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku Kyoto 606-8502, Japan, Department of Materials Science and Chemistry, Faculty of Systems Engineering, Wakayama University, 930 Sakaedani Wakayama 640-8510, Japan, Department of Cellular and Molecular Biology, Hiroshima University, Hiroshima 734-8553, Japan, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba Meguro-ku Tokyo 153-8904, Japan, and Institute for Integrated Cell-Material
| | - Hidetoshi Tahara
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku Kyoto 606-8502, Japan, Department of Materials Science and Chemistry, Faculty of Systems Engineering, Wakayama University, 930 Sakaedani Wakayama 640-8510, Japan, Department of Cellular and Molecular Biology, Hiroshima University, Hiroshima 734-8553, Japan, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba Meguro-ku Tokyo 153-8904, Japan, and Institute for Integrated Cell-Material
| | - Yan Xu
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku Kyoto 606-8502, Japan, Department of Materials Science and Chemistry, Faculty of Systems Engineering, Wakayama University, 930 Sakaedani Wakayama 640-8510, Japan, Department of Cellular and Molecular Biology, Hiroshima University, Hiroshima 734-8553, Japan, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba Meguro-ku Tokyo 153-8904, Japan, and Institute for Integrated Cell-Material
| | - Takashi Kawase
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku Kyoto 606-8502, Japan, Department of Materials Science and Chemistry, Faculty of Systems Engineering, Wakayama University, 930 Sakaedani Wakayama 640-8510, Japan, Department of Cellular and Molecular Biology, Hiroshima University, Hiroshima 734-8553, Japan, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba Meguro-ku Tokyo 153-8904, Japan, and Institute for Integrated Cell-Material
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku Kyoto 606-8502, Japan, Department of Materials Science and Chemistry, Faculty of Systems Engineering, Wakayama University, 930 Sakaedani Wakayama 640-8510, Japan, Department of Cellular and Molecular Biology, Hiroshima University, Hiroshima 734-8553, Japan, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba Meguro-ku Tokyo 153-8904, Japan, and Institute for Integrated Cell-Material
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku Kyoto 606-8502, Japan, Department of Materials Science and Chemistry, Faculty of Systems Engineering, Wakayama University, 930 Sakaedani Wakayama 640-8510, Japan, Department of Cellular and Molecular Biology, Hiroshima University, Hiroshima 734-8553, Japan, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba Meguro-ku Tokyo 153-8904, Japan, and Institute for Integrated Cell-Material
| |
Collapse
|