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Roy S, Maiti B, Banerjee N, Kaulage MH, Muniyappa K, Chatterjee S, Bhattacharya S. New Xanthone Derivatives as Potent G-Quadruplex Binders for Developing Anti-Cancer Therapeutics. ACS Pharmacol Transl Sci 2023; 6:546-566. [PMID: 37082748 PMCID: PMC10111628 DOI: 10.1021/acsptsci.2c00205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Indexed: 04/22/2023]
Abstract
Xanthone is an important scaffold for various medicinally relevant compounds. However, it has received scant attention in the design of agents that are cytotoxic to cancer cells via targeting the stabilization of G-quadruplex (G4) nucleic acids. Specific G4 DNA recognition against double-stranded (ds) DNA is receiving epoch-making interest for the development of G4-mediated anticancer agents. Toward this goal, we have synthesized xanthone-based derivatives with various functionalized side-arm substituents that exhibited significant selectivity for G4 DNA as compared to dsDNA. The specific interaction has been demonstrated by performing various biophysical experiments. Based on the computational study as well as the competitive ligand binding assay, it is inferred that the potent compounds exhibit an end-stacking mode of binding with G4 DNA. Additionally, compound-induced conformational changes in the flanking nucleotides form the binding pocket for effective interaction. Selective action of the compounds on cancer cells suggests their effectiveness as potent anti-cancer agents. This study promotes the importance of structure-based screening approaches to get molecular insights for new scaffolds toward desired specific recognition of non-canonical G4 DNA structures.
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Affiliation(s)
- Soma Roy
- Department
of Organic Chemistry, Indian Institute of
Science, Bangalore 560012, India
- School
of Applied & Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Bappa Maiti
- School
of Applied & Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Nilanjan Banerjee
- Department
of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata 700054, India
| | - Mangesh H. Kaulage
- Department
of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Kalappa Muniyappa
- Department
of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Subhrangsu Chatterjee
- Department
of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata 700054, India
| | - Santanu Bhattacharya
- Department
of Organic Chemistry, Indian Institute of
Science, Bangalore 560012, India
- School
of Applied & Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
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2
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Roy S, Chakraborty N, Maiti B, Muniyappa K, Bhattacharya S. Design and Synthesis of Xanthone Analogues Conjugated with Aza-aromatic Substituents as Promising G-Quadruplex Stabilizing Ligands and their Selective Cancer Cell Cytotoxic Action. Chembiochem 2023; 24:e202200609. [PMID: 36455103 DOI: 10.1002/cbic.202200609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/24/2022] [Accepted: 11/25/2022] [Indexed: 12/03/2022]
Abstract
We have examined the stabilization of higher-order noncanonical G-quadruplex (G4) DNA structures formed by the G-rich sequences in the promoter region of oncogenes such as c-MYC, c-KIT, VEGF and BCl2 by newly synthesized, novel nitrogen-containing aromatics conjugated to xanthone moiety. Compounds with N-heterocyclic substituents such as pyridine (XNiso), benzimidazole (XBIm), quinoxaline (XQX) and fluorophore dansyl (XDan) showed greater effectiveness in stabilizing the G4 DNA as well as selective cytotoxicity for cancer cells (mainly A549) over normal cells both in terms of UV-Vis spectral titrations and cytotoxicity assay. Both fluorescence spectral titrimetric measurements and circular dichroism (CD) melting experiments further substantiated the G4 stabilization phenomenon by these small-molecular ligands. In addition, these compounds could induce the formation of parallel G4 structures in the absence of any added salt condition in Tris⋅HCl buffer at 25 °C. In a polymerase stop assay, the formation of stable G4 structures in the promoter of oncogenes and halting of DNA synthesis in the presence of the above-mentioned compounds was demonstrated by using oncogene promoter as the DNA synthesis template. Apoptosis-mediated cell death of the cancer cells was proved by Annexin V-PI dual staining assay and cell-cycle arrest occurred in the S phase of the cell cycles. The plausible mode of binding involves the stacking of the xanthone core on the G4 DNA plane with the possibility of interaction with the 5'-overhang as indicated by molecular dynamics simulation studies.
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Affiliation(s)
- Soma Roy
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, 560012, India.,School of Applied & Interdisciplinary Sciences Indian Association for the Cultivation of Science, Kolkata, 700032, India
| | - Nirmal Chakraborty
- School of Applied & Interdisciplinary Sciences Indian Association for the Cultivation of Science, Kolkata, 700032, India
| | - Bappa Maiti
- School of Applied & Interdisciplinary Sciences Indian Association for the Cultivation of Science, Kolkata, 700032, India
| | - Kalappa Muniyappa
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Santanu Bhattacharya
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, 560012, India.,School of Applied & Interdisciplinary Sciences Indian Association for the Cultivation of Science, Kolkata, 700032, India
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Singh M, Gupta R, Comez L, Paciaroni A, Rani R, Kumar V. BCL2 G quadruplex-binding small molecules: Current status and prospects for the development of next-generation anticancer therapeutics. Drug Discov Today 2022; 27:2551-2561. [PMID: 35709931 DOI: 10.1016/j.drudis.2022.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 06/01/2022] [Accepted: 06/08/2022] [Indexed: 11/03/2022]
Abstract
B cell lymphoma 2 (BCL2) overexpression in a range of human tumors is often related to chemotherapy resistance and poor prognosis. GC-rich regions upstream of the P1 promoter in human BCL2 can form G-quadruplex (G4) structures through the stacking of four Hoogsteen-paired guanine bases. Stabilizing the G4 fold implies the inhibition of BCL2 expression and, thus, small molecules that selectively bind to the G4 are promising anticancer candidates. In this review, we discuss the structural aspects, binding affinity, selectivity, and biological activity of well-characterized BCL2 G4 binding ligands in vitro and in vivo. We also explore future directions in the research and development of G4-based anticancer therapeutics.
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Affiliation(s)
- Mamta Singh
- Amity Institute of Molecular Medicine and Stem Cell Research, Amity University, Noida, UP, 201303, India
| | - Rajat Gupta
- Amity Institute of Molecular Medicine and Stem Cell Research, Amity University, Noida, UP, 201303, India
| | - Lucia Comez
- IOM-CNR National Research Council, Via Pascoli, Perugia I-06123, Italy
| | - Alessandro Paciaroni
- Department of Physics and Geology, University of Perugia, via Pascoli, 06123, Italy
| | - Reshma Rani
- Drug Discovery Unit, Jubilant Biosys Ltd, Sector 58, Noida, UP 201301, India.
| | - Vinit Kumar
- Amity Institute of Molecular Medicine and Stem Cell Research, Amity University, Noida, UP, 201303, India.
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Ongaro A, Desiderati G, Oselladore E, Auricchio D, Memo M, Ribaudo G, Sissi C, Gianoncelli A. Amino-Acid-Anthraquinone Click Chemistry Conjugates Selectively Target Human Telomeric G-Quadruplexes. ChemMedChem 2021; 17:e202100665. [PMID: 34882992 DOI: 10.1002/cmdc.202100665] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/07/2021] [Indexed: 11/06/2022]
Abstract
Guanine-rich sequences are known to fold into G-quadruplex (G4) arrangements, which are present in oncogenes and in the telomeric regions of chromosomes. In particular, G4s represent an obstacle to functioning of telomerase, an enzyme overexpressed in cancer cells causing their immortalization. Therefore, G4 stabilization using small molecules represents an appealing strategy for the medicinal chemist. Ligands based on an anthraquinone scaffold, to which peptidic side chains were attached by an amide bond, were previously reported. We envisioned improving this ligand concept leveraging the click chemistry approach, which, besides representing a flexible, high yielding synthetic strategy, allows an elongation of the side chains and an increase of π-π stacking and H-bond interactions with the nucleobases through the triazole ring. Compounds were tested for their ability to interact with G4 DNA with a multiple analytical approach, demonstrating an elevated aptitude to stabilize the G4 and high selectivity over double stranded DNA.
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Affiliation(s)
- Alberto Ongaro
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123, Brescia, Italy
| | - Giovanni Desiderati
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, 35131, Padova, Italy
| | - Erika Oselladore
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123, Brescia, Italy
| | - Davide Auricchio
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, 35131, Padova, Italy
| | - Maurizio Memo
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123, Brescia, Italy
| | - Giovanni Ribaudo
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123, Brescia, Italy
| | - Claudia Sissi
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, 35131, Padova, Italy
| | - Alessandra Gianoncelli
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123, Brescia, Italy
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Largy E, König A, Ghosh A, Ghosh D, Benabou S, Rosu F, Gabelica V. Mass Spectrometry of Nucleic Acid Noncovalent Complexes. Chem Rev 2021; 122:7720-7839. [PMID: 34587741 DOI: 10.1021/acs.chemrev.1c00386] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nucleic acids have been among the first targets for antitumor drugs and antibiotics. With the unveiling of new biological roles in regulation of gene expression, specific DNA and RNA structures have become very attractive targets, especially when the corresponding proteins are undruggable. Biophysical assays to assess target structure as well as ligand binding stoichiometry, affinity, specificity, and binding modes are part of the drug development process. Mass spectrometry offers unique advantages as a biophysical method owing to its ability to distinguish each stoichiometry present in a mixture. In addition, advanced mass spectrometry approaches (reactive probing, fragmentation techniques, ion mobility spectrometry, ion spectroscopy) provide more detailed information on the complexes. Here, we review the fundamentals of mass spectrometry and all its particularities when studying noncovalent nucleic acid structures, and then review what has been learned thanks to mass spectrometry on nucleic acid structures, self-assemblies (e.g., duplexes or G-quadruplexes), and their complexes with ligands.
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Affiliation(s)
- Eric Largy
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Alexander König
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Anirban Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Debasmita Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Sanae Benabou
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Frédéric Rosu
- Univ. Bordeaux, CNRS, INSERM, IECB, UMS 3033, F-33600 Pessac, France
| | - Valérie Gabelica
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
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Ribaudo G, Ongaro A, Zagotto G, Memo M, Gianoncelli A. Evidence on selective binding to G-quadruplex DNA of isoflavones from Maclura pomifera by mass spectrometry and molecular docking. Nat Prod Res 2019; 35:2583-2587. [PMID: 31631705 DOI: 10.1080/14786419.2019.1680670] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
G-quadruplex DNA stabilization mediated by small molecules is an attractive approach to modulate the transcription of guanine-rich sequences and contrast unregulated cell proliferation. Natural alkaloids have been reported to target this macromolecular arrangement, and such mechanism may be among these underlying the antiproliferative effect of some flavonoids. The binding affinity for G-quadruplex and double stranded DNA of 4 isoflavones from Maclura pomifera, namely osajin, pomiferin, scandenone and auriculasin, was evaluated using electrospray mass spectrometry (ESI-MS). The experiments pointed out that osajin and scandenone preferentially bind G-quadruplex. Moreover, since G-quadruplex stabilization is a crucial aim for triggering biological effects such as gene expression, collision-induced dissociation (CID) assays were performed to study the relative gas-phase kinetic stability of the DNA/ligand complexes. Osajin was identified as the best G-quadruplex stabilizer of the set, and in silico docking studies indicate that stacking is the preferred interaction motif of this natural compound.
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Affiliation(s)
- Giovanni Ribaudo
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Alberto Ongaro
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Giuseppe Zagotto
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
| | - Maurizio Memo
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Alessandra Gianoncelli
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
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G-Quadruplex surveillance in BCL-2 gene: a promising therapeutic intervention in cancer treatment. Drug Discov Today 2017; 22:1165-1186. [PMID: 28506718 DOI: 10.1016/j.drudis.2017.05.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 03/20/2017] [Accepted: 05/05/2017] [Indexed: 02/07/2023]
Abstract
Recently, therapeutic implications of BCL-2 quadruplex invigorated the field of clinical oncology. This Keynote review discusses how a BCL-2 quadruplex-selective approach circumvents the limitations of existing therapeutics; and which improvisations might ameliorate the recent trends of quadruplex-based treatment.
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Micheli E, Altieri A, Cianni L, Cingolani C, Iachettini S, Bianco A, Leonetti C, Cacchione S, Biroccio A, Franceschin M, Rizzo A. Perylene and coronene derivatives binding to G-rich promoter oncogene sequences efficiently reduce their expression in cancer cells. Biochimie 2016; 125:223-31. [DOI: 10.1016/j.biochi.2016.04.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 04/08/2016] [Indexed: 11/28/2022]
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9
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Shen R, Chen Y, Li Z, Qi H, Wang Y. Synthesis and biological evaluation of disubstituted amidoxanthones as potential telomeric G-quadruplex DNA-binding and apoptosis-inducing agents. Bioorg Med Chem 2016; 24:619-26. [DOI: 10.1016/j.bmc.2015.12.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 12/12/2015] [Accepted: 12/15/2015] [Indexed: 11/26/2022]
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10
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Pany SPP, Bommisetti P, Diveshkumar KV, Pradeepkumar PI. Benzothiazole hydrazones of furylbenzamides preferentially stabilize c-MYC and c-KIT1 promoter G-quadruplex DNAs. Org Biomol Chem 2016; 14:5779-93. [DOI: 10.1039/c6ob00138f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The stabilization of G-quadruplex DNA structures by using small molecule ligands having simple structural scaffolds has the potential to be harnessed for developing next generation anticancer agents.
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Affiliation(s)
| | - Praneeth Bommisetti
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
| | - K. V. Diveshkumar
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
| | - P. I. Pradeepkumar
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
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11
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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]
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12
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Liu QL, Wu XY, Gao F, Bao D, Wang FM. 9-(2-Chlorophenyl)-4a-hydroxy-3,4,4a,5,6,7,9,9a-octahydro-2 H-xanthene-1,8-dione. Acta Crystallogr Sect E Struct Rep Online 2014; 70:o442-3. [PMID: 24826146 PMCID: PMC3998631 DOI: 10.1107/s1600536814005297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Accepted: 03/07/2014] [Indexed: 11/10/2022]
Abstract
In the title compound, C19H19ClO4, the dihydropyran ring and the cyclohexane ring adopt a half-chair conformation and a chair conformation, respectively. The cyclohexene ring has an envelope conformation with the central CH2 C atom as the flap. This atom is disordered over two positions [site-occupancy ratio = 0.744 (12):0.256 (12)] above and below the mean plane formed by the other five atoms. In the crystal, O—H⋯O hydrogen bonds between hydroxy and carbonyl groups link molecules into chains propagating along [001].
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Franceschin M, Nocioni D, Biroccio A, Micheli E, Cacchione S, Cingolani C, Venditti A, Zizza P, Bianco A, Altieri A. Design and synthesis of a new dimeric xanthone derivative: enhancement of G-quadruplex selectivity and telomere damage. Org Biomol Chem 2014; 12:9572-82. [DOI: 10.1039/c4ob01658k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Dimerization of the xanthone core greatly enhances G-quadruplex binding and biological activity.
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Affiliation(s)
- Marco Franceschin
- University of Rome “Sapienza”
- Department of Chemistry
- Roma 00185, Italy
| | - Daniele Nocioni
- University of Rome “Sapienza”
- Department of Chemistry
- Roma 00185, Italy
| | - Annamaria Biroccio
- Experimental Chemotherapy Laboratory
- Regina Elena National Cancer Institute
- Italy
| | - Emanuela Micheli
- University of Rome “Sapienza”
- Department of Biology and Biotechnology “Charles Darwin”
- Roma 00185, Italy
- Istituto Pasteur-Fondazione Cenci-Bolognetti
- Roma 00185, Italy
| | - Stefano Cacchione
- University of Rome “Sapienza”
- Department of Biology and Biotechnology “Charles Darwin”
- Roma 00185, Italy
- Istituto Pasteur-Fondazione Cenci-Bolognetti
- Roma 00185, Italy
| | - Chiara Cingolani
- Experimental Chemotherapy Laboratory
- Regina Elena National Cancer Institute
- Italy
| | | | - Pasquale Zizza
- Experimental Chemotherapy Laboratory
- Regina Elena National Cancer Institute
- Italy
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