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Choudhury SD, Kumar P, Choudhury D. Bioactive nutraceuticals as G4 stabilizers: potential cancer prevention and therapy-a critical review. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024; 397:3585-3616. [PMID: 38019298 DOI: 10.1007/s00210-023-02857-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 11/13/2023] [Indexed: 11/30/2023]
Abstract
G-quadruplexes (G4) are non-canonical, four-stranded, nucleic acid secondary structures formed in the guanine-rich sequences, where guanine nucleotides associate with each other via Hoogsteen hydrogen bonding. These structures are widely found near the functional regions of the mammalian genome, such as telomeres, oncogenic promoters, and replication origins, and play crucial regulatory roles in replication and transcription. Destabilization of G4 by various carcinogenic agents allows oncogene overexpression and extension of telomeric ends resulting in dysregulation of cellular growth-promoting oncogenesis. Therefore, targeting and stabilizing these G4 structures with potential ligands could aid cancer prevention and therapy. The field of G-quadruplex targeting is relatively nascent, although many articles have demonstrated the effect of G4 stabilization on oncogenic expressions; however, no previous study has provided a comprehensive analysis about the potency of a wide variety of nutraceuticals and some of their derivatives in targeting G4 and the lattice of oncogenic cell signaling cascade affected by them. In this review, we have discussed bioactive G4-stabilizing nutraceuticals, their sources, mode of action, and their influence on cellular signaling, and we believe our insight would bring new light to the current status of the field and motivate researchers to explore this relatively poorly studied arena.
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Affiliation(s)
- Satabdi Datta Choudhury
- Department of Chemistry and Biochemistry, Thapar Institute of Engineering and Technology, Patiala, Punjab, 147004, India
| | - Prateek Kumar
- School of Basic Sciences, Indian Institute of Technology (IIT), Mandi, Himachal Pradesh, 175005, India
| | - Diptiman Choudhury
- Department of Chemistry and Biochemistry, Thapar Institute of Engineering and Technology, Patiala, Punjab, 147004, India.
- Centre for Excellence in Emerging Materials, Thapar Institute of Engineering and Technology, Patiala, Punjab, 147004, India.
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2
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Liu XY, Tan Q, Li LX. A pan-cancer analysis of Dyskeratosis congenita 1 (DKC1) as a prognostic biomarker. Hereditas 2023; 160:38. [PMID: 38082360 PMCID: PMC10712082 DOI: 10.1186/s41065-023-00302-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Dyskeratosis congenita 1 (DKC1), a critical component of telomerase complex, is highly expressed in a variety of human cancers. However, the association of DKC1 with cancer occurrence and development stages is not clear, making a pan-cancer analysis crucial. METHODS We conducted a study using various bioinformatic databases such as TIMER, GEPIA, UALCAN, and KM plotter Analysis to examine the different expressions of DKC1 in multiple tissues and its correlation with pathological stages. Through KEGG analysis, GO enrichment analysis and Venn analysis, we were able to reveal DKC1-associated genes and signaling pathways. In addition, we performed several tests including the CCK, wound healing assay, cell cycle arrest assay, transwell assay and Sa-β-gal staining on DKC1-deleted MDA-231 cells. RESULTS Our study demonstrates that DKC1 has relatively low expression specificity in different tissues. Furthermore, we found that in ACC, KICH, KIRP and LIHC, the expression level of DKC1 is positively correlated with pathological stages. Conversely, in NHSC, KIRP, LGG, LIHC, MESO and SARC, we observed a negative influence of DKC1 expression level on the overall survival rate. We also found a significant positive correlation between DKC1 expression and Tumor Mutational Burden in 14 tumors. Additionally, we observed a significantly negative impact of DKC1 DNA methylation on gene expression at the promoter region in BRCA. We also identified numerous phosphorylation sites concentrated at the C-terminus of the DKC1 protein. Our GO analysis revealed a correlation between DKC1 and ribosomal biosynthesis pathways, and the common element UTP14A was identified. We also observed decreased rates of cell proliferation, migration and invasion abilities in DKC1-knockout MDA-MB-231 cell lines. Furthermore, DKC1-knockout induced cell cycle arrest and caused cell senescence. CONCLUSIONS Our findings suggest that the precise expression of DKC1 is closely associated with the occurrence and developmental stages of cancer in multiple tissues. Depletion of DKC1 can inhibit the abilities of cancer cells to proliferate, migrate, and invade by arresting the cell cycle and inducing cell senescence. Therefore, DKC1 may be a valuable prognostic biomarker for the diagnosis and treatment of cancer in various tissues.
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Affiliation(s)
- Xin-Ying Liu
- School of Life and Health Sciences, Huzhou College, Huzhou, 313000, China
- Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, China
| | - Qing Tan
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100005, China
| | - Lin-Xiao Li
- School of Life and Health Sciences, Huzhou College, Huzhou, 313000, China.
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Fukuda H, Zou T, Fujii S, Sato S, Wakahara D, Higashi S, Tseng TY, Chang TC, Yada N, Matsuo K, Habu M, Tominaga K, Takeuchi H, Takenaka S. Cyclic anthraquinone derivatives, unique G-quadruplex binders, selectively induce cancer cell apoptosis and inhibit tumor growth. PNAS NEXUS 2023; 2:pgad211. [PMID: 37416876 PMCID: PMC10319625 DOI: 10.1093/pnasnexus/pgad211] [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: 04/04/2023] [Revised: 05/23/2023] [Accepted: 06/14/2023] [Indexed: 07/08/2023]
Abstract
Cyclic anthraquinone derivatives (cAQs), which link two side chains of 1,5-disubstituted anthraquinone as a threading DNA intercalator, have been developed as G-quartet (G4) DNA-specific ligands. Among the cAQs, cAQ-mBen linked through the 1,3-position of benzene had the strongest affinity for G4 recognition and stabilization in vitro and was confirmed to bind to the G4 structure in vivo, selectively inhibiting cancer cell proliferation in correlation with telomerase expression levels and triggering cell apoptosis. RNA-sequencing analysis further indicated that differentially expressed genes regulated by cAQ-mBen were profiled with more potential quadruplex-forming sequences. In the treatment of the tumor-bearing mouse model, cAQ-mBen could effectively reduce tumor tissue and had less adverse effects on healthy tissue. These results suggest that cAQ-mBen can be a potential cancer therapeutic agent as a G4 binder.
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Affiliation(s)
| | | | | | | | - Daiki Wakahara
- Department of Applied Chemistry, Kyushu Institute of Technology, Fukuoka 804-8550, Japan
| | - Sen Higashi
- Division of Applied Pharmacology, Department of Health Promotion, Kyushu Dental University, Fukuoka 803-8580, Japan
| | - Ting-Yuan Tseng
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan
| | - Ta-Chau Chang
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan
| | - Naomi Yada
- Division of Oral Pathology, Department of Health Promotion, Kyushu Dental University, Fukuoka 803-8580, Japan
| | - Kou Matsuo
- Division of Oral Pathology, Department of Health Promotion, Kyushu Dental University, Fukuoka 803-8580, Japan
| | - Manabu Habu
- Division of Oral and Maxillofacial Surgery, Department of Science of Physical Functions, Kyushu Dental University, Fukuoka 803-8580, Japan
| | - Kazuhiro Tominaga
- Division of Oral and Maxillofacial Surgery, Department of Science of Physical Functions, Kyushu Dental University, Fukuoka 803-8580, Japan
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Satange R, Chang CC, Li L, Lin SH, Neidle S, Hou MH. Synergistic binding of actinomycin D and echinomycin to DNA mismatch sites and their combined anti-tumour effects. Nucleic Acids Res 2023; 51:3540-3555. [PMID: 36919604 PMCID: PMC10164580 DOI: 10.1093/nar/gkad156] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 02/07/2023] [Accepted: 02/23/2023] [Indexed: 03/16/2023] Open
Abstract
Combination cancer chemotherapy is one of the most useful treatment methods to achieve a synergistic effect and reduce the toxicity of dosing with a single drug. Here, we use a combination of two well-established anticancer DNA intercalators, actinomycin D (ActD) and echinomycin (Echi), to screen their binding capabilities with DNA duplexes containing different mismatches embedded within Watson-Crick base-pairs. We have found that combining ActD and Echi preferentially stabilised thymine-related T:T mismatches. The enhanced stability of the DNA duplex-drug complexes is mainly due to the cooperative binding of the two drugs to the mismatch duplex, with many stacking interactions between the two different drug molecules. Since the repair of thymine-related mismatches is less efficient in mismatch repair (MMR)-deficient cancer cells, we have also demonstrated that the combination of ActD and Echi exhibits enhanced synergistic effects against MMR-deficient HCT116 cells and synergy is maintained in a MMR-related MLH1 gene knockdown in SW620 cells. We further accessed the clinical potential of the two-drug combination approach with a xenograft mouse model of a colorectal MMR-deficient cancer, which has resulted in a significant synergistic anti-tumour effect. The current study provides a novel approach for the development of combination chemotherapy for the treatment of cancers related to DNA-mismatches.
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Affiliation(s)
- Roshan Satange
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung402, Taiwan
- Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung402, Taiwan
| | - Chih-Chun Chang
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung402, Taiwan
| | - Long‐Yuan Li
- Department of Life Sciences, National Chung Hsing University, Taichung402, Taiwan
| | - Sheng-Hao Lin
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung402, Taiwan
- Division of Chest Medicine, Changhua Christian Hospital, Changhua City, Taiwan
- Departement of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung402, Taiwan
| | - Stephen Neidle
- The School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Ming-Hon Hou
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung402, Taiwan
- Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung402, Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung402, Taiwan
- Department of Life Sciences, National Chung Hsing University, Taichung402, Taiwan
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5
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Teloxantron inhibits the processivity of telomerase with preferential DNA damage on telomeres. Cell Death Dis 2022; 13:1005. [PMID: 36437244 PMCID: PMC9701690 DOI: 10.1038/s41419-022-05443-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 11/09/2022] [Accepted: 11/15/2022] [Indexed: 11/29/2022]
Abstract
Telomerase reactivation is one of the hallmarks of cancer, which plays an important role in cellular immortalization and the development and progression of the tumor. Chemical telomerase inhibitors have been shown to trigger replicative senescence and apoptotic cell death both in vitro and in vivo. Due to its upregulation in various cancers, telomerase is considered a potential target in cancer therapy. In this study, we identified potent, small-molecule telomerase inhibitors using a telomerase repeat amplification protocol assay. The results of the assay are the first evidence of telomerase inhibition by anthraquinone derivatives that do not exhibit G-quadruplex-stabilizing properties. The stability of telomerase in the presence of its inhibitor was evaluated under nearly physiological conditions using a cellular thermal shift assay. Our data showed that the compound induced aggregation of the catalytic subunit (hTERT) of human telomerase, and molecular studies confirmed the binding of the hit compound with the active site of the enzyme. The ability of new derivatives to activate DNA double-strand breaks (DSBs) was determined by high-resolution microscopy and flow cytometry in tumor cell lines differing in telomere elongation mechanism. The compounds triggered DSBs in TERT-positive A549 and H460 lung cancer cell lines, but not in TERT-negative NHBE normal human bronchial epithelial and ALT-positive U2OS osteosarcoma cell lines, which indicates that the induction of DSBs was dependent on telomerase inhibition. The observed DNA damage activated DNA damage response pathways involving ATM/Chk2 and ATR/Chk1 cascades. Additionally, the compounds induced apoptotic cell death through extrinsic and intrinsic pathways in lung cancer cells. Taken together, our study demonstrated that anthraquinone derivatives can be further developed into novel telomerase-related anticancer agents.
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Malik MS, Alsantali RI, Jassas RS, Alsimaree AA, Syed R, Alsharif MA, Kalpana K, Morad M, Althagafi II, Ahmed SA. Journey of anthraquinones as anticancer agents - a systematic review of recent literature. RSC Adv 2021; 11:35806-35827. [PMID: 35492773 PMCID: PMC9043427 DOI: 10.1039/d1ra05686g] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 10/06/2021] [Indexed: 12/19/2022] Open
Abstract
Anthraquinones are privileged chemical scaffolds that have been used for centuries in various therapeutic applications. The anthraquinone moiety forms the core of various anticancer agents. However, the emergence of drug-resistant cancers warrants the development of new anticancer agents. The research endeavours towards new anthraquinone-based compounds are increasing rapidly in recent years. They are used as a core chemical template to achieve structural modifications, resulting in the development of new anthraquinone-based compounds as promising anticancer agents. Mechanistically, most of the anthraquinone-based compounds inhibit cancer progression by targeting essential cellular proteins. Herein, we review new anthraquinone analogues that have been developed in recent years as anticancer agents. This includes a systematic review of the recent literature (2005-2021) on anthraquinone-based compounds in cell-based models and key target proteins such as kinases, topoisomerases, telomerases, matrix metalloproteinases and G-quadruplexes involved in the viability of cancer cells. In addition to this, the developments in PEG-based delivery of anthraquinones and the toxicity aspects of anthraquinone derivatives are also discussed. The review dispenses a compact background knowledge to understanding anthraquinones for future research on the expansion of anticancer therapeutics.
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Affiliation(s)
- M Shaheer Malik
- Department of Chemistry, Faculty of Applied Sciences, Umm Al-Qura University Makkah 21955 Saudi Arabia
| | - Reem I Alsantali
- Department of Pharmaceutical Chemistry, College of Pharmacy, Taif University P. O. Box 11099 Taif 21944 Saudi Arabia
| | - Rabab S Jassas
- Department of Chemistry, Jamoum University College, Umm Al-Qura University 21955 Makkah Saudi Arabia
| | - Abdulrahman A Alsimaree
- Department of Basic Science (Chemistry), College of Science and Humanities, Shaqra University Afif Saudi Arabia
| | - Riyaz Syed
- Centalla Discovery, JHUB, Jawaharlal Nehru Technological University Hyderabad Kukatpally Hyderabad 500085 India
| | - Meshari A Alsharif
- Department of Chemistry, Faculty of Applied Sciences, Umm Al-Qura University Makkah 21955 Saudi Arabia
| | - Kulkarni Kalpana
- Department of Humanities and Sciences (Chemistry), Gokaraju Rangaraju Institute of Engineering and Technology Bachupally Hyderabad 500090 India
| | - Moataz Morad
- Department of Chemistry, Faculty of Applied Sciences, Umm Al-Qura University Makkah 21955 Saudi Arabia
| | - Ismail I Althagafi
- Department of Chemistry, Faculty of Applied Sciences, Umm Al-Qura University Makkah 21955 Saudi Arabia
| | - Saleh A Ahmed
- Department of Chemistry, Faculty of Applied Sciences, Umm Al-Qura University Makkah 21955 Saudi Arabia
- Department of Chemistry, Faculty of Science, Assiut University 71516 Assiut Egypt
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7
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Lozynskyi A, Holota S, Yushyn I, Sabadakh O, Karpenko O, Novikov V, Lesyk R. Synthesis and Biological Activity Evaluation of Polyfunctionalized Anthraquinonehydrazones. LETT DRUG DES DISCOV 2021. [DOI: 10.2174/1570180817999200802032844] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background :
Anthraquinone derivatives, frequently occurring motifs in many various
natural compounds, have attracted a great deal of interest as compounds with a wide spectrum of
biological activities.
Introduction:
The hybrid pharmacophore approach has become an object of considerable interest
due to the incorporation of a five- or six-membered heterocyclic rings in the structure of various
natural compounds, especially anthraquinone derivatives.
Methods:
A series of polyfunctionalized anthraquinonehydrazones have been synthesized via the
azo-coupling reaction between anthraquinone-based triazenes and methylene active compounds. The
structures of synthesized compounds were confirmed by spectral data. Some of the synthesized
compounds were screened for their in vitro anticancer activity according to US NCI protocols. The
screening of antimicrobial and antifungal activities against Candida albicans and Lactobacillus sp.
was carried out. The synthesized compounds were evaluated for their antioxidant (DPPH free radical
scavenging assay) and herbicidal activity.
Results:
The synthesized 1-[N'-(5-oxo-2-thioxoimidazolidin-4-ylidene)-hydrazino]-anthraquinone
1.5 displayed a high level of antimitotic activity against tested human tumor cells with mean
GI50/TGI values 4.06/78.52μM. The screening of antimicrobial and antifungal activities led to the
identification of 1.8 and 1.9 with a moderate effect on Candida albicans and Lactobacillus sp. Antioxidant
activity evaluation allowed the identification of 1-[N'-(3-methyl-5-oxo-1-phenyl-1,5-
dihydropyrazol-4-ylidene)-hydrazino]-anthraquinone 1.8 with an IC50 value of 3.715 mM. The herbicidal
activity screening led to compound identification 1.8 with growth inhibition of Agrostis stolonifera
at 25 %.
Conclusion:
The obtained anthraquinonehydrazones constitute an interesting template for the design
of new synthetic agents with polypharmacological activities.
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Affiliation(s)
- Andrii Lozynskyi
- Department of Pharmaceutical, Organic and Bioorganic Chemistry, Danylo Halytsky Lviv National Medical University, Pekarska 69, Lviv 79010, Ukraine
| | - Serhii Holota
- Department of Pharmaceutical, Organic and Bioorganic Chemistry, Danylo Halytsky Lviv National Medical University, Pekarska 69, Lviv 79010, Ukraine
| | - Ihor Yushyn
- Department of Pharmaceutical, Organic and Bioorganic Chemistry, Danylo Halytsky Lviv National Medical University, Pekarska 69, Lviv 79010, Ukraine
| | - Oksana Sabadakh
- Department of Environmental Chemistry and Chemistry Education, Vasyl Stefanyk Precarpathian National University, Halytska 201, Ivano-Frankivsk 76000, Ukraine
| | | | - Volodymyr Novikov
- Department of Technology of Biologically Active Substances, Pharmacy and Biotechnology, Lviv Polytechnic National University, Bandery 12, Lviv 79013, Ukraine
| | - Roman Lesyk
- Department of Pharmaceutical, Organic and Bioorganic Chemistry, Danylo Halytsky Lviv National Medical University, Pekarska 69, Lviv 79010, Ukraine
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Anthraquinone: a promising scaffold for the discovery and development of therapeutic agents in cancer therapy. Future Med Chem 2020; 12:1037-1069. [PMID: 32349522 DOI: 10.4155/fmc-2019-0198] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Cancer, characterized by uncontrolled malignant neoplasm, is a leading cause of death in both advanced and emerging countries. Although, ample drugs are accessible in the market to intervene with tumor progression, none are totally effective and safe. Natural anthraquinone (AQ) equivalents such as emodin, aloe-emodin, alchemix and many synthetic analogs extend their antitumor activity on different targets including telomerase, topoisomerases, kinases, matrix metalloproteinases, DNA and different phases of cell lines. Nano drug delivery strategies are advanced tools which deliver drugs into tumor cells with minimum drug leakage to normal cells. This review delineates the way AQ derivatives are binding on these targets by abolishing tumor cells to produce anticancer activity and purview of nanoformulations related to AQ analogs.
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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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10
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Wu PC, Tzeng SL, Chang CK, Kao YF, Waring MJ, Hou MH. Cooperative recognition of T:T mismatch by echinomycin causes structural distortions in DNA duplex. Nucleic Acids Res 2019; 46:7396-7404. [PMID: 29741655 PMCID: PMC6101601 DOI: 10.1093/nar/gky345] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 04/25/2018] [Indexed: 12/16/2022] Open
Abstract
Small-molecule compounds that target mismatched base pairs in DNA offer a novel prospective for cancer diagnosis and therapy. The potent anticancer antibiotic echinomycin functions by intercalating into DNA at CpG sites. Surprisingly, we found that the drug strongly prefers to bind to consecutive CpG steps separated by a single T:T mismatch. The preference appears to result from enhanced cooperativity associated with the binding of the second echinomycin molecule. Crystallographic studies reveal that this preference originates from the staggered quinoxaline rings of the two neighboring antibiotic molecules that surround the T:T mismatch forming continuous stacking interactions within the duplex. These and other associated changes in DNA conformation allow the formation of a minor groove pocket for tight binding of the second echinomycin molecule. We also show that echinomycin displays enhanced cytotoxicity against mismatch repair-deficient cell lines, raising the possibility of repurposing the drug for detection and treatment of mismatch repair-deficient cancers.
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Affiliation(s)
- Pei-Ching Wu
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 40227, Taiwan
| | - Shu-Ling Tzeng
- Institute of Medicine, Chung Shan Medical University, Taichung 40201, Taiwan
| | - Chung-Ke Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Ya-Fen Kao
- Institute of Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan
| | - Michael J Waring
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, England
| | - Ming-Hon Hou
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 40227, Taiwan.,Institute of Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan
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11
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Challenges and current status of computational methods for docking small molecules to nucleic acids. Eur J Med Chem 2019; 168:414-425. [PMID: 30831409 DOI: 10.1016/j.ejmech.2019.02.046] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 02/12/2019] [Accepted: 02/12/2019] [Indexed: 01/29/2023]
Abstract
Since the development of the first docking program in 1982, the use of docking-based in silico screening for potentially bioactive molecule discovery has become a common strategy in academia and pharmaceutical industry. Up until recently, application of docking programs has largely focused on drugs binding to proteins. However, with the discovery of promising drug targets in nucleic acids, including RNA riboswitches, DNA G-quadruplexes, and extended repeats in RNA, there has been greater interests in developing drugs for nucleic acids. However, due to major biochemical and physical differences in charges, binding pockets, and solvation, existing docking programs, developed for proteins, face difficulties when adopted directly for nucleic acids. In this review, we cover the current field of in silico docking to nucleic acids, available programs, as well as challenges faced in the field.
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12
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Tikhomirov AS, Tsvetkov VB, Kaluzhny DN, Volodina YL, Zatonsky GV, Schols D, Shchekotikhin AE. Tri-armed ligands of G-quadruplex on heteroarene-fused anthraquinone scaffolds: Design, synthesis and pre-screening of biological properties. Eur J Med Chem 2018; 159:59-73. [DOI: 10.1016/j.ejmech.2018.09.054] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 09/18/2018] [Accepted: 09/19/2018] [Indexed: 01/30/2023]
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13
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Mikek C, West SJ, Gwin JC, Dayal N, Sintim HO, Lewis EA. Berenil Binds Tightly to Parallel and Mixed Parallel/Antiparallel G-Quadruplex Motifs with Varied Thermodynamic Signatures. ACS OMEGA 2018; 3:11582-11591. [PMID: 30320266 PMCID: PMC6173502 DOI: 10.1021/acsomega.8b01621] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 09/06/2018] [Indexed: 06/08/2023]
Abstract
Diminazene, DMZ, (or berenil) has been reported as a tight binder of G-quadruplexes. G-Quadruplex structures are often located in the promotor regions of oncogenes and may play a regulatory role in gene expression based on the stability of the folding topology. In this study, attempts have been made to characterize the specificity of DMZ binding toward multiple G-quadruplex topologies or foldamers. Mutant sequences of the G-quadruplex forming promotor regions of several oncogenes were designed to exhibit restricted loop lengths and folding topologies. Circular dichroism was used to confirm the quadruplex topology of mutant BCL2, KRAS, and c-MYC sequences, human telomere (Na+ and K+) G-quadruplexes and their complexes with DMZ and analogs thereof. Isothermal titration calorimetry was used to generate a complete thermodynamic profile (ΔG, ΔH, -TΔS) for the formation of DMZ and analog complexes with the target G-quadruplexes. DMZ binds to parallel and/or mixed parallel/antiparallel quadruplex DNA motifs with stoichiometries up to 8:1 and via three binding modes with varying affinities. In the case of the parallel G-quadruplexes, with the exception of the long-looped c-MYC mutant, the highest affinity binding event (mode 1) is driven by enthalpy. DMZ binding to the long-looped c-MYC mutant exhibits a very favorable entropy change in addition to a moderately favorable enthalpy change. Mode 1 binding to the antiparallel and mixed parallel/antiparallel hTel quadruplexes is also driven by favorable enthalpy changes. In all cases, the intermediate DMZ affinity binding (mode 2) is driven almost entirely by entropy, with small or unfavorable enthalpic contributions. The weakest binding event (mode 3) is also entropically driven with small or moderate enthalpic contributions.
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Affiliation(s)
- Clinton
G. Mikek
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
- Center
for Drug Discovery, Purdue University, 720 Clinic Drive, West Lafayette, Indiana 47907, United States
| | - Savannah J. West
- Department
of Chemistry, Mississippi State University, 310 President’s Circle, Mississippi, Mississippi State 39762, United States
| | - J. Cole Gwin
- Department
of Chemistry, Mississippi State University, 310 President’s Circle, Mississippi, Mississippi State 39762, United States
| | - Neetu Dayal
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
- Center
for Drug Discovery, Purdue University, 720 Clinic Drive, West Lafayette, Indiana 47907, United States
| | - Herman O. Sintim
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
- Center
for Drug Discovery, Purdue University, 720 Clinic Drive, West Lafayette, Indiana 47907, United States
| | - Edwin A. Lewis
- Department
of Chemistry, Mississippi State University, 310 President’s Circle, Mississippi, Mississippi State 39762, United States
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14
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Głuszyńska A, Juskowiak B, Kuta-Siejkowska M, Hoffmann M, Haider S. Carbazole ligands as c-myc G-quadruplex binders. Int J Biol Macromol 2018; 114:479-490. [DOI: 10.1016/j.ijbiomac.2018.03.135] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 03/16/2018] [Accepted: 03/21/2018] [Indexed: 10/24/2022]
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15
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Ethyl-substitutive Thioflavin T as a highly-specific fluorescence probe for detecting G-quadruplex structure. Sci Rep 2018; 8:2666. [PMID: 29422637 PMCID: PMC5805748 DOI: 10.1038/s41598-018-20960-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 01/26/2018] [Indexed: 12/31/2022] Open
Abstract
G-quadruplex has attracted considerable attention due to their prevalent distribution in functional genomic regions and transcripts, which can importantly influence biological processes such as regulation of telomere maintenance, gene transcription and gene translation. Artificial receptor study has been developed for accurate identification of G-quadruplex from DNA species, since it is important for the G-quadruplex related basic research, clinical diagnosis, and therapy. Herein, fluorescent dye ThT-E, a derivative of the known fluorescence probe Thioflavin T (ThT), was designed and synthesized to effectively differentiate various G-quadruplex structures from other nucleic acid forms. Compared with methyl groups in ThT, three ethyl groups were introduced to ThT-E, which leads to strengthened affinity, selectivity and little inducing effect on the G-quadruplex formation. More importantly, ThT-E could be served as a visual tool to directly differentiate G-quadruplex solution even with naked eyes under illumination of ultraviolet light. Thus, this probe reported herein may hold great promise for high-throughput assay to screen G-quadruplex, which may widely apply to G-quadruplex-based potential diagnosis and therapy.
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