1
|
Pal S, Fatma K, Ravichandiran V, Dash J. Triazolyl Dibenzo[ a,c]phenazines Stabilize Telomeric G-quadruplex and Inhibit Telomerase. ASIAN J ORG CHEM 2021; 10:2921-2926. [PMID: 37823002 PMCID: PMC7614908 DOI: 10.1002/ajoc.202100468] [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: 07/27/2021] [Indexed: 11/10/2022]
Abstract
We herein report the synthesis and biophysical evaluation of triazolyl dibenzo[a,c]phenazine derivatives as a novel class of G-quadruplex ligands. The aromatic core facilitates π-π interaction and the flexible, protonatable side chains interact with the phosphate backbone of DNA via electrostatic interactions. Förster resonance energy transfer (FRET) melting assay and isothermal titration calorimetry (ITC) studies suggest that these ligands show binding preference for the hTELO G-quadruplex over G-quadruplexes found in the promoter region of various oncogenes and duplex DNA. The in vitro telomeric repeat amplification protocol (Q-TRAP) assay reveals that these ligands reduce telomerase activity in cancer cells.
Collapse
Affiliation(s)
- Sarmistha Pal
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India
- Department of Medicinal Chemistry, NIPER-KOLKATA, Chunilal Bhawan (Adjacent to BCPL), 168, Maniktala Main Road P.O. Bengal Chemicals, P.S. Phoolbagan, Kolkata – 700054, West Bengal
| | - Khushnood Fatma
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India
| | - Velayutham Ravichandiran
- Department of Medicinal Chemistry, NIPER-KOLKATA, Chunilal Bhawan (Adjacent to BCPL), 168, Maniktala Main Road P.O. Bengal Chemicals, P.S. Phoolbagan, Kolkata – 700054, West Bengal
| | - Jyotirmayee Dash
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India
| |
Collapse
|
2
|
Chaudhuri R, Fatma K, Dash J. Regulation of gene expression by targeting DNA secondary structures. J CHEM SCI 2021. [DOI: 10.1007/s12039-021-01898-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
3
|
Yang NN, Zhou LJ, Li P, Sui Q, Gao EQ. Space-confined indicator displacement assay inside a metal-organic framework for fluorescence turn-on sensing. Chem Sci 2019; 10:3307-3314. [PMID: 30996917 PMCID: PMC6428140 DOI: 10.1039/c9sc00032a] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 01/29/2019] [Indexed: 12/15/2022] Open
Abstract
The indicator displacement assay (IDA) is for the first time performed within a metal-organic framework (MOF) to achieve ultrasensitive fluorescence turn-on sensing. A Zr(iv) ion MOF (UiO-67-DQ-PsO) furnished with electron-deficient diquat units (DQ2+, as the receptor) on the wall and electron-rich 1-pyrenesulfonate anions (PsO-, as the fluorescent indicator) in the pores was prepared by postsynthetic anion exchange. The MOF is capable of sensing alkylamines owing to the competing PsO--DQ2+ and alkylamine-DQ2+ charge-transfer interactions, the former interaction causing a fluorescence OFF state and the latter displacing PsO- to trigger its emission. Significant advantages have been demonstrated for the IDA inside the MOF. The turn-on assay exhibits much higher sensitivity and anti-interference than the turn-off sensing using the MOF without indicators (the sensitivity is enhanced by as much as six orders of magnitude to the subnanomolar level). The integration of both the receptor and indicator in the porous solid enables facile regeneration and recyclability of the IDA ensemble. Furthermore, we show that the confined space provided by the MOF significantly enhances the supramolecular interactions to make possible the IDA impossible in solution. This work not only demonstrates a novel conceptual approach to fabricate superior fluorescence turn-on sensors using porous materials but also has important implications for supramolecular chemistry in porous materials.
Collapse
Affiliation(s)
- Ning-Ning Yang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes , School of Chemistry and Molecular Engineering , East China Normal University , Shanghai 200062 , P. R. China .
| | - Li-Jiao Zhou
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes , School of Chemistry and Molecular Engineering , East China Normal University , Shanghai 200062 , P. R. China .
| | - Peng Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes , School of Chemistry and Molecular Engineering , East China Normal University , Shanghai 200062 , P. R. China .
| | - Qi Sui
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes , School of Chemistry and Molecular Engineering , East China Normal University , Shanghai 200062 , P. R. China .
| | - En-Qing Gao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes , School of Chemistry and Molecular Engineering , East China Normal University , Shanghai 200062 , P. R. China .
| |
Collapse
|
4
|
Abstract
DNA has played an early and powerful role in the development of bottom-up nanotechnologies, not least because of DNA's precise, predictable, and controllable properties of assembly on the nanometer scale. Watson-Crick complementarity has been used to build complex 2D and 3D architectures and design a number of nanometer-scale systems for molecular computing, transport, motors, and biosensing applications. Most of such devices are built with classical B-DNA helices and involve classical A-T/U and G-C base pairs. However, in addition to the above components underlying the iconic double helix, a number of alternative pairing schemes of nucleobases are known. This review focuses on two of these noncanonical classes of DNA helices: G-quadruplexes and the i-motif. The unique properties of these two classes of DNA helix have been utilized toward some remarkable constructions and applications: G-wires; nanostructures such as DNA origami; reconfigurable structures and nanodevices; the formation and utilization of hemin-utilizing DNAzymes, capable of generating varied outputs from biosensing nanostructures; composite nanostructures made up of DNA as well as inorganic materials; and the construction of nanocarriers that show promise for the therapeutics of diseases.
Collapse
Affiliation(s)
- Jean-Louis Mergny
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering , Nanjing University , Nanjing 210023 , China.,ARNA Laboratory , Université de Bordeaux, Inserm U 1212, CNRS UMR5320, IECB , Pessac 33600 , France.,Institute of Biophysics of the CAS , v.v.i., Královopolská 135 , 612 65 Brno , Czech Republic
| | - Dipankar Sen
- Department of Molecular Biology & Biochemistry , Simon Fraser University , Burnaby , British Columbia V5A 1S6 , Canada.,Department of Chemistry , Simon Fraser University , Burnaby , British Columbia V5A 1S6 , Canada
| |
Collapse
|
5
|
Zhang R, Chen A, Yu Y, Chai Y, Zhuo Y, Yuan R. Electrochemiluminescent carbon dot-based determination of microRNA-21 by using a hemin/G-wire supramolecular nanostructure as co-reaction accelerator. Mikrochim Acta 2018; 185:432. [DOI: 10.1007/s00604-018-2959-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 08/10/2018] [Indexed: 01/10/2023]
|
6
|
Maiti S, Saha P, Das T, Bessi I, Schwalbe H, Dash J. Human Telomeric G-Quadruplex Selective Fluoro-Isoquinolines Induce Apoptosis in Cancer Cells. Bioconjug Chem 2018; 29:1141-1154. [DOI: 10.1021/acs.bioconjchem.7b00781] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Subhadip Maiti
- Department of Organic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Puja Saha
- Department of Organic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Tania Das
- Department of Organic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Irene Bessi
- Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University, Frankfurt, Max-von-Laue Strasse 7, 60438 Frankfurt am Main, Germany
| | - Harald Schwalbe
- Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University, Frankfurt, Max-von-Laue Strasse 7, 60438 Frankfurt am Main, Germany
| | - Jyotirmayee Dash
- Department of Organic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| |
Collapse
|
7
|
Panda D, Saha P, Das T, Dash J. Target guided synthesis using DNA nano-templates for selectively assembling a G-quadruplex binding c-MYC inhibitor. Nat Commun 2017; 8:16103. [PMID: 28706243 PMCID: PMC5519986 DOI: 10.1038/ncomms16103] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Accepted: 05/30/2017] [Indexed: 02/06/2023] Open
Abstract
The development of small molecules is essential to modulate the cellular functions of biological targets in living system. Target Guided Synthesis (TGS) approaches have been used for the identification of potent small molecules for biological targets. We herein demonstrate an innovative example of TGS using DNA nano-templates that promote Huisgen cycloaddition from an array of azide and alkyne fragments. A G-quadruplex and a control duplex DNA nano-template have been prepared by assembling the DNA structures on gold-coated magnetic nanoparticles. The DNA nano-templates facilitate the regioselective formation of 1,4-substituted triazole products, which are easily isolated by magnetic decantation. The G-quadruplex nano-template can be easily recovered and reused for five reaction cycles. The major triazole product, generated by the G-quadruplex inhibits c-MYC expression by directly targeting the c-MYC promoter G-quadruplex. This work highlights that the nano-TGS approach may serve as a valuable strategy to generate target-selective ligands for drug discovery. Identification of inhibitors can be accelerated by using the target as a template for ligand formation. Here the authors show that DNA-functionalised magnetic nanoparticles guide templating of G-quadruplex binding c-MYC inhibitors from an array of building blocks, and can be isolated by magnetic decanting.
Collapse
Affiliation(s)
- Deepanjan Panda
- Department of Organic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India
| | - Puja Saha
- Department of Organic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India
| | - Tania Das
- Department of Organic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India
| | - Jyotirmayee Dash
- Department of Organic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India
| |
Collapse
|
8
|
Pavan Kumar Y, Saha P, Saha D, Bessi I, Schwalbe H, Chowdhury S, Dash J. Fluorescent Dansyl-Guanosine Conjugates that Bindc-MYCPromoter G-Quadruplex and Downregulatec-MYCExpression. Chembiochem 2016; 17:388-93. [DOI: 10.1002/cbic.201500631] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Indexed: 01/15/2023]
Affiliation(s)
- Y. Pavan Kumar
- Department of Organic Chemistry; Indian Association for the Cultivation of Science; Jadavpur University; 2A ∞ B Raja S. C. Mullick Road Jadavpur Kolkata 700032 India
| | - Puja Saha
- Department of Organic Chemistry; Indian Association for the Cultivation of Science; Jadavpur University; 2A ∞ B Raja S. C. Mullick Road Jadavpur Kolkata 700032 India
| | - Dhurjhoti Saha
- CSIR-Institute of Genomics and Integrative Biology; Mathura Road Delhi 110 025 India
| | - Irene Bessi
- Institute of Organic Chemistry and Chemical Biology; Goethe University Frankfurt; and Center for Biomolecular Magnetic Resonance; Max-von-Laue Strasse 7 60438 Frankfurt am Main Germany
| | - Harald Schwalbe
- Institute of Organic Chemistry and Chemical Biology; Goethe University Frankfurt; and Center for Biomolecular Magnetic Resonance; Max-von-Laue Strasse 7 60438 Frankfurt am Main Germany
| | - Shantanu Chowdhury
- CSIR-Institute of Genomics and Integrative Biology; Mathura Road Delhi 110 025 India
| | - Jyotirmayee Dash
- Department of Organic Chemistry; Indian Association for the Cultivation of Science; Jadavpur University; 2A ∞ B Raja S. C. Mullick Road Jadavpur Kolkata 700032 India
| |
Collapse
|
9
|
Chauhan A, Paladhi S, Debnath M, Dash J. Selective recognition of c-MYC G-quadruplex DNA using prolinamide derivatives. Org Biomol Chem 2016; 14:5761-7. [DOI: 10.1039/c6ob00177g] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein we report the design, synthesis, biophysical and biological evaluation of triazole containing prolinamide derivatives as selectivec-MYCG-quadruplex binding ligands.
Collapse
Affiliation(s)
- Ajay Chauhan
- Department of Chemical Sciences
- Indian Institute of Science Education and Research Kolkata
- Mohanpur
- India
| | - Sushovan Paladhi
- Department of Chemical Sciences
- Indian Institute of Science Education and Research Kolkata
- Mohanpur
- India
- Department of Organic Chemistry
| | - Manish Debnath
- Department of Organic Chemistry
- Indian Association for the Cultivation of Science
- Kolkata-700032
- India
| | - Jyotirmayee Dash
- Department of Chemical Sciences
- Indian Institute of Science Education and Research Kolkata
- Mohanpur
- India
- Department of Organic Chemistry
| |
Collapse
|
10
|
Panda D, Debnath M, Mandal S, Bessi I, Schwalbe H, Dash J. A Nucleus-Imaging Probe That Selectively Stabilizes a Minor Conformation of c-MYC G-quadruplex and Down-regulates c-MYC Transcription in Human Cancer Cells. Sci Rep 2015; 5:13183. [PMID: 26286633 PMCID: PMC4541407 DOI: 10.1038/srep13183] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 07/17/2015] [Indexed: 12/27/2022] Open
Abstract
The c-MYC proto-oncogene is a regulator of fundamental cellular processes such as cell cycle progression and apoptosis. The development of novel c-MYC inhibitors that can act by targeting the c-MYC DNA G-quadruplex at the level of transcription would provide potential insight into structure-based design of small molecules and lead to a promising arena for cancer therapy. Herein we report our finding that two simple bis-triazolylcarbazole derivatives can inhibit c-MYC transcription, possibly by stabilizing the c-MYC G-quadruplex. These compounds are prepared using a facile and modular approach based on Cu(I) catalysed azide and alkyne cycloaddition. A carbazole ligand with carboxamide side chains is found to be microenvironment-sensitive and highly selective for "turn-on" detection of c-MYC quadruplex over duplex DNA. This fluorescent probe is applicable to visualize the cellular nucleus in living cells. Interestingly, the ligand binds to c-MYC in an asymmetric fashion and selects the minor-populated conformer via conformational selection.
Collapse
Affiliation(s)
- Deepanjan Panda
- Department of Organic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India
| | - Manish Debnath
- Department of Organic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India
| | - Samir Mandal
- Department of Organic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India
| | - Irene Bessi
- Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt and Centre for Biomolecular, Magnetic Resonance, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Harald Schwalbe
- Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt and Centre for Biomolecular, Magnetic Resonance, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Jyotirmayee Dash
- Department of Organic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India
| |
Collapse
|