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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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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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Shen R, Li X, Chen Y, Yang A, Kou X. Xanthone derivatives as potential telomeric G-quadruplex stabilizing and cytotoxic agents: Effects of substitution on quadruplex binding affinity and cytotoxicity. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Shen R, Chen Y, Wu J, Zhao L, Yang A, Kou X. Effect of Bis-Dimethylamine Substitution on DNA Binding Property and Cytotoxic Activity of Polyhydroxyxanthone. Chem Biodivers 2022; 19:e202101021. [PMID: 35324082 DOI: 10.1002/cbdv.202101021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 03/24/2022] [Indexed: 12/30/2022]
Abstract
A bis-dimethylamine substituted xanthone (Xan-2) was obtained by cationic modification of the free C3 and C6 hydroxy groups of 1,3,6-trihydroxyxanthone (Xan-1) which was isolated from Polygala hongkongensis Hemsl.. The results of the spectroscopic analysis, melting profiles, electrophoretic migration, PCR assay and molecular docking indicated that the hydrophobic plane of Xan-1 and Xan-2 could intercalate into the DNA base pairs meanwhile the basic amine alkyl chain of Xan-2 could bind with DNA phosphate framework via electrostatic interaction. Thus, Xan-2 exhibited higher DNA binding affinity than Xan-1. Further study showed that Xan-2 could inhibit the proliferation of HeLa, SGC-7901 and A549 cells effectively by MTT assay and induce apoptosis of HeLa cells as detected by AO/EB staining and flow cytometry assay. Interestingly, Xan-2 exhibited selective cytotoxicity to cells, which was proved by its relatively low inhibitory effect on Raw 264.7 cell. What these studies mean is that disubstituted amine alkyl chains will play an important role in DNA binding property and cytotoxic activity, providing a direction for the development of novel potential antitumor agents.
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Affiliation(s)
- Rui Shen
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Yuhong Chen
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Jianhua Wu
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Lihua Zhao
- Tianjin Renai College, Tianjin, 301636, China
| | - Aihong Yang
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Xiaodi Kou
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
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Synthesis and biological evaluation of xanthone derivatives as anti-cancer agents targeting topoisomerase II and DNA. Med Chem Res 2022. [DOI: 10.1007/s00044-022-02862-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Andreeva DV, Tikhomirov AS, Shchekotikhin AE. Ligands of G-quadruplex nucleic acids. RUSSIAN CHEMICAL REVIEWS 2021. [DOI: 10.1070/rcr4968] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Roy S, Ali A, Kamra M, Muniyappa K, Bhattacharya S. Specific stabilization of promoter G-Quadruplex DNA by 2,6-disubstituted amidoanthracene-9,10-dione based dimeric distamycin analogues and their selective cancer cell cytotoxicity. Eur J Med Chem 2020; 195:112202. [PMID: 32302880 DOI: 10.1016/j.ejmech.2020.112202] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/19/2020] [Accepted: 03/01/2020] [Indexed: 10/24/2022]
Abstract
We have designed and synthesized anthraquinone containing compounds which have oligopyrrole side chains of varying lengths. These compounds stabilized the G-quadruplex DNA formed in the promoter regions of c-MYC oncogenes selectively over the duplex DNA. These observations were recorded using UV-vis spectroscopic titrations, fluorescence measurements and circular dichroism (CD) spectral titrations. The potency of the compounds to stabilize the G4 DNA has been shown from the thermal denaturation experiments. The compound interacts with c-MYC G-quadruplex DNA through stacking mode as obtained from ethidium bromide displacement assay, cyclic voltammetric titration, and docking experiments. Molecular modeling studies suggested that the stacking of the anthraquinone moiety over the G-tetrad of the G4 structures are responsible for the stability of such quadruplex secondary structure. Furthermore, polymerase stop assay also supported the formation of stable G4 structures in the presence of the above-mentioned compounds. The compounds have shown selective cancer cell (HeLa and HEK293T) cytotoxicity over normal cells (NIH3T3 and HDFa) under in vitro conditions as determined from MTT based cell viability assay. Apoptosis was found to be the mechanistic pathway underlying the cancer cell cytotoxicity as obtained from Annexin V-FITC and PI dual staining assay which was further substantiated by nuclear morphological changes as observed by AO/EB dual staining assay. Cellular morphological changes, as well as nuclear condensation and fragmentation upon treatment with these compounds, were observed under bright field and confocal microscopy.
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Affiliation(s)
- Soma Roy
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Asfa Ali
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Mohini Kamra
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, 560012, 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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Resende DISP, Durães F, Maia M, Sousa E, Pinto MMM. Recent advances in the synthesis of xanthones and azaxanthones. Org Chem Front 2020. [DOI: 10.1039/d0qo00659a] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A useful chemical toolbox for (aza)xanthones from 2012 to 2020 that covers the optimization of known procedures and novel methodologies.
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Affiliation(s)
- Diana I. S. P. Resende
- CIIMAR – Centro Interdisciplinar de Investigação Marinha e Ambiental
- Terminal de Cruzeiros do Porto de Leixões
- 4450-208 Matosinhos
- Portugal
- Laboratório de Química Orgânica e Farmacêutica
| | - Fernando Durães
- CIIMAR – Centro Interdisciplinar de Investigação Marinha e Ambiental
- Terminal de Cruzeiros do Porto de Leixões
- 4450-208 Matosinhos
- Portugal
- Laboratório de Química Orgânica e Farmacêutica
| | - Miguel Maia
- CIIMAR – Centro Interdisciplinar de Investigação Marinha e Ambiental
- Terminal de Cruzeiros do Porto de Leixões
- 4450-208 Matosinhos
- Portugal
- Laboratório de Química Orgânica e Farmacêutica
| | - Emília Sousa
- CIIMAR – Centro Interdisciplinar de Investigação Marinha e Ambiental
- Terminal de Cruzeiros do Porto de Leixões
- 4450-208 Matosinhos
- Portugal
- Laboratório de Química Orgânica e Farmacêutica
| | - Madalena M. M. Pinto
- CIIMAR – Centro Interdisciplinar de Investigação Marinha e Ambiental
- Terminal de Cruzeiros do Porto de Leixões
- 4450-208 Matosinhos
- Portugal
- Laboratório de Química Orgânica e Farmacêutica
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Huang S, Liang Y, Cui J, Xie J, Liu Y, Hu B, Xiao Q. Comparative investigation of binding interactions with three steroidal derivatives of d(GGGT) 4 G-quadruplex aptamer. Steroids 2018; 132:46-55. [PMID: 29458054 DOI: 10.1016/j.steroids.2018.02.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 02/04/2018] [Accepted: 02/13/2018] [Indexed: 11/19/2022]
Abstract
Steroidal derivatives have attracted tremendous attentions in biological and biomedical areas, due to their variety biological activities. The investigation of structural influences helps in understanding their biological activities. The interactions of steroidal derivatives with DNA may play important roles in biological activities, however only a few investigations were reported on this issue. Herein, the structural influences of three steroidal derivatives were investigated based on their binding interactions with d(GGGT)4 G-quadruplex aptamer by spectroscopic approaches, nuclear magnetic resonance (NMR), electrochemical methods, and molecular modeling techniques. Three compounds were found to selectively bind with parallel G-quadruplex aptamer to form three complexes through end-stacking binding modes. Three compounds stabilized the G-quadruplex structure of the aptamer at different levels, which enhanced the biological activity of this aptamer to some extent. The space steric hindrance was responsible for differences in the binding interactions between d(GGGT)4 G-quadruplex aptamer and three compounds. These results provide new information for the molecular understanding of binding interactions of steroidal derivatives with DNA and the strategy for research of structural influences.
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Affiliation(s)
- Shan Huang
- College of Chemistry and Materials Science, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Guangxi Teachers Education University, Nanning 530001, PR China; Key Laboratory of Beibu Gulf Environment Change and Resources Utilization (Guangxi Teachers Education University), Ministry of Education, Nanning 530001, PR China
| | - Yu Liang
- College of Chemistry and Materials Science, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Guangxi Teachers Education University, Nanning 530001, PR China
| | - Jianguo Cui
- College of Chemistry and Materials Science, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Guangxi Teachers Education University, Nanning 530001, PR China.
| | - Jiangning Xie
- College of Chemistry and Materials Science, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Guangxi Teachers Education University, Nanning 530001, PR China
| | - Yi Liu
- College of Chemistry and Materials Science, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Guangxi Teachers Education University, Nanning 530001, PR China; College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, PR China
| | - Baoqing Hu
- Key Laboratory of Beibu Gulf Environment Change and Resources Utilization (Guangxi Teachers Education University), Ministry of Education, Nanning 530001, PR China
| | - Qi Xiao
- College of Chemistry and Materials Science, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Guangxi Teachers Education University, Nanning 530001, PR China; College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, PR China; Key Laboratory of Beibu Gulf Environment Change and Resources Utilization (Guangxi Teachers Education University), Ministry of Education, Nanning 530001, PR China.
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Studies on interactions of carbazole derivatives with DNA, cell image, and cytotoxicity. Bioorg Med Chem 2018; 26:285-294. [DOI: 10.1016/j.bmc.2017.11.044] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 11/26/2017] [Accepted: 11/29/2017] [Indexed: 11/19/2022]
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