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Li Y, Li Z, Yun P, Sun D, Niu Y, Yao B, Wang K. Studying the Effects and Competitive Mechanisms of YOYO-1 on the Binding Characteristics of DOX and DNA Molecules Based on Surface-Enhanced Raman Spectroscopy and Molecular Docking Techniques. Int J Mol Sci 2024; 25:3804. [PMID: 38612614 PMCID: PMC11011392 DOI: 10.3390/ijms25073804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 03/21/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024] Open
Abstract
Revealing the interaction mechanisms between anticancer drugs and target DNA molecules at the single-molecule level is a hot research topic in the interdisciplinary fields of biophysical chemistry and pharmaceutical engineering. When fluorescence imaging technology is employed to carry out this kind of research, a knotty problem due to fluorescent dye molecules and drug molecules acting on a DNA molecule simultaneously is encountered. In this paper, based on self-made novel solid active substrates NpAA/(ZnO-ZnCl2)/AuNPs, we use a surface-enhanced Raman spectroscopy method, inverted fluorescence microscope technology, and a molecular docking method to investigate the action of the fluorescent dye YOYO-1 and the drug DOX on calf thymus DNA (ctDNA) molecules and the influencing effects and competitive relationships of YOYO-1 on the binding properties of the ctDNA-DOX complex. The interaction sites and modes of action between the YOYO-1 and the ctDNA-DOX complex are systematically examined, and the DOX with the ctDNA-YOYO-1 are compared, and the impact of YOYO-1 on the stability of the ctDNA-DOX complex and the competitive mechanism between DOX and YOYO-1 acting with DNA molecules are elucidated. This study has helpful experimental guidance and a theoretical foundation to expound the mechanism of interaction between drugs and biomolecules at the single-molecule level.
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Affiliation(s)
- Yanjie Li
- Key Laboratory of Photoelectric Technology of Shaanxi Province, National Center for International Research of Photoelectric Technology & Nano-Functional Materials and Application, Institute of Photonics and Photon-Technology, Northwest University, Xi’an 710127, China (D.S.)
| | - Zhiwei Li
- Key Laboratory of Photoelectric Technology of Shaanxi Province, National Center for International Research of Photoelectric Technology & Nano-Functional Materials and Application, Institute of Photonics and Photon-Technology, Northwest University, Xi’an 710127, China (D.S.)
| | - Penglun Yun
- Key Laboratory of Photoelectric Technology of Shaanxi Province, National Center for International Research of Photoelectric Technology & Nano-Functional Materials and Application, Institute of Photonics and Photon-Technology, Northwest University, Xi’an 710127, China (D.S.)
| | - Dan Sun
- Key Laboratory of Photoelectric Technology of Shaanxi Province, National Center for International Research of Photoelectric Technology & Nano-Functional Materials and Application, Institute of Photonics and Photon-Technology, Northwest University, Xi’an 710127, China (D.S.)
| | - Yong Niu
- Key Laboratory of Photoelectric Technology of Shaanxi Province, National Center for International Research of Photoelectric Technology & Nano-Functional Materials and Application, Institute of Photonics and Photon-Technology, Northwest University, Xi’an 710127, China (D.S.)
| | - Baoli Yao
- State Key Laboratory of Transient Optics and Photonics, Xi’an Institute of Optics and Precision Mechanics, Chinese Academy of Sciences, Xi’an 710119, China
| | - Kaige Wang
- Key Laboratory of Photoelectric Technology of Shaanxi Province, National Center for International Research of Photoelectric Technology & Nano-Functional Materials and Application, Institute of Photonics and Photon-Technology, Northwest University, Xi’an 710127, China (D.S.)
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2
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Bag S, Ghosal S, Karmakar S, Pramanik G, Bhowmik S. Uncovering the Contrasting Binding Behavior of Plant Flavonoids Fisetin and Morin Having Subsidiary Hydroxyl Groups (-OH) with HRAS1 and HRAS2 i-Motif DNA Structures: Decoding the Structural Alterations and Positional Influences. ACS OMEGA 2023; 8:30315-30329. [PMID: 37636929 PMCID: PMC10448647 DOI: 10.1021/acsomega.3c03105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 07/18/2023] [Indexed: 08/29/2023]
Abstract
Research on the interactions of naturally existing flavonoids with various noncanonical DNA such as i-motif (IM) DNA structures is helpful in comprehending the molecular basis of binding mode as well as providing future direction for the application and invention of novel effective therapeutic drugs. IM DNA structures have been identified as prospective anticancer therapeutic targets, and flavonoids are smaller molecules with a variety of health-promoting attributes, including anticancer activities. The extensive investigation comprising a series of techniques reveals the contrasting mode of the binding behavior of fisetin and morin with various IM DNA structures. We have discovered that structural alterations of hydroxyl groups located at different places of aromatic rings influence flavonoid's reactivity. This minor structural alteration appears to be critical for fisetin and morin's capacity to interact differentially with HRAS1 and HRAS2 IM DNA. Hence, fisetin appears to be an efficient ligand for HRAS1 and morin is considered to be an efficient ligand for HRAS2 IM DNA. This novel exploration opens up the possibility of employing the strategy for regulation of gene expression in cancerous cells. Our finding also reveals the flavonoid-mediated specific interaction with IM DNA while pointing toward tangible strategies for drug discovery and other essential cellular functions.
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Affiliation(s)
- Sagar Bag
- Department
of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, A.P.C. Road, Kolkata 700009, India
| | - Souvik Ghosal
- Mahatma
Gandhi Medical Advanced Research Institute (MGMARI), Sri Balaji Vidyapeeth
(Deemed to be University), Pondy−Cuddalore Main Road, Pillaiyarkuppam, Pondicherry 607402, India
| | - Sudip Karmakar
- UGC−DAE
Consortium for Scientific Research, Kolkata Centre, Sector III, LB-8, Bidhan Nagar, Kolkata 700 106, India
| | - Goutam Pramanik
- UGC−DAE
Consortium for Scientific Research, Kolkata Centre, Sector III, LB-8, Bidhan Nagar, Kolkata 700 106, India
| | - Sudipta Bhowmik
- Department
of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, A.P.C. Road, Kolkata 700009, India
- Mahatma
Gandhi Medical Advanced Research Institute (MGMARI), Sri Balaji Vidyapeeth
(Deemed to be University), Pondy−Cuddalore Main Road, Pillaiyarkuppam, Pondicherry 607402, India
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3
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Chen XM, Zhou JY, Liu SQ, Song LH, Wang HL, Wang Q, Liang SM, Lu L, Wei JH, Huang R, Zhang Y. Design, synthesis, and antitumor evaluation of morpholine substituted bisnaphthalimides as DNA targeting agents. Bioorg Med Chem Lett 2023; 85:129218. [PMID: 36894107 DOI: 10.1016/j.bmcl.2023.129218] [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: 12/14/2022] [Revised: 02/25/2023] [Accepted: 03/03/2023] [Indexed: 03/09/2023]
Abstract
A series of mono- and bisnaphthalimides derivatives containing 3-nitro and 4-morpholine moieties were designed, synthesized, and evaluated for their in vitro anticancer activities against four cancer cell lines. Some compounds exhibited relatively good antiproliferative activity on the cell lines tested, in comparison with mitonafide and amonafide. It is noteworthy that bisnaphthalimide A6 was identified as the most potent compound in anti-proliferation against MGC-803 cells, with an IC50 lowered to 0.09 μM, a far greater potency than that of mono-naphthalimide A7, mitonafide, and amonafide. A gel electrophoresis assay revealed that DNA and Topo I were the potential targets of compounds A6 and A7. The treatment of CNE-2 cells with compounds A6 and A7 resulted in an S phase cell cycle arrest, accompanied by the upregulation of the expression levels of the antioncogene p27 and the down-regulation of the expression levels of CDK2 and cyclin E. In addition, compounds A6 and A7-induced apoptosis was further confirmed by flow cytometry, ROS generation assay, and Hoechst 33,258 staining. In particular, in vivo antitumor assay results revealed that bisnaphthalimide A6 exhibited potent anticancer efficiency in an MGC-803 xenograft tumor model, in comparison with mitonafide, and had lower toxicity than mono-naphthalimide A7. In brief, the results suggested that bisnaphthalimide derivatives containing 3-nitro and 4-morpholine moieties might serve as DNA binding agents for the development of new antitumor agents.
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Affiliation(s)
- Xiao-Man Chen
- Guangxi Key Laboratory for Pharmaceutical Molecular Discovery and Druggability Optimization, School of Pharmacy, Guilin Medical University, Guilin 541199, China; Guangxi Engineering Research Center for Pharmaceutical Molecular Screening and Druggability Evaluation, School of Pharmacy, Guilin Medical University, Guilin 5411199, China
| | - Jian-Yu Zhou
- Guangxi Key Laboratory for Pharmaceutical Molecular Discovery and Druggability Optimization, School of Pharmacy, Guilin Medical University, Guilin 541199, China; Guangxi Engineering Research Center for Pharmaceutical Molecular Screening and Druggability Evaluation, School of Pharmacy, Guilin Medical University, Guilin 5411199, China
| | - Shuang-Qiang Liu
- Guangxi Key Laboratory for Pharmaceutical Molecular Discovery and Druggability Optimization, School of Pharmacy, Guilin Medical University, Guilin 541199, China; Guangxi Engineering Research Center for Pharmaceutical Molecular Screening and Druggability Evaluation, School of Pharmacy, Guilin Medical University, Guilin 5411199, China
| | - Long-Hao Song
- Guangxi Key Laboratory for Pharmaceutical Molecular Discovery and Druggability Optimization, School of Pharmacy, Guilin Medical University, Guilin 541199, China; Guangxi Engineering Research Center for Pharmaceutical Molecular Screening and Druggability Evaluation, School of Pharmacy, Guilin Medical University, Guilin 5411199, China
| | - Hui-Ling Wang
- Guangxi Key Laboratory for Pharmaceutical Molecular Discovery and Druggability Optimization, School of Pharmacy, Guilin Medical University, Guilin 541199, China; Guangxi Engineering Research Center for Pharmaceutical Molecular Screening and Druggability Evaluation, School of Pharmacy, Guilin Medical University, Guilin 5411199, China
| | - Qi Wang
- Guangxi Key Laboratory for Pharmaceutical Molecular Discovery and Druggability Optimization, School of Pharmacy, Guilin Medical University, Guilin 541199, China; Guangxi Engineering Research Center for Pharmaceutical Molecular Screening and Druggability Evaluation, School of Pharmacy, Guilin Medical University, Guilin 5411199, China
| | - Si-Min Liang
- Guangxi Key Laboratory for Pharmaceutical Molecular Discovery and Druggability Optimization, School of Pharmacy, Guilin Medical University, Guilin 541199, China; Guangxi Engineering Research Center for Pharmaceutical Molecular Screening and Druggability Evaluation, School of Pharmacy, Guilin Medical University, Guilin 5411199, China
| | - Lin Lu
- Guangxi Key Laboratory for Pharmaceutical Molecular Discovery and Druggability Optimization, School of Pharmacy, Guilin Medical University, Guilin 541199, China; Guangxi Engineering Research Center for Pharmaceutical Molecular Screening and Druggability Evaluation, School of Pharmacy, Guilin Medical University, Guilin 5411199, China
| | - Jian-Hua Wei
- Guangxi Key Laboratory for Pharmaceutical Molecular Discovery and Druggability Optimization, School of Pharmacy, Guilin Medical University, Guilin 541199, China; Guangxi Engineering Research Center for Pharmaceutical Molecular Screening and Druggability Evaluation, School of Pharmacy, Guilin Medical University, Guilin 5411199, China.
| | - Rizhen Huang
- Guangxi Key Laboratory for Pharmaceutical Molecular Discovery and Druggability Optimization, School of Pharmacy, Guilin Medical University, Guilin 541199, China; Guangxi Engineering Research Center for Pharmaceutical Molecular Screening and Druggability Evaluation, School of Pharmacy, Guilin Medical University, Guilin 5411199, China.
| | - Ye Zhang
- Guangxi Key Laboratory for Pharmaceutical Molecular Discovery and Druggability Optimization, School of Pharmacy, Guilin Medical University, Guilin 541199, China; Guangxi Engineering Research Center for Pharmaceutical Molecular Screening and Druggability Evaluation, School of Pharmacy, Guilin Medical University, Guilin 5411199, China.
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Miranda de Souza Duarte-Filho LA, Ortega de Oliveira PC, Yanaguibashi Leal CE, de Moraes MC, Picot L. Ligand fishing as a tool to screen natural products with anticancer potential. J Sep Sci 2023:e2200964. [PMID: 36808885 DOI: 10.1002/jssc.202200964] [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: 11/24/2022] [Revised: 02/07/2023] [Accepted: 02/07/2023] [Indexed: 02/23/2023]
Abstract
Cancer is the second leading cause of death in the world and its incidence is expected to increase with the aging of the world's population and globalization of risk factors. Natural products and their derivatives have provided a significant number of approved anticancer drugs and the development of robust and selective screening assays for the identification of lead anticancer natural products are essential in the challenge of developing personalized targeted therapies tailored to the genetic and molecular characteristics of tumors. To this end, a ligand fishing assay is a remarkable tool to rapidly and rigorously screen complex matrices, such as plant extracts, for the isolation and identification of specific ligands that bind to relevant pharmacological targets. In this paper, we review the application of ligand fishing with cancer-related targets to screen natural product extracts for the isolation and identification of selective ligands. We provide critical analysis of the system configurations, targets, and key phytochemical classes related to the field of anticancer research. Based on the data collected, ligand fishing emerges as a robust and powerful screening system for the rapid discovery of new anticancer drugs from natural resources. It is currently an underexplored strategy according to its considerable potential.
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Affiliation(s)
| | | | - Cíntia Emi Yanaguibashi Leal
- Departamento de Ciências Farmacêuticas, Pós-Graduação em Biociências (PGB) Universidade Federal do Vale do São Francisco, Petrolina, Brazil
| | - Marcela Cristina de Moraes
- Departamento de Química Orgânica, Laboratório BIOCROM, Instituto de Química, Universidade Federal Fluminense, Niterói, Brazil
| | - Laurent Picot
- UMR CNRS 7266 LIENSs, Département de Biotechnologie, La Rochelle Université, La Rochelle, France
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5
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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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6
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Mikra C, Mitrakas A, Ghizzani V, Katsani KR, Koffa M, Koukourakis M, Psomas G, Protti S, Fagnoni M, Fylaktakidou KC. Effect of Arylazo Sulfones on DNA: Binding, Cleavage, Photocleavage, Molecular Docking Studies and Interaction with A375 Melanoma and Non-Cancer Cells. Int J Mol Sci 2023; 24:ijms24031834. [PMID: 36768159 PMCID: PMC9915714 DOI: 10.3390/ijms24031834] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 01/04/2023] [Accepted: 01/12/2023] [Indexed: 01/19/2023] Open
Abstract
A set of arylazo sulfones, known to undergo N-S bond cleavage upon light exposure, has been synthesized, and their activity in the dark and upon irradiation towards DNA has been investigated. Their interaction with calf-thymus DNA has been examined, and the significant affinity observed (most probably due to DNA intercalation) was analyzed by means of molecular docking "in silico" calculations that pointed out polar contacts, mainly via the sulfonyl moiety. Incubation with plasmid pBluescript KS II revealed DNA cleavage that has been studied over time and concentration. UV-A irradiation considerably improved DNA damage for most of the compounds, whereas under visible light the effect was slightly lower. Moving to in vitro experiments, irradiation was found to slightly enhance the death of the cells in the majority of the compounds. Naphthylazosulfone 1 showed photo-disruptive effect under UV-A irradiation (IC50 ~13 μΜ) followed by derivatives 14 and 17 (IC50 ~100 μΜ). Those compounds were irradiated in the presence of two non-cancer cell lines and were found equally toxic only upon irradiation and not in the dark. The temporal and spatial control of light, therefore, might provide a chance for these novel scaffolds to be useful for the development of phototoxic pharmaceuticals.
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Affiliation(s)
- Chrysoula Mikra
- Laboratory of Organic Chemistry, Faculty of Chemistry, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Achilleas Mitrakas
- Laboratory of Cellular Biology and Cell Cycle, Molecular Biology and Genetics Department, Democritus University of Thrace, University Campus, Dragana, 68100 Alexandroupolis, Greece
- Department of Radiotherapy and Oncology, Democritus University of Thrace, University General Hospital of Alexandroupolis, 68100 Alexandroupolis, Greece
| | - Virginia Ghizzani
- PhotoGreen Lab, Department of Chemistry, University of Pavia, V. Le Taramelli 12, 27100 Pavia, Italy
| | - Katerina R. Katsani
- Laboratory of Biochemistry and Molecular Virology, Molecular Biology and Genetics Department, Democritus University of Thrace, Dragana, 68100 Alexandroupolis, Greece
| | - Maria Koffa
- Laboratory of Cellular Biology and Cell Cycle, Molecular Biology and Genetics Department, Democritus University of Thrace, University Campus, Dragana, 68100 Alexandroupolis, Greece
| | - Michael Koukourakis
- Department of Radiotherapy and Oncology, Democritus University of Thrace, University General Hospital of Alexandroupolis, 68100 Alexandroupolis, Greece
| | - George Psomas
- Laboratory of Inorganic Chemistry, Faculty of Chemistry, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Stefano Protti
- PhotoGreen Lab, Department of Chemistry, University of Pavia, V. Le Taramelli 12, 27100 Pavia, Italy
| | - Maurizio Fagnoni
- PhotoGreen Lab, Department of Chemistry, University of Pavia, V. Le Taramelli 12, 27100 Pavia, Italy
- Correspondence: (M.F.); (K.C.F.)
| | - Konstantina C. Fylaktakidou
- Laboratory of Organic Chemistry, Faculty of Chemistry, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
- Correspondence: (M.F.); (K.C.F.)
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Schmoeller LA, Wodtke F, Pietezak D, Leite DC, da Rocha JC, Xavier FR, Gariani RA. Structural and electronic investigation of 3,4-dihydropyrimidin-2(1H)-ones (DHPMs): Correlations between spectroscopic and molecular docking features upon salmon sperm DNA. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133546] [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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ARSLANTAS A, AĞIRTAŞ MS. The Study of Interaction Activity of Nickel (ll) Phthalocyanine Complex Bearing Tetra Substituted Phenoxy-3-Methoxybenzoic Acid Groups with DNA. GAZI UNIVERSITY JOURNAL OF SCIENCE 2022. [DOI: 10.35378/gujs.1089316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Nickel phthalocyanine complex containing 4-(3,4-dicyanophenoxy)-3-methoxybenzoic acid group was synthesized and specified by way of FT-IR, NMR, UV/Vis procedures. The binding of PcNi complex to CT-DNA was examined via electronic absorption titration, emission titration, melting temperature, viscosity measurement, and agarose gel electrophoresis technics, respectively. The DNA interaction activity of PcNi against CT-DNA was studied by way of UV/Vi titrations, fluorescence spectra, farther by conducting melting point, viscosity procedures in the buffer of a pH 7.02. The obtained outcomes from these methods demonstrated that PcNi indicated substantial binding affinity to the DNA via intercalating by the binding constant of 1.31 x 106 m-1. Further, the interaction activity of the complex on CT-DNA was investigated by which the electrophoresis technique and this procedure indicated that PcNi complex exhibits strong binding affinity on the DNA.
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Wang H, Bai X, Huang Y, Chen Y, Dong G, Ou T, Wu S, Xu D, Sheng C. Discovery of novel triple targeting G‑quadruplex and topoisomerase 1/2 ligands from natural products evodiamine and rutaecarpine. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.07.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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10
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Farajzadeh N, Güler Kuşçulu N, Yenilmez HY, Bahar D, Altuntas Bayir Z. Anticancer and Biological Properties of New Axially Disubstituted Silicon Phthalocyanines. Dalton Trans 2022; 51:7539-7550. [DOI: 10.1039/d2dt01033j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This study reports the synthesis of three novel axially disubstituted silicon phthalocyanines (1-3-Si) and their quaternized phthalocyanines (1-3-QSi). The resulting compounds were characterized by applying spectroscopic techniques including 1H NMR,...
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Franco Pinto J, Fillion A, Duchambon P, Bombard S, Granzhan A. Acridine-O 6-benzylguanine hybrids: Synthesis, DNA binding, MGMT inhibition and antiproliferative activity. Eur J Med Chem 2021; 227:113909. [PMID: 34731767 DOI: 10.1016/j.ejmech.2021.113909] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 09/24/2021] [Accepted: 10/06/2021] [Indexed: 12/13/2022]
Abstract
O6-Methylguanine-DNA-methyltransferase (MGMT) is a key DNA repair enzyme involved in chemoresistance to DNA-alkylating anti-cancer drugs such as Temozolomide (TMZ) through direct repair of drug-induced O6-methylguanine residues in DNA. MGMT substrate analogues, such as O6-benzylguanine (BG), efficiently inactivate MGMT in vitro and in cells; however, these drugs failed to reach the clinic due to adverse side effects. Here, we designed hybrid drugs combining a BG residue covalently linked to a DNA-interacting moiety (6-chloro-2-methoxy-9-aminoacridine). Specifically, two series of hybrids, encompassing three compounds each, were obtained by varying the position of the attachment point of BG (N9 of guanine vs. the benzyl group) and the length and nature of the linker. UV/vis absorption and fluorescence data indicate that all six hybrids adopt an intramolecularly stacked conformation in aqueous solutions in a wide range of temperatures. All hybrids interact with double-stranded DNA, as clearly evidenced by spectrophotometric titrations, without intercalation of the acridine ring and do not induce thermal stabilization of the duplex. All hybrids, as well as the reference DNA intercalator (6-chloro-2-methoxy-9-aminoacridine 8), irreversibly inhibit MGMT in vitro with variable efficiency, comparable to that of BG. In a multidrug-resistant glioblastoma cell line T98G, benzyl-linked hybrids 7a-c and the N9-linked hybrid 19b are moderately cytotoxic (GI50 ≥ 15 μM after 96 h), while N9-linked hybrids 19a and 19c are strongly cytotoxic (GI50 = 1-2 μM), similarly to acridine 8 (GI50 = 0.6 μM). Among all compounds, hybrids 19a and 19c, similarly to BG, display synergic cytotoxic effect upon co-treatment with subtoxic doses of TMZ, with combination index (CI) values as low as 0.2-0.3. In agreement with in vitro results, compound 19a inactivates cellular MGMT but, unlike BG, does not induce significant levels of DNA damage, either alone or in combination with TMZ, as indicated by the results of γH2AX immunostaining experiments. Instead, and unlike BG, compound 19a alone induces significant apoptosis of T98G cells, which is not further increased in a combination with TMZ. These results indicate that molecular mechanisms underlying the cytotoxicity of 19a and its combination with TMZ are distinct from that of BG. The strongly synergic properties of this combination represent an interesting therapeutic opportunity in treating TMZ-resistant cancers.
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Affiliation(s)
- Jaime Franco Pinto
- CNRS UMR9187, Inserm U1196, Institut Curie, PSL Research University, 91405, Orsay, France; CNRS UMR9187, Inserm U1196, Université Paris Saclay, 91405, Orsay, France
| | - Alexandra Fillion
- CNRS UMR9187, Inserm U1196, Institut Curie, PSL Research University, 91405, Orsay, France; CNRS UMR9187, Inserm U1196, Université Paris Saclay, 91405, Orsay, France
| | - Patricia Duchambon
- CNRS UMR9187, Inserm U1196, Institut Curie, PSL Research University, 91405, Orsay, France; CNRS UMR9187, Inserm U1196, Université Paris Saclay, 91405, Orsay, France
| | - Sophie Bombard
- CNRS UMR9187, Inserm U1196, Institut Curie, PSL Research University, 91405, Orsay, France; CNRS UMR9187, Inserm U1196, Université Paris Saclay, 91405, Orsay, France.
| | - Anton Granzhan
- CNRS UMR9187, Inserm U1196, Institut Curie, PSL Research University, 91405, Orsay, France; CNRS UMR9187, Inserm U1196, Université Paris Saclay, 91405, Orsay, France.
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12
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Günsel A, Taslimi P, Atmaca GY, Bilgiçli AT, Pişkin H, Ceylan Y, Erdoğmuş A, Yarasir MN, Gülçin İ. Novel potential metabolic enzymes inhibitor, photosensitizer and antibacterial agents based on water-soluble phthalocyanine bearing imidazole derivative. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130402] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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13
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Günsel A, Kalkan F, Atmaca GY, Barut B, Bilgiçli AT, Pişkin H, Özel A, Erdoğmuş A, Yarasir MN. Synthesis of water‐soluble phthalocyanines containing 1‐methyl‐1
H
‐imidazole‐2‐thiol: Investigation of DNA nuclease, α‐glucosidase inhibitory, and photo‐physicochemical properties. Appl Organomet Chem 2021. [DOI: 10.1002/aoc.6202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Armağan Günsel
- Department of Chemistry, Faculty of Arts and Sciences Sakarya University Serdivan Turkey
| | - Fatma Kalkan
- Department of Chemistry, Faculty of Arts and Sciences Sakarya University Serdivan Turkey
| | - Göknur Yaşa Atmaca
- Department of Chemistry, Faculty of Arts and Sciences Yıldız Technical University Istanbul Turkey
| | - Burak Barut
- Faculty of Pharmacy, Department of Biochemistry Karadeniz Technical University Trabzon Turkey
| | - Ahmet T. Bilgiçli
- Department of Chemistry, Faculty of Arts and Sciences Sakarya University Serdivan Turkey
| | - Hasan Pişkin
- Department of Physics, Faculty of Arts and Sciences Boğaziçi University İstanbul Turkey
| | - Arzu Özel
- Faculty of Pharmacy, Department of Biochemistry Karadeniz Technical University Trabzon Turkey
- Drug and Pharmaceutical Technology Application and Research Center Karadeniz Technical University Trabzon Turkey
| | - Ali Erdoğmuş
- Department of Chemistry, Faculty of Arts and Sciences Yıldız Technical University Istanbul Turkey
| | - M. Nilüfer Yarasir
- Department of Chemistry, Faculty of Arts and Sciences Sakarya University Serdivan Turkey
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14
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Bortolozzi R, Ihmels H, Schulte R, Stremmel C, Viola G. Synthesis, DNA-binding and antiproliferative properties of diarylquinolizinium derivatives. Org Biomol Chem 2021; 19:878-890. [PMID: 33410854 DOI: 10.1039/d0ob02298e] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
A series of ten 2,7- and 2,8-diarylquinolizinium derivatives was synthesized and their DNA-binding and cytotoxic properties were investigated. Except for one nitro-substituted derivative all tested diarylquinolizinium ions bind to DNA with sufficient affinity (2 × 104 M-1-2 × 105 M-1). It was shown with photometric, fluorimetric and polarimetric titrations as well as with flow-LD analysis that the ligands bind mainly by intercalation to duplex DNA, however, depending on the ligand-DNA ratio, groove binding and backbone association were also observed with some derivatives. The biological activity was further investigated with tests of cytotoxicity and antiproliferative properties towards non-tumor cells and selected cancer cells, along with cell cycle analysis and an annexin-V assay. Notably, substrates that carry donor-functionalities in the 4-position of the phenyl substituents revealed a strong, and in some cases selective, antiproliferative activity as quantified by the growth inhibition, GI50, at very low micromolar and even submicromolar level both in leukemia and solid tumors.
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Affiliation(s)
- Roberta Bortolozzi
- Department of Women's and Child's health, Oncohematology laboratory, University of Padova, Via Giustiniani 2, I-35128 Padova, Italy. giampietro,
| | - Heiko Ihmels
- Department of Chemistry and Biology, University of Siegen, Adolf-Reichwein-Str. 2, 57068 Siegen, Germany.
| | - Robin Schulte
- Department of Chemistry and Biology, University of Siegen, Adolf-Reichwein-Str. 2, 57068 Siegen, Germany.
| | - Christopher Stremmel
- Department of Chemistry and Biology, University of Siegen, Adolf-Reichwein-Str. 2, 57068 Siegen, Germany.
| | - Giampietro Viola
- Department of Women's and Child's health, Oncohematology laboratory, University of Padova, Via Giustiniani 2, I-35128 Padova, Italy. giampietro,
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15
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Usman M, Khan RA, Khan MR, Abul Farah M, BinSharfan II, Alharbi W, Shaik JP, Parine NR, Alsalme A, Tabassum S. A novel biocompatible formate bridged 1D-Cu(ii) coordination polymer induces apoptosis selectively in human lung adenocarcinoma (A549) cells. Dalton Trans 2021; 50:2253-2267. [PMID: 33506238 DOI: 10.1039/d0dt03782f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Copper compounds are promising candidates for next-generation metal anticancer drugs. Therefore, we synthesized and characterized a formate bridged 1D coordination polymer [Cu(L)(HCOO)2]n, (L = 2-methoxy-6-methyl-3-((quinolin-8-ylimino)methyl)chroman-4-ol), PCU1, wherein the Cu(ii) center adopts a square pyramidal coordination environment with adjacent CuCu distances of 5.28 Å. Primarily, in vitro DNA interaction studies revealed a metallopolymer which possesses high DNA binding propensity and cleaves DNA via the oxidative pathway. We further analysed its potential on cancerous cells MCF-7, HeLa, A549, and two non-tumorigenic cells HEK293 and HBE. The selective cytotoxicity potential of PCU1 against A549 cells driven us to examine the mechanistic pathways comprehensively by carrying out various assays viz, cell cycle arrest, Annexin V-FTIC/PI assay, autophagy, intercellular localization, mitochondrial membrane potential 'MMP', antiproliferative assay, and gene expression of TGF-β and MMP-2.
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Affiliation(s)
- Mohammad Usman
- Department of Chemistry, Aligarh Muslim University, Aligarh-202002, India.
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16
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Alves JEF, de Oliveira JF, de Lima Souza TRC, de Moura RO, de Carvalho Júnior LB, Alves de Lima MDC, de Almeida SMV. Novel indole-thiazole and indole-thiazolidinone derivatives as DNA groove binders. Int J Biol Macromol 2021; 170:622-635. [PMID: 33359805 DOI: 10.1016/j.ijbiomac.2020.12.153] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/18/2020] [Accepted: 12/19/2020] [Indexed: 10/22/2022]
Abstract
In this study, we report the synthesis of eight novel indole-thiazole and indole-thiazolidinone derivatives, as well as their ability to interact with DNA, analysed through the UV-vis absorption, fluorescence, circular dichroism (CD), viscosity techniques and molecular docking. The ctDNA interaction analysis demonstrated different spectroscopic effects and the affinity constants (Kb) calculated by the UV-vis absorption method were between 2.08 × 105 and 6.99 × 106 M-1, whereas in the fluorescence suppression constants (Ksv) ranged between 0.38 and 0.77 × 104 M-1 and 0.60-7.59 × 104 M-1 using Ethidium Bromide (EB) and 4',6-Diamidino-2-phenylindole (DAPI) as fluorescent probes, respectively. Most derivatives did not alter significantly the secondary structure of the ctDNA according to the CD results. None of the compounds was able to change the relative viscosity of the ctDNA. These results prove that compounds interact with ctDNA via groove binding, which was confirmed by A-T rich oligonucleotide sequence assay with compound JF-252, suggesting the importance of both the phenyl ring coupled to C-4 thiazole ring and the bromo-unsubstituted indole nucleus.
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Affiliation(s)
| | | | | | - Ricardo Olímpio de Moura
- Departamento de Ciências Farmacêuticas, Centro de Ciências Biológicas e da Saúde, Universidade Estadual da Paraíba e Bodocongo, Campina Grande, PB 58429-500, Brazil
| | | | - Maria do Carmo Alves de Lima
- Laboratório de Química e Inovação Terapêutica (LQIT) - Departamento de Antibióticos, Universidade Federal de Pernambuco, 50670-901, Brazil
| | - Sinara Mônica Vitalino de Almeida
- Laboratório de Imunopatologia Keizo Asami (LIKA), Universidade Federal de Pernambuco, 50670-901, Brazil; Laboratório de Biologia Molecular, Universidade de Pernambuco (UPE), Multicampi Garanhuns, Garanhuns, PE 55290-000, Brazil.
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17
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Kumar P, Singh P, Saren S, Pakira S, Sivakumar S, Patra AK. Kinetically labile ruthenium(II) complexes of terpyridines and saccharin: effect of substituents on photoactivity, solvation kinetics, and photocytotoxicity. Dalton Trans 2021; 50:8196-8217. [PMID: 34031678 DOI: 10.1039/d1dt00246e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein, we designed six kinetically labile ruthenium(ii) complexes containing saccharin (sac) and 4'-substituted-2,2':6',2''-terpyridines (R-tpy), viz. trans-[Ru(sac)2(H2O)3(dmso-S)] (1) and [RuII(R-tpy)(sac)2(X)] [X = solvent molecule] (2-6). We intentionally kept the labile hydrolysable Ru-X bonds that were potentially activated via solvent-exchange reactions. This strategy generates a coordinative vacancy that allows further binding with potential biological targets. To gain insight into the electronic effects of ancillary ligands on Ru-X ligand-exchange kinetics or photoreactions, we have used a series of substituted terpyridines (R-tpy) and studied their solvation kinetics. The ternary complexes were also studied for their potential utility in Ru-assisted photoactivated chemotherapy (PACT) synergized with release of saccharin as a highly selective carbonic anhydrase IX (CA-IX) inhibitor, over-expressed in hypoxic tumors. The ternary complexes exhibit distorted octahedral geometry around Ru(ii) from two monodentate transoidal saccharin in the axial position, and tridentate terpyridines and labile solvent molecules at the basal plane (2-6). We studied their speciation, solvation kinetics, and photoreactivity in the presence of green LED light (λirr = 530 nm). All the complexes are relatively labile and undergo solvation in coordinating solvents (e.g. DMSO/DMF). The complexes undergo the ligand-substitution reaction, and their speciation and kinetics were studied by UV-Vis, ESI-MS, 1H-NMR, and structural analysis. We also attempted to assess the effect of various substituents on the ancillary terpyridine ligand (R-tpy) in photo-reactivity and ligand-exchange reactions. The photo-induced absorption and emission measurements suggested dissociation of the saccharin from the Ru-center supporting PACT pathways. The complexes display a significant binding affinity with CT-DNA (Kb ∼ 104-105 M-1) and bovine serum albumin (BSA) (KBSA ∼ 105 M-1). Cytotoxicity was studied in the dark and the presence of low energy UV-A light (365 nm) in cervical cancer cells (HeLa) and breast cancer cells (MCF7). Photoirradiation of the complexes induces the generation of reactive oxygen species (ROS) assessed using 1,3-diphenylisobenzofuran (DPBF) and intracellular DCFDA assays. The complexes are sufficiently internalized in cancer cells throughout the cytoplasm and nucleus and induce apoptosis as studied by staining with dual dyes using confocal microscopy.
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Affiliation(s)
- Priyaranjan Kumar
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, Uttar Pradesh, India.
| | - Prerana Singh
- Department of Chemical Engineering, DST Thematic Unit of Excellence on Soft Nanofabrication, Indian Institute of Technology Kanpur, Kanpur 208016, Uttar Pradesh, India and Department of Biological Sciences & Bioengineering, Indian Institute of Technology Kanpur, Uttar Pradesh 208016, India
| | - Sanjoy Saren
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, Uttar Pradesh, India.
| | - Sandip Pakira
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, Uttar Pradesh, India.
| | - Sri Sivakumar
- Department of Chemical Engineering, DST Thematic Unit of Excellence on Soft Nanofabrication, Indian Institute of Technology Kanpur, Kanpur 208016, Uttar Pradesh, India
| | - Ashis K Patra
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, Uttar Pradesh, India.
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18
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Ray B, Mehrotra R. Nucleic acid binding mechanism of flavone derivative, riviciclib: Structural analysis to unveil anticancer potential. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2020; 211:111990. [PMID: 32858336 DOI: 10.1016/j.jphotobiol.2020.111990] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 07/17/2020] [Accepted: 08/07/2020] [Indexed: 10/23/2022]
Abstract
Despite burgeoned knowledge about the origin, growth, tissue interactions, and spread of cancer in recent years, the functional complexity and unique survival ability of cancer cells still make it difficult to target them. Riviciclib is a semi-synthetic derivative of rohitukine and possesses anticancer potential. Inhibition of nucleic acid activity in an uncontrolled dividing cell can form the basis for the development of new-age cancer therapeutics. The present study reports the molecular interaction between riviciclib and nucleic acid (DNA/tRNA) using spectroscopic and molecular docking studies in an attempt to comprehend its cellular toxicity as well as the nature and mode of binding between them. Vibrational spectroscopic results suggest that riviciclib intercalates DNA duplex and primarily binds with guanine, adenine, and thymine nucleobases. While in the case of riviciclib-tRNA complexation, riviciclib interacts mostly with uracil residues of the tRNA molecule. Besides nucleobases, riviciclib interacts with the sugar-phosphate backbone of both biomacromolecules. Conformationally, DNA alters from B-form to C-form, whereas tRNA shows no change in its native A-form. The order (104 M-1) of binding constant for riviciclib-nucleic acid complexation infer moderate to strong affinity of riviciclib with DNA and tRNA, respectively. Molecular docking explorations are further in corroboration with our spectroscopic outcomes.
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Affiliation(s)
- Bhumika Ray
- CSIR-National Physical Laboratory, Dr. K. S. Krishnan Marg, New Delhi 110012, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Ranjana Mehrotra
- CSIR-National Physical Laboratory, Dr. K. S. Krishnan Marg, New Delhi 110012, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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19
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Turky A, Bayoumi AH, Sherbiny FF, El-Adl K, Abulkhair HS. Unravelling the anticancer potency of 1,2,4-triazole-N-arylamide hybrids through inhibition of STAT3: synthesis and in silico mechanistic studies. Mol Divers 2020; 25:403-420. [PMID: 32830299 DOI: 10.1007/s11030-020-10131-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 08/06/2020] [Indexed: 12/26/2022]
Abstract
The discovery of potent STAT3 inhibitors has gained noteworthy impetus in the last decade. In line with this trend, considering the proven biological importance of 1,2,4-triazoles, herein, we are reporting the design, synthesis, pharmacokinetic profiles, and in vitro anticancer activity of novel C3-linked 1,2,4-triazole-N-arylamide hybrids and their in silico proposed mechanism of action via inhibition of STAT3. The 1,2,4-triazole scaffold was selected as a privilege ring system that is embedded in core structures of a variety of anticancer drugs which are either in clinical use or still under clinical trials. The designed 1,2,4-triazole derivatives were synthesized by linking the triazole-thione moiety through amide hydrophilic linkers with diverse lipophilic fragments. In silico study to predict cytotoxicity of the new hybrids against different kinds of human cancer cell lines as well as the non-tumor cells was conducted. The multidrug-resistant human breast adenocarcinoma cells (MDA-MB-231) was found most susceptible to the cytotoxic effect of synthesized compounds and hence were selected to evaluate the in vitro anticancer activity. Four of the designed derivatives showed promising cytotoxicity effects against selected cancer cells, among which compound 12 showed the highest potency (IC50 = 3.61 µM), followed by 21 which displayed IC50 value of 3.93 µM. Also, compounds 14 and 23 revealed equipotent activity with the reference cytotoxic agent doxorubicin. To reinforce these observations, the obtained data of in vitro cytotoxicity have been validated in terms of ligand-protein interaction and new compounds were analyzed for ADMET properties to evaluate their potential to build up as good drug candidates. This study led us to identify two novel C3-linked 1,2,4-triazole-N-arylamide hybrids of interesting antiproliferative potentials as probable lead inhibitors of STAT3 with promising pharmacokinetic profiles.
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Affiliation(s)
- Abdallah Turky
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Al-Azhar University, Nasr City, Cairo, 11884, Egypt
| | - Ashraf H Bayoumi
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Al-Azhar University, Nasr City, Cairo, 11884, Egypt
| | - Farag F Sherbiny
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Al-Azhar University, Nasr City, Cairo, 11884, Egypt
- Pharmaceutical Organic Chemistry Department, College of Pharmacy, Misr University for Science and Technology (MUST), 6th October City, Egypt
| | - Khaled El-Adl
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Al-Azhar University, Cairo, Egypt
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Heliopolis University for Sustainable Development, Cairo, Egypt
| | - Hamada S Abulkhair
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Al-Azhar University, Nasr City, Cairo, 11884, Egypt.
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Horus University - Egypt, International Costal Road, New Damietta, Egypt.
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20
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Zhirov AM, Kovalev DA, Ulshina DV, Pisarenko SV, Demidov OP, Borovlev IV. Diazapyrenes: interaction with nucleic acids and biological activity. Chem Heterocycl Compd (N Y) 2020; 56:674-693. [PMID: 32836316 PMCID: PMC7366485 DOI: 10.1007/s10593-020-02717-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 11/26/2019] [Indexed: 12/22/2022]
Abstract
The review summarizes data on the practical aspects of the interaction of nucleic acids with diazapyrene derivatives. The information on biological activity is given and the probable mechanisms underlying the action of diazapyrenes are analyzed. It contains 119 references.
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Affiliation(s)
- Andrey M. Zhirov
- Stavropol Research Anti-Plague Institute, 13-15 Sovetskaya St, Stavropol, 355035 Russia
| | - Dmitry A. Kovalev
- Stavropol Research Anti-Plague Institute, 13-15 Sovetskaya St, Stavropol, 355035 Russia
| | - Diana V. Ulshina
- Stavropol Research Anti-Plague Institute, 13-15 Sovetskaya St, Stavropol, 355035 Russia
| | - Sergey V. Pisarenko
- Stavropol Research Anti-Plague Institute, 13-15 Sovetskaya St, Stavropol, 355035 Russia
| | - Oleg P. Demidov
- North Caucasus Federal University, 1a Pushkina St, Stavropol, 355017 Russia
| | - Ivan V. Borovlev
- North Caucasus Federal University, 1a Pushkina St, Stavropol, 355017 Russia
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21
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Bisceglie F, Orsoni N, Pioli M, Bonati B, Tarasconi P, Rivetti C, Amidani D, Montalbano S, Buschini A, Pelosi G. Cytotoxic activity of copper(ii), nickel(ii) and platinum(ii) thiosemicarbazone derivatives: interaction with DNA and the H2A histone peptide. Metallomics 2020; 11:1729-1742. [PMID: 31502621 DOI: 10.1039/c9mt00166b] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Metal complexes still represent promising pharmacological tools in the development of new anticancer drugs. Bis(citronellalthiosemicarbazonate)nickel(ii) is a metal compound extremely effective against leukemic and NCS cancer cell lines. Preliminary experiments performed with this compound and with its Cu(ii) and Pt(ii) analogues evidenced alterations, detectable by comet assay, in the DNA of treated U937 cells. In addition, [Cu(tcitr)2] and [Pt(tcitr)2] were also able to induce gene mutations and produce frameshift events. To gain further insights into the mechanism of action of these metal compounds, we carried out a multidisciplinary study to investigate whether their biological activity can be ascribed to the direct interaction with DNA or with chromatin. The DNA interaction was investigated by means of CD and UV-Vis spectroscopic techniques and by AFM, whereas the chromatin interaction was studied by analyzing the effects of the compounds on the structure of a peptide that mimicks the potential metal binding site in the "C-tail" region of histone H2A by means of NMR, CD, UV-Vis and MS. The intensities of the effects induced by the metal compounds on the peptide follow the order [Ni(tcitr)2] > [Pt(tcitr)2] ≫ [Cu(tcitr)2]. From the AFM data, a remarkable DNA compaction was observed in the presence of [Pt(tcitr)2], while [Ni(tcitr)2] causes the formation of large interlaced DNA aggregates.
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Affiliation(s)
- Franco Bisceglie
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/a, 43124 Parma, Italy.
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22
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Tessaro F, Scapozza L. How 'Protein-Docking' Translates into the New Emerging Field of Docking Small Molecules to Nucleic Acids? Molecules 2020; 25:E2749. [PMID: 32545835 PMCID: PMC7355999 DOI: 10.3390/molecules25122749] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 06/05/2020] [Accepted: 06/11/2020] [Indexed: 11/16/2022] Open
Abstract
In this review, we retraced the '40-year evolution' of molecular docking algorithms. Over the course of the years, their development allowed to progress from the so-called 'rigid-docking' searching methods to the more sophisticated 'semi-flexible' and 'flexible docking' algorithms. Together with the advancement of computing architecture and power, molecular docking's applications also exponentially increased, from a single-ligand binding calculation to large screening and polypharmacology profiles. Recently targeting nucleic acids with small molecules has emerged as a valuable therapeutic strategy especially for cancer treatment, along with bacterial and viral infections. For example, therapeutic intervention at the mRNA level allows to overcome the problematic of undruggable proteins without modifying the genome. Despite the promising therapeutic potential of nucleic acids, molecular docking programs have been optimized mostly for proteins. Here, we have analyzed literature data on nucleic acid to benchmark some of the widely used docking programs. Finally, the comparison between proteins and nucleic acid targets docking highlighted similarity and differences, which are intrinsically related to their chemical and structural nature.
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Affiliation(s)
- Francesca Tessaro
- Pharmaceutical Biochemistry, School of Pharmaceutical Sciences, University of Geneva CMU, Rue Michel-Servet 1, 1211 Geneva 4, Switzerland;
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, 1211 Geneva, Switzerland
| | - Leonardo Scapozza
- Pharmaceutical Biochemistry, School of Pharmaceutical Sciences, University of Geneva CMU, Rue Michel-Servet 1, 1211 Geneva 4, Switzerland;
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, 1211 Geneva, Switzerland
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23
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Ballı Z, Arslantaş A, Güngördü Solǧun D, Ağırtaş MS. DNA binding studies of the 2,10,16,24–tetrakis (phenoxy-3-methoxybenzoic acid)phthalocyaninato) Co(II) and Cu(II) compounds. SN APPLIED SCIENCES 2020. [DOI: 10.1007/s42452-020-2640-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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24
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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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25
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Gritzapis PS, Varras PC, Andreou NP, Katsani KR, Dafnopoulos K, Psomas G, Peitsinis ZV, Koumbis AE, Fylaktakidou KC. p-Pyridinyl oxime carbamates: synthesis, DNA binding, DNA photocleaving activity and theoretical photodegradation studies. Beilstein J Org Chem 2020; 16:337-350. [PMID: 32256851 PMCID: PMC7082612 DOI: 10.3762/bjoc.16.33] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 02/19/2020] [Indexed: 12/23/2022] Open
Abstract
A number of p-pyridinyl oxime carbamate derivatives were prepared upon the reaction of the corresponding oximes with isocyanates. These novel compounds reacted photochemically in the presence of supercoiled plasmid DNA. Structure-activity relationship (SAR) studies revealed that the substituent on the imine group was not affecting the extend of the DNA damage, whereas the substituent of the carbamate group was critical, with the halogenated derivatives to be able to cause extensive single and double stranded DNA cleavages, acting as "synthetic nucleases", independently of oxygen and pH. Calf thymus-DNA affinity studies showed a good-to-excellent affinity of selected both active and non-active derivatives. Preliminary theoretical studies were performed, in an effort to explain the reasons why some derivatives cause photocleavage and some others not, which were experimentally verified using triplet state activators and quenchers. These theoretical studies seem to allow the prediction of the activity of derivatives able to pass intersystem crossing to their triplet energy state and thus create radicals able to damage DNA. With this study, it is shown that oxime carbamate derivatives have the potential to act as novel effective photobase generating DNA-photocleavers, and are proposed as new leads for "on demand" biotechnological applications in drug discovery and medicine.
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Affiliation(s)
- Panagiotis S Gritzapis
- Laboratory of Organic, Bioorganic and Natural Product Chemistry, Molecular Biology and Genetics Department, Democritus University of Thrace, University Campus, Dragana, 68100, Alexandroupolis, Greece
| | - Panayiotis C Varras
- Laboratory of Organic, Bioorganic and Natural Product Chemistry, Molecular Biology and Genetics Department, Democritus University of Thrace, University Campus, Dragana, 68100, Alexandroupolis, Greece
| | - Nikolaos-Panagiotis Andreou
- Laboratory of Organic, Bioorganic and Natural Product Chemistry, Molecular Biology and Genetics Department, Democritus University of Thrace, University Campus, Dragana, 68100, Alexandroupolis, Greece
| | - Katerina R Katsani
- Laboratory of Biochemistry and Molecular Virology, Molecular Biology and Genetics Department, Democritus University of Thrace, University Campus, Dragana, 68100, Alexandroupolis, Greece
| | - Konstantinos Dafnopoulos
- Laboratory of Organic, Bioorganic and Natural Product Chemistry, Molecular Biology and Genetics Department, Democritus University of Thrace, University Campus, Dragana, 68100, Alexandroupolis, Greece
- Laboratory of Inorganic Chemistry, Chemistry Department, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - George Psomas
- Laboratory of Inorganic Chemistry, Chemistry Department, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Zisis V Peitsinis
- Laboratory of Organic Chemistry, Chemistry Department, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Alexandros E Koumbis
- Laboratory of Organic Chemistry, Chemistry Department, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Konstantina C Fylaktakidou
- Laboratory of Organic, Bioorganic and Natural Product Chemistry, Molecular Biology and Genetics Department, Democritus University of Thrace, University Campus, Dragana, 68100, Alexandroupolis, Greece
- Laboratory of Organic Chemistry, Chemistry Department, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
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26
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Nguyen TM, Nakata E, Zhang Z, Saimura M, Dinh H, Morii T. Rational design of a DNA sequence-specific modular protein tag by tuning the alkylation kinetics. Chem Sci 2019; 10:9315-9325. [PMID: 32110294 PMCID: PMC7006624 DOI: 10.1039/c9sc02990g] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 08/19/2019] [Indexed: 01/03/2023] Open
Abstract
Sequence-selective chemical modification of DNA by synthetic ligands has been a long-standing challenge in the field of chemistry. Even when the ligand consists of a sequence-specific DNA binding domain and reactive group, sequence-selective reactions by these ligands are often accompanied by off-target reactions. A basic principle to design DNA modifiers that react at specific sites exclusively governed by DNA sequence recognition remains to be established. We have previously reported selective DNA modification by a self-ligating protein tag conjugated with a DNA-binding domain, termed as a modular adaptor, and orthogonal application of modular adaptors by relying on the chemoselectivity of the protein tag. The sequence-specific crosslinking reaction by the modular adaptor is thought to proceed in two steps: the first step involves the formation of a DNA-protein complex, while in the second step, a proximity-driven intermolecular crosslinking occurs. According to this scheme, the specific crosslinking reaction of a modular adaptor would be driven by the DNA recognition process only when the dissociation rate of the DNA complex is much higher than the rate constant for the alkylation reaction. In this study, as a proof of principle, a set of combinations for modular adaptors and their substrates were utilized to evaluate the reactions. Three types of modular adaptors consisting of a single type of self-ligating tag and three types of DNA binding proteins fulfill the kinetic requirements for the reaction of the self-ligating tag with a substrate and the dissociation of the DNA-protein complex. These modular adaptors actually undergo sequence-specific crosslinking reactions exclusively driven by the recognition of a specific DNA sequence. The design principle of sequence-specific modular adaptors based on the kinetic aspects of complex formation and chemical modification is applicable for developing recognition-driven selective modifiers for proteins and other biological macromolecules.
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Affiliation(s)
- Thang Minh Nguyen
- Institute of Advanced Energy , Kyoto University , Uji , Kyoto 611-0011 , Japan .
| | - Eiji Nakata
- Institute of Advanced Energy , Kyoto University , Uji , Kyoto 611-0011 , Japan .
| | - Zhengxiao Zhang
- Institute of Advanced Energy , Kyoto University , Uji , Kyoto 611-0011 , Japan .
| | - Masayuki Saimura
- Institute of Advanced Energy , Kyoto University , Uji , Kyoto 611-0011 , Japan .
| | - Huyen Dinh
- Institute of Advanced Energy , Kyoto University , Uji , Kyoto 611-0011 , Japan .
| | - Takashi Morii
- Institute of Advanced Energy , Kyoto University , Uji , Kyoto 611-0011 , Japan .
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27
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Nakano SI, Ayusawa T, Tanino Y, Sugimoto N. Stabilization of DNA Loop Structures by Large Cations. J Phys Chem B 2019; 123:7687-7694. [PMID: 31465227 DOI: 10.1021/acs.jpcb.9b06074] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The DNA-binding properties of large cations differ from those of metal ions due to steric exclusion from base-paired regions. In this study, the thermal stability of DNA secondary structures, including duplexes, internal loops, bulge loops, hairpin loops, dangling ends, and G-quadruplexes, was investigated in the presence of cations of different sizes. Large cations, such as tetrabutylammonium and tetrapentylammonium ions, reduced the stability of fully matched duplexes but increased the stability of duplexes with a long loop. The cations also increased the stability of G-quadruplexes with a long loop, and the degree of stabilization was greater for low-stability G-quadruplexes. Analysis of the salt concentration dependence indicates that large cations bind to the loop nucleotides, leading to counteracting the destabilization effect on base pairing. It is likely that binding occurs when loop nucleotides are sufficiently flexible to allow for greater accessibility for large cations. These results provide insight into nucleic acid interactions with large cationic molecules and suggest a potential method for stabilizing noncanonical DNA structures under intracellular conditions.
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Affiliation(s)
- Shu-Ichi Nakano
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST) , Konan University , 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe , 650-0047 , Japan
| | - Toshiya Ayusawa
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST) , Konan University , 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe , 650-0047 , Japan
| | - Yuichi Tanino
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST) , Konan University , 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe , 650-0047 , Japan
| | - Naoki Sugimoto
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST) , Konan University , 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe , 650-0047 , Japan.,Frontier Institute for Biomolecular Engineering Research (FIBER) , Konan University , 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe , 650-0047 , Japan
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28
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Das AK, Ihmels H, Kölsch S. Diphenylaminostyryl-substituted quinolizinium derivatives as fluorescent light-up probes for duplex and quadruplex DNA. Photochem Photobiol Sci 2019; 18:1373-1381. [PMID: 30916703 DOI: 10.1039/c9pp00096h] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
(E)-2-[1'-((Diphenylamino)styryl)quinolizinium (3a) and 2,2'-{(phenylimino)-bis[(E)-1'',1'''-styryl]}-bis[quinolizinium] (3b) were synthesized, and their interactions with duplex DNA and quadruplex DNA were investigated with a particular focus on their ability to operate as DNA-sensitive fluorescent probes. Due to the significantly different size and steric demand of these quinolizinium derivatives they exhibit different binding modes. Thus, 3a intercalates into duplex DNA and binds through π stacking to quadruplex DNA, whereas 3b favours groove binding to both DNA forms. The emission intensity of these compounds is very low in aqueous solution, but it increases drastically upon association with duplex DNA by a factor of 11 (3a) and >100 (3b) and with quadruplex DNA by a factor of >100 (3a) and 10 (3b), with emission bands between 600 and 750 nm.
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Affiliation(s)
- Avijit Kumar Das
- Department of Chemistry and Biology, University of Siegen, Center of Micro- and Nanochemistry and Engineering, Adolf-Reichwein-Str. 2, 57068 Siegen, Germany.
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29
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Sumran G, Aggarwal R, Mittal A, Aggarwal A, Gupta A. Design, synthesis and photoinduced DNA cleavage studies of [1,2,4]-triazolo[4,3-a]quinoxalin-4(5H)-ones. Bioorg Chem 2019; 88:102932. [DOI: 10.1016/j.bioorg.2019.102932] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 03/20/2019] [Accepted: 04/15/2019] [Indexed: 12/19/2022]
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30
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Ihmels H, Karbasiyoun M, Löhl K, Stremmel C. Structural flexibility versus rigidity of the aromatic unit of DNA ligands: binding of aza- and azoniastilbene derivatives to duplex and quadruplex DNA. Org Biomol Chem 2019; 17:6404-6413. [PMID: 31225566 DOI: 10.1039/c9ob00809h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The known azastilbene (E)-1,2-di(quinolin-3-yl)ethane (2a) and the novel azoniastilbene derivatives (E)-2-(2-(naphthalen-2-yl)vinyl)quinolizinium (2b) and (E)-3,3'-(ethane-1,2-diyl)bis(1-methylquinolinin-1-ium) (2c) were synthesized. Their interactions with duplex and quadruplex DNA (G4-DNA) were studied by photometric, fluorimetric, polarimetric and flow-LD analysis, and by thermal DNA denaturation studies, as well as by 1H-NMR spectroscopy. The main goal of this study was a comparison of these conformationally flexible compounds with the known G4-DNA-binding diazoniadibenzo[b,k]chrysenes, that have a comparable π-system extent, but a rigid structure. We have observed that the aza- and azoniastilbene derivatives 2a-c, i.e. compounds with almost the same spatial dimensions and steric demand, bind to DNA with an affinity and selectivity that depends significantly on the number of positive charges. Whereas the charge neutral derivative 2a binds unspecifically to the DNA backbone of duplex DNA, the ionic compounds 2b and 2c are typical DNA intercalators. Notably, the bis-quinolinium derivative 2c binds to G4-DNA with moderate affinity (Kb = 4.8 × 105 M-1) and also stabilizes the G4-DNA towards thermal denaturation (ΔTm = 11 °C at ligand-DNA ratio = 5.0). Strikingly, the corresponding rigid counterpart, 4a,12a-diazonia-8,16-dimethyldibenzo[b,k]chrysene, stabilizes the G4-DNA to an even greater extent under identical conditions (ΔTm = 27 °C). These results indicate that the increased flexibility of a G4-DNA ligand does not necessarily lead to stronger interactions with the G4-DNA as compared with rigid ligands that have essentially the same size and π system extent.
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Affiliation(s)
- H Ihmels
- Department of Chemistry and Biology, University of Siegen, Adolf-Reichwein-Str. 2, 57068 Siegen, Germany.
| | - M Karbasiyoun
- Department of Chemistry and Biology, University of Siegen, Adolf-Reichwein-Str. 2, 57068 Siegen, Germany.
| | - K Löhl
- Department of Chemistry and Biology, University of Siegen, Adolf-Reichwein-Str. 2, 57068 Siegen, Germany.
| | - C Stremmel
- Department of Chemistry and Biology, University of Siegen, Adolf-Reichwein-Str. 2, 57068 Siegen, Germany.
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31
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Dai P, He Y, Luo G, Deng J, Jiang N, Fang T, Li Y, Cheng Y. Screening candidate microRNA-mRNA network for predicting the response to chemoresistance in osteosarcoma by bioinformatics analysis. J Cell Biochem 2019; 120:16798-16810. [PMID: 31090103 DOI: 10.1002/jcb.28938] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 03/16/2019] [Accepted: 03/22/2019] [Indexed: 01/16/2023]
Abstract
The search for biomarkers is important for providing more targeted treatments for osteosarcoma patients with chemoresistance. In this study, differentially expressed microRNAs (miRNAs) were identified from miRNA expression profiles. And the target messenger RNAs (mRNAs) of miRNA were obtained from two websites in public domains. Analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway by these miRNA targets suggests that they may have potential links to osteosarcoma chemoresistance. In the protein-protein interaction (PPI) network, we screened three subnetworks and 10 hub RNAs, and analyzed through KEGG pathway and searched the PubMed database, indicating that they were significantly associated with drug resistance. Then we found 12 key mRNAs by analyzing the mRNA expression profile. Survival analyses showed that most of the 10 hub mRNAs and 12 key mRNAs had a significant influence on the prognosis of patients with chemoresistance osteosarcoma. A miRNA-mRNA network is constructed by integrating mRNAs and miRNAs information. The network biomarkers in this study have an advantage over traditional single-molecule biomarkers in terms of predictive power. And the mRNAs in this network biomarkers are supported by survival analysis or by existing theories. These results will contribute to the choice of chemotherapy before treatment and the prediction of patient prognosis.
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Affiliation(s)
- Penggao Dai
- College of Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan, China
| | - Yancheng He
- College of Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan, China
| | - Guosong Luo
- Department of Health Management, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Jiaqi Deng
- Department of Ultrasound Medicine, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Nan Jiang
- College of Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan, China
| | - Tingting Fang
- College of Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan, China
| | - Yujuan Li
- Department of Health Management, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Ying Cheng
- College of Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan, China
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32
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Hassan AA, Aly AA, Mohamed NK, El Shaieb KM, Makhlouf MM, Abdelhafez ESMN, Bräse S, Nieger M, Dalby KN, Kaoud TS. Design, synthesis, and DNA interaction studies of furo-imidazo[3.3.3]propellane derivatives: Potential anticancer agents. Bioorg Chem 2019; 85:585-599. [PMID: 30878891 PMCID: PMC6543821 DOI: 10.1016/j.bioorg.2019.02.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 02/10/2019] [Accepted: 02/11/2019] [Indexed: 11/26/2022]
Abstract
A large number of natural products containing the propellane scaffold have been reported to exhibit cytotoxicity against several cancers; however, their mechanism of action is still unknown. Anticancer drugs targeting DNA are mainly composed of small planar molecule/s that can interact with the DNA helix, causing DNA malfunction and cell death. The aim of this study was to design and synthesize propellane derivatives that can act as DNA intercalators and/or groove binders. The unique structure of the propellane derivatives and their ability to display planar ligands with numerous possible geometries, renders them potential starting points to design new drugs targeting DNA in cancer cells. New substituted furo-imidazo[3.3.3]propellanes were synthesized via the reaction of substituted alkenylidene-hydrazinecarbothioamides with 2-(1,3-dioxo-2,3-dihydro-1H-2-ylidene)propanedinitrile in tetrahydrofuran at room temperature. The structures of the products were confirmed by a combination of elemental analysis, NMR, ESI-MS, IR and single crystal X-ray analysis. Interestingly, 5c, 5d and 5f showed an ability to interact with Calf Thymus DNA (CT-DNA). Their DNA-binding mode was investigated using a combination of absorption spectroscopy, DNA melting, viscosity, CD spectroscopy measurements, as well as competitive binding studies with several dyes. Their cytotoxicity was evaluated against the NCI-60 panel of cancer cell lines. 5c, 5d and 5f exhibited similar anti-proliferative activity against the A549 non-small cell lung cancer (NSCLC) cell line. Further mechanistic studies revealed their ability to induce DNA damage in the A549 cell line, as well as apoptosis, evidenced by elevated Annexin V expression, enhanced caspase 3/7 activation and PARP cleavage. In this study, we present the potential for designing novel propellanes to provoke cytotoxic activity, likely through DNA binding-induced DNA damage and apoptosis.
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Affiliation(s)
- Alaa A Hassan
- Chemistry Department, Faculty of Science, Minia University, El-Minia 61519, Egypt.
| | - Ashraf A Aly
- Chemistry Department, Faculty of Science, Minia University, El-Minia 61519, Egypt
| | - Nasr K Mohamed
- Chemistry Department, Faculty of Science, Minia University, El-Minia 61519, Egypt
| | - Kamal M El Shaieb
- Chemistry Department, Faculty of Science, Minia University, El-Minia 61519, Egypt
| | - Maysa M Makhlouf
- Chemistry Department, Faculty of Science, Minia University, El-Minia 61519, Egypt
| | | | - Stefan Bräse
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, Karlsruhe 76131, Germany; Institute of Toxicology and Genetics, Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany
| | - Martin Nieger
- Department of Chemistry, University of Helsinki, P.O. Box 55, A.I. Virtasen aukio I, Helsinki 00014, Finland
| | - Kevin N Dalby
- Division of Chemical Biology and Medicinal Chemistry, The University of Texas at Austin, Austin, TX 78712, USA
| | - Tamer S Kaoud
- Department of Medicinal Chemistry, Faculty of Pharmacy, Minia University, El-Minia 61519, Egypt; Division of Chemical Biology and Medicinal Chemistry, The University of Texas at Austin, Austin, TX 78712, USA.
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33
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Salerno S, La Pietra V, Hyeraci M, Taliani S, Robello M, Barresi E, Milite C, Simorini F, García-Argáez AN, Marinelli L, Novellino E, Da Settimo F, Marini AM, Dalla Via L. Benzothiopyranoindole- and pyridothiopyranoindole-based antiproliferative agents targeting topoisomerases. Eur J Med Chem 2019; 165:46-58. [PMID: 30660826 DOI: 10.1016/j.ejmech.2019.01.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 12/21/2018] [Accepted: 01/07/2019] [Indexed: 11/20/2022]
Abstract
New benzothiopyranoindoles (5a-l) and pyridothiopyranoindoles (5m-t), featuring different combinations of substituents (H, Cl, OCH3) at R2-R4 positions and protonatable R1-dialkylaminoalkyl chains, were synthesized and biologically assayed on three human tumor cell lines, showing significant antiproliferative activity (GI50 values spanning from 0.31 to 6.93 μM) and pro-apoptotic effect. Linear flow dichroism experiments indicate the ability of both chromophores to form a molecular complex with DNA, following an intercalative mode of binding. All compounds displayed a moderate ability to inhibit the relaxation activity of both topoisomerases I and II, reasonably correlated to their intercalative capacities. Cleavable assay performed with topoisomerase I revealed a significant poisoning effect for compounds 5g, 5h, 5s, and 5t. A theoretical model provided by hydrated docking calculations clarified the role of the R1-R4 substituents on the topoisomerase I poison activity, revealing a crucial role of the R2-OCH3 group.
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Affiliation(s)
- Silvia Salerno
- Dipartimento di Farmacia, Università di Pisa, Via Bonanno 6, 56126, Pisa, Italy
| | - Valeria La Pietra
- Dipartimento di Farmacia, Università di Napoli "Federico II", Via D. Montesano 49, 80131, Napoli, Italy
| | - Mariafrancesca Hyeraci
- Dipartimento di Scienze del Farmaco, Università di Padova, Via Marzolo 5, 35131, Padova, Italy
| | - Sabrina Taliani
- Dipartimento di Farmacia, Università di Pisa, Via Bonanno 6, 56126, Pisa, Italy.
| | - Marco Robello
- Synthetic Bioactive Molecules Section LBC, NIDDK, NIH, 8 Center Dr., 20982, Bethesda, MD, USA
| | - Elisabetta Barresi
- Dipartimento di Farmacia, Università di Pisa, Via Bonanno 6, 56126, Pisa, Italy
| | - Ciro Milite
- Dipartimento di Farmacia, Università di Salerno, Via Giovanni Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Francesca Simorini
- Dipartimento di Farmacia, Università di Pisa, Via Bonanno 6, 56126, Pisa, Italy
| | - Aída Nelly García-Argáez
- Dipartimento di Scienze del Farmaco, Università di Padova, Via Marzolo 5, 35131, Padova, Italy; Fondazione per la Biologia e la Medicina della Rigenerazione T.E.S., Via Marzolo 13, 35131, Padova, Italy
| | - Luciana Marinelli
- Dipartimento di Farmacia, Università di Napoli "Federico II", Via D. Montesano 49, 80131, Napoli, Italy.
| | - Ettore Novellino
- Dipartimento di Farmacia, Università di Napoli "Federico II", Via D. Montesano 49, 80131, Napoli, Italy
| | - Federico Da Settimo
- Dipartimento di Farmacia, Università di Pisa, Via Bonanno 6, 56126, Pisa, Italy
| | - Anna Maria Marini
- Dipartimento di Farmacia, Università di Pisa, Via Bonanno 6, 56126, Pisa, Italy
| | - Lisa Dalla Via
- Dipartimento di Scienze del Farmaco, Università di Padova, Via Marzolo 5, 35131, Padova, Italy
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34
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Arciszewska K, Pućkowska A, Wróbel A, Drozdowska D. Carbocyclic Analogues of Distamycin and Netropsin. Mini Rev Med Chem 2019; 19:98-113. [PMID: 30626311 DOI: 10.2174/1389557518666181009143203] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 07/02/2018] [Accepted: 07/04/2018] [Indexed: 11/22/2022]
Abstract
The DNA as the depository of genetic information is a natural target for chemotherapy. A lot of anticancer and antimicrobial agents derive their biological activity from their selective interaction with DNA in the minor groove and from their ability to interfere with biological processes such as enzyme catalysis, replication and transcription. The discovery of the details of minor groove binding drugs, such as netropsin and distamycin A, oligoamides built of 4-amino-1-methylpyrrole-2-carboxylic acid residues, allowed to develop various DNA sequence-reading molecules, named lexitropsins, capable of interacting with DNA precisely, strongly and with a high specificity, and at the same time exhibiting significant cytotoxic potential. Among such compounds, lexitropsins built of carbocyclic sixmembered aromatic rings occupy a quite prominent place in drug research. This work is an attempt to present current findings in the study of carbocyclic lexitropins, their structures, syntheses and biological investigations such as DNA-binding and antiproliferative activity.
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Affiliation(s)
| | - Anna Pućkowska
- Department of Organic Chemistry, Medical University, Bialystok 15-222, Mickiewicza Street 2c, Poland
| | - Agnieszka Wróbel
- Department of Organic Chemistry, Medical University, Bialystok 15-222, Mickiewicza Street 2c, Poland
| | - Danuta Drozdowska
- Department of Organic Chemistry, Medical University, Bialystok 15-222, Mickiewicza Street 2c, Poland
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35
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Sedghi Masoud S, Nagasawa K. i-Motif-Binding Ligands and Their Effects on the Structure and Biological Functions of i-Motif. Chem Pharm Bull (Tokyo) 2018; 66:1091-1103. [DOI: 10.1248/cpb.c18-00720] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Shadi Sedghi Masoud
- Department of Life Science and Biotechnology, Faculty of Technology, Tokyo University of Agriculture and Technology
| | - Kazuo Nagasawa
- Department of Life Science and Biotechnology, Faculty of Technology, Tokyo University of Agriculture and Technology
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36
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Sullivan HJ, Readmond C, Radicella C, Persad V, Fasano TJ, Wu C. Binding of Telomestatin, TMPyP4, BSU6037, and BRACO19 to a Telomeric G-Quadruplex-Duplex Hybrid Probed by All-Atom Molecular Dynamics Simulations with Explicit Solvent. ACS OMEGA 2018; 3:14788-14806. [PMID: 30555989 PMCID: PMC6289566 DOI: 10.1021/acsomega.8b01574] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Accepted: 09/11/2018] [Indexed: 06/09/2023]
Abstract
A promising anticancer therapeutic strategy is the stabilization of telomeric G-quadruplexes using G-quadruplex-binding small molecules. Although many G-quadruplex-specific ligands have been developed, their low potency and selectivity to G-quadruplexes over duplex remains unsolved. Recently, a crystal structure of a telomeric 3' quadruplex-duplex hybrid was reported and the quadruplex-duplex interface was suggested to a good target to address the issues. However, there are no high-resolution complex structures reported for G-quadruplex ligands except for a docked BSU6037. In this study, molecular dynamic (MD) binding simulations with a free ligand were used to study binding poses and dynamics of four representative ligands: telomestatin, TMPyP4, BSU6037, and BRACO19. The MD data showed that BSU6037 was able to fully intercalate into the interface whereas TMPyP4 and BRACO19 could only maintain partial intercalation into the interface and telomestatin only binds at the quadruplex and duplex ends. Both linear ligands, BSU6037 and BRACO19, were able to interact with the interface, yet they were not selective over duplex DNA. The DNA geometry, binding modes, and binding pathways were systematically characterized, and the binding energy was calculated and compared for each system. The interaction of the ligands to the interface was by the means of an induced-fit binding mechanism rather than a lock-key mechanism, consisting of the DNA unfolding at the interface to allow entrance of the drug and then the refolding and repacking of the DNA and the ligand to further stabilize the G-quadruplex. On the basis of the findings in this study, modifications were suggested to optimize the interface binding for TMPyp4 and telomestatin.
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Affiliation(s)
- Holli-Joi Sullivan
- Chemistry
& Biochemistry and Department of Molecular & Cellular Biosciences, College of Science and Mathematics, Rowan University, Glassboro, New Jersey 08028, United States
| | - Carolyn Readmond
- Chemistry
& Biochemistry and Department of Molecular & Cellular Biosciences, College of Science and Mathematics, Rowan University, Glassboro, New Jersey 08028, United States
| | - Christina Radicella
- Chemistry
& Biochemistry and Department of Molecular & Cellular Biosciences, College of Science and Mathematics, Rowan University, Glassboro, New Jersey 08028, United States
| | - Victoria Persad
- Chemistry
& Biochemistry and Department of Molecular & Cellular Biosciences, College of Science and Mathematics, Rowan University, Glassboro, New Jersey 08028, United States
| | - Thomas J. Fasano
- Chemistry
& Biochemistry and Department of Molecular & Cellular Biosciences, College of Science and Mathematics, Rowan University, Glassboro, New Jersey 08028, United States
| | - Chun Wu
- Chemistry
& Biochemistry and Department of Molecular & Cellular Biosciences, College of Science and Mathematics, Rowan University, Glassboro, New Jersey 08028, United States
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37
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Calabrese DR, Chen X, Leon EC, Gaikwad SM, Phyo Z, Hewitt WM, Alden S, Hilimire TA, He F, Michalowski AM, Simmons JK, Saunders LB, Zhang S, Connors D, Walters KJ, Mock BA, Schneekloth JS. Chemical and structural studies provide a mechanistic basis for recognition of the MYC G-quadruplex. Nat Commun 2018; 9:4229. [PMID: 30315240 PMCID: PMC6185959 DOI: 10.1038/s41467-018-06315-w] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 08/16/2018] [Indexed: 01/06/2023] Open
Abstract
G-quadruplexes (G4s) are noncanonical DNA structures that frequently occur in the promoter regions of oncogenes, such as MYC, and regulate gene expression. Although G4s are attractive therapeutic targets, ligands capable of discriminating between different G4 structures are rare. Here, we describe DC-34, a small molecule that potently downregulates MYC transcription in cancer cells by a G4-dependent mechanism. Inhibition by DC-34 is significantly greater for MYC than other G4-driven genes. We use chemical, biophysical, biological, and structural studies to demonstrate a molecular rationale for the recognition of the MYC G4. We solve the structure of the MYC G4 in complex with DC-34 by NMR spectroscopy and illustrate specific contacts responsible for affinity and selectivity. Modification of DC-34 reveals features required for G4 affinity, biological activity, and validates the derived NMR structure. This work advances the design of quadruplex-interacting small molecules to control gene expression in therapeutic areas such as cancer. Targeting noncoding nucleic acids with small molecules represents an important and significant challenge in chemical biology and drug discovery. Here the authors characterize DC-34, a small molecule that exhibits selective binding to specific G4 structures, and provide a structural basis for its selectivity
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Affiliation(s)
- David R Calabrese
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD, 21702, USA
| | - Xiang Chen
- Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD, 21702, USA
| | - Elena C Leon
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Snehal M Gaikwad
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Zaw Phyo
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - William M Hewitt
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD, 21702, USA
| | - Stephanie Alden
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD, 21702, USA
| | - Thomas A Hilimire
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD, 21702, USA
| | - Fahu He
- Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD, 21702, USA
| | | | - John K Simmons
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Lindsey B Saunders
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD, 21702, USA
| | - Shuling Zhang
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Daniel Connors
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Kylie J Walters
- Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD, 21702, USA.
| | - Beverly A Mock
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA.
| | - John S Schneekloth
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD, 21702, USA.
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38
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Tassinari M, Cimino-Reale G, Nadai M, Doria F, Butovskaya E, Recagni M, Freccero M, Zaffaroni N, Richter SN, Folini M. Down-Regulation of the Androgen Receptor by G-Quadruplex Ligands Sensitizes Castration-Resistant Prostate Cancer Cells to Enzalutamide. J Med Chem 2018; 61:8625-8638. [PMID: 30188709 DOI: 10.1021/acs.jmedchem.8b00502] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Stabilization of the G-quadruplexes (G4s) within the androgen receptor (AR) gene promoter to block transcription may represent an innovative approach to interfere with aberrant AR signaling in castration resistant prostate cancer (CRPC). A library of differently functionalized naphthalene diimides (NDIs) was screened for their ability to stabilize AR G4s: the core-extended NDI (7) stood out as the most promising ligand. AR-positive cells were remarkably sensitive to 7 in comparison to AR-negative CRCP or normal prostate epithelial cells; 7 induced remarkable impairment of AR mRNA and protein amounts and significant perturbations in the expression levels of KLK3 and of genes involved in the activation of AR program via feedback mechanisms. Moreover, 7 synergistically interacted with Enzalutamide, an inhibitor of AR signaling used in second-line therapies. Overall, our data show that stabilization of AR G4s may represent an alternative treatment options for CRPC and other malignancies relying on aberrant androgen signaling.
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Affiliation(s)
- Martina Tassinari
- Department of Molecular Medicine , University of Padua , via A. Gabelli 63 , 35121 Padua , Italy
| | - Graziella Cimino-Reale
- Department of Applied Research and Technological Development , Fondazione IRCCS Istituto Nazionale dei Tumori di Milano , Via G. A. Amadeo 42 , 20133 Milan , Italy
| | - Matteo Nadai
- Department of Molecular Medicine , University of Padua , via A. Gabelli 63 , 35121 Padua , Italy
| | - Filippo Doria
- Department of Chemistry , University of Pavia , v. le Taramelli 10 , 27100 , Pavia , Italy
| | - Elena Butovskaya
- Department of Molecular Medicine , University of Padua , via A. Gabelli 63 , 35121 Padua , Italy
| | - Marta Recagni
- Department of Applied Research and Technological Development , Fondazione IRCCS Istituto Nazionale dei Tumori di Milano , Via G. A. Amadeo 42 , 20133 Milan , Italy
| | - Mauro Freccero
- Department of Chemistry , University of Pavia , v. le Taramelli 10 , 27100 , Pavia , Italy
| | - Nadia Zaffaroni
- Department of Applied Research and Technological Development , Fondazione IRCCS Istituto Nazionale dei Tumori di Milano , Via G. A. Amadeo 42 , 20133 Milan , Italy
| | - Sara N Richter
- Department of Molecular Medicine , University of Padua , via A. Gabelli 63 , 35121 Padua , Italy
| | - Marco Folini
- Department of Applied Research and Technological Development , Fondazione IRCCS Istituto Nazionale dei Tumori di Milano , Via G. A. Amadeo 42 , 20133 Milan , Italy
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39
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Ghashghaei O, Caputo S, Sintes M, Revés M, Kielland N, Estarellas C, Luque FJ, Aviñó A, Eritja R, Serna-Gallego A, Marrugal-Lorenzo JA, Pachón J, Sánchez-Céspedes J, Treadwell R, de Moliner F, Vendrell M, Lavilla R. Multiple Multicomponent Reactions: Unexplored Substrates, Selective Processes, and Versatile Chemotypes in Biomedicine. Chemistry 2018; 24:14513-14521. [PMID: 29974986 DOI: 10.1002/chem.201802877] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 07/04/2018] [Indexed: 01/01/2023]
Abstract
Multiple multicomponent reactions rapidly assemble complex structures. Despite being very productive, the lack of selectivity and the reduced number of viable transformations restrict their general application in synthesis. Hereby, we describe a rationale for a selective version of these processes based in the preferential generation of intermediates which are less reactive than the initial substrates. In this way, applying the Groebke-Blackburn-Bienaymé reaction on a range of α-polyamino-polyazines, we prepared a family compact heterocyclic scaffolds with relevant applications in medicinal and biological chemistry (live cell imaging probes, selective binders for DNA quadruplexes, and antiviral agents against human adenoviruses). The approach has general character and yields complex molecular targets in a selective, tunable and direct manner.
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Affiliation(s)
- Ouldouz Ghashghaei
- Laboratory of Medicinal Chemistry, Faculty of Pharmacy and Institute of, Biomedicine (IBUB), University of Barcelona, Barcelona Science Park, Baldiri Reixac 10-12, Barcelona, 08028, Spain.,CIBER-BBN, Networking Centre for Bioengineering, Biomaterials & Nanomedicine, Baldiri Reixac 10-12, Barcelona, 08028, Spain
| | - Samantha Caputo
- Laboratory of Medicinal Chemistry, Faculty of Pharmacy and Institute of, Biomedicine (IBUB), University of Barcelona, Barcelona Science Park, Baldiri Reixac 10-12, Barcelona, 08028, Spain.,CIBER-BBN, Networking Centre for Bioengineering, Biomaterials & Nanomedicine, Baldiri Reixac 10-12, Barcelona, 08028, Spain
| | - Miquel Sintes
- Laboratory of Medicinal Chemistry, Faculty of Pharmacy and Institute of, Biomedicine (IBUB), University of Barcelona, Barcelona Science Park, Baldiri Reixac 10-12, Barcelona, 08028, Spain.,CIBER-BBN, Networking Centre for Bioengineering, Biomaterials & Nanomedicine, Baldiri Reixac 10-12, Barcelona, 08028, Spain
| | - Marc Revés
- Laboratory of Medicinal Chemistry, Faculty of Pharmacy and Institute of, Biomedicine (IBUB), University of Barcelona, Barcelona Science Park, Baldiri Reixac 10-12, Barcelona, 08028, Spain.,CIBER-BBN, Networking Centre for Bioengineering, Biomaterials & Nanomedicine, Baldiri Reixac 10-12, Barcelona, 08028, Spain
| | - Nicola Kielland
- Laboratory of Medicinal Chemistry, Faculty of Pharmacy and Institute of, Biomedicine (IBUB), University of Barcelona, Barcelona Science Park, Baldiri Reixac 10-12, Barcelona, 08028, Spain.,CIBER-BBN, Networking Centre for Bioengineering, Biomaterials & Nanomedicine, Baldiri Reixac 10-12, Barcelona, 08028, Spain
| | - Carolina Estarellas
- Departament de Fisicoquímica, Facultat de Farmàcia, and IBUB, Universitat de Barcelona, Prat de la Riba 171, 08921, Santa Coloma, de Gramenet, Spain
| | - F Javier Luque
- Departament de Fisicoquímica, Facultat de Farmàcia, and IBUB, Universitat de Barcelona, Prat de la Riba 171, 08921, Santa Coloma, de Gramenet, Spain
| | - Anna Aviñó
- Department of Chemical & Biomolecular Nanotechnology, Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, Jordi Girona 18-26, 08034-, Barcelona, Spain
| | - Ramón Eritja
- Department of Chemical & Biomolecular Nanotechnology, Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, Jordi Girona 18-26, 08034-, Barcelona, Spain
| | - Ana Serna-Gallego
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, University Hospital Virgen del Rocío/Institute of Biomedicine of, Seville (IBiS)/CSIC/, University of Seville, Spain
| | - José Antonio Marrugal-Lorenzo
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, University Hospital Virgen del Rocío/Institute of Biomedicine of, Seville (IBiS)/CSIC/, University of Seville, Spain
| | - Jerónimo Pachón
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, University Hospital Virgen del Rocío/, Institute of Biomedicine of Seville (IBiS)/CSIC/, University of Seville &, Department of Medicine, University of Seville, Seville, Spain
| | - Javier Sánchez-Céspedes
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, University Hospital Virgen del Rocío/, Institute of Biomedicine of Seville (IBiS)/CSIC/, University of Seville &, Department of Medicine, University of Seville, Seville, Spain
| | - Ryan Treadwell
- MRC/UoE Centre for Inflammation Research, The University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Fabio de Moliner
- MRC/UoE Centre for Inflammation Research, The University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Marc Vendrell
- MRC/UoE Centre for Inflammation Research, The University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Rodolfo Lavilla
- Laboratory of Medicinal Chemistry, Faculty of Pharmacy and Institute of, Biomedicine (IBUB), University of Barcelona, Barcelona Science Park, Baldiri Reixac 10-12, Barcelona, 08028, Spain.,CIBER-BBN, Networking Centre for Bioengineering, Biomaterials & Nanomedicine, Baldiri Reixac 10-12, Barcelona, 08028, Spain
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40
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Wu C, Wang W, Fang L, Su W. Programmable pyrrole-imidazole polyamides: A potent tool for DNA targeting. CHINESE CHEM LETT 2018. [DOI: 10.1016/j.cclet.2018.05.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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41
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Rakers V, Cadinu P, Edel JB, Vilar R. Development of microfluidic platforms for the synthesis of metal complexes and evaluation of their DNA affinity using online FRET melting assays. Chem Sci 2018; 9:3459-3469. [PMID: 29780475 PMCID: PMC5933291 DOI: 10.1039/c8sc00528a] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 02/28/2018] [Indexed: 11/21/2022] Open
Abstract
Guanine-rich DNA sequences can fold into quadruple-stranded structures known as G-quadruplexes. These structures have been proposed to play important biological roles and have been identified as potential drug targets. As a result, there is increasing interest in developing small molecules that can bind to G-quadruplexes. So far, these efforts have been mostly limited to conventional batch synthesis. Furthermore, no quick on-line method to assess new G-quadruplex binders has been developed. Herein, we report on two new microfluidic platforms to: (a) readily prepare G-quadruplex binders (based on metal complexes) in flow, quantitatively and without the need for purification before testing; (b) a microfluidic platform (based on FRET melting assays of DNA) that enables the real-time and on-line assessment of G-quadruplex binders in continuous flow.
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Affiliation(s)
- Viktoria Rakers
- Department of Chemistry , Imperial College London , London SW7 2AZ , UK . ;
- Institute of Chemical Biology , Imperial College London , London SW7 2AZ , UK
| | - Paolo Cadinu
- Department of Chemistry , Imperial College London , London SW7 2AZ , UK . ;
- Institute of Chemical Biology , Imperial College London , London SW7 2AZ , UK
| | - Joshua B Edel
- Department of Chemistry , Imperial College London , London SW7 2AZ , UK . ;
- Institute of Chemical Biology , Imperial College London , London SW7 2AZ , UK
| | - Ramon Vilar
- Department of Chemistry , Imperial College London , London SW7 2AZ , UK . ;
- Institute of Chemical Biology , Imperial College London , London SW7 2AZ , UK
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42
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43
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Ji L, Yang S, Li S, Liu S, Tang S, Liu Z, Meng X, Yu S. A novel triazolonaphthalimide induces apoptosis and inhibits tumor growth by targeting DNA and DNA-associated processes. Oncotarget 2018; 8:37394-37408. [PMID: 28445124 PMCID: PMC5514917 DOI: 10.18632/oncotarget.16962] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 03/27/2017] [Indexed: 12/28/2022] Open
Abstract
DNA and DNA-associated processes have been classes of the most important targets of chemotherapeutic drugs. As classic DNA intercalators and topoisomerase inhibitors, naphthalimides have been extensively investigated as potential anti-cancer drugs. We recently synthesized a novel series of triazolonaphthalimides with excellent anti-cancer activities. In the present study, one of the most potent triazolonaphthalimides, LSS-11, was investigated. LSS-11 bound to DNA in vitro and in cell mainly by minor groove binding and significantly increased the stability of DNA, which could be fundamental for the biological activities of LSS-11. In addition to inhibiting DNA topoisomerase II-catalyzed decatenation of knotted circulated DNA, LSS-11 dramatically inhibited DNA replication mediated by polymerase chain reaction and isothermal helicase-dependent amplification, as well as the expression of luciferase driven by a minimal TA promoter in cell. Furthermore, LSS-11 exhibited strong cytotoxicity in selected human colon cancer cell lines by inducing cell cycle arrest and apoptosis, which was accompanied by DNA damage response. Finally, LSS-11 potently inhibited the growth of S180 murine sarcoma and SW480 human colorectal cancer xenografts in vivo without significant major toxicities. These results suggest that LSS-11 deserves further research and development as a novel anti-cancer agent, and provided new understandings of mechanisms by which LSS-11 inhibited multiple DNA-associated processes and tumor growth.
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Affiliation(s)
- Liyan Ji
- Department of Chemical Biology, Peking University School of Pharmaceutical Sciences, Beijing 100191, China.,International Institute for Translational Chinese Medicine, Guangzhou Traditional Chinese Medicine University, Guangzhou 510006, China
| | - Simin Yang
- Department of Chemical Biology, Peking University School of Pharmaceutical Sciences, Beijing 100191, China
| | - Shasha Li
- Department of Chemical Biology, Peking University School of Pharmaceutical Sciences, Beijing 100191, China
| | - Shan Liu
- Department of Chemical Biology, Peking University School of Pharmaceutical Sciences, Beijing 100191, China
| | - Shunan Tang
- Department of Chemical Biology, Peking University School of Pharmaceutical Sciences, Beijing 100191, China
| | - Zhongqiu Liu
- International Institute for Translational Chinese Medicine, Guangzhou Traditional Chinese Medicine University, Guangzhou 510006, China
| | - Xiangbao Meng
- Department of Chemical Biology, Peking University School of Pharmaceutical Sciences, Beijing 100191, China
| | - Siwang Yu
- Department of Chemical Biology, Peking University School of Pharmaceutical Sciences, Beijing 100191, China
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44
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Iodine mediated pyrazolo-quinoline derivatives as potent anti-proliferative agents. Bioorg Med Chem Lett 2018; 28:664-667. [DOI: 10.1016/j.bmcl.2018.01.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 01/02/2018] [Accepted: 01/15/2018] [Indexed: 01/04/2023]
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45
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Ali A, Kamra M, Bhan A, Mandal SS, Bhattacharya S. New Fe(iii) and Co(ii) salen complexes with pendant distamycins: selective targeting of cancer cells by DNA damage and mitochondrial pathways. Dalton Trans 2018; 45:9345-53. [PMID: 27186601 DOI: 10.1039/c5dt04374c] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Minor groove binding distamycin like moieties were conjugated with core salens and the corresponding Fe(iii) and Co(ii) complexes were synthesized. Herein, we have shown efficient DNA minor groove binding specificities along with excellent DNA cleavage capacities with metallosalen conjugates. The metal complexes showed toxicity toward various cancer cells over normal cells with high specificity. Interestingly, the Co(ii) complexes exhibited greater activity than the Fe(iii) complexes in accordance with the stronger affinity of the former in the biophysical studies. Active DNA damage, and prominent nuclear condensation along with the release of cytochrome-c from the mitochondria unanimously showed that the metal complexes followed apoptotic pathways to induce cell death.
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Affiliation(s)
- Asfa Ali
- Department of Organic Chemistry, Indian Institute of Science, Bangalore 560 012, India
| | - Mohini Kamra
- Department of Organic Chemistry, Indian Institute of Science, Bangalore 560 012, India
| | - Arunoday Bhan
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX 76019, USA
| | - Subhrangsu S Mandal
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX 76019, USA
| | - Santanu Bhattacharya
- Department of Organic Chemistry, Indian Institute of Science, Bangalore 560 012, India and Indian Association for the Cultivation of Science, Kolkata, West Bengal 700 032, India.
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46
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Varrica MG, Zagni C, Mineo PG, Floresta G, Monciino G, Pistarà V, Abbadessa A, Nicosia A, Castilho RM, Amata E, Rescifina A. DNA intercalators based on (1,10-phenanthrolin-2-yl)isoxazolidin-5-yl core with better growth inhibition and selectivity than cisplatin upon head and neck squamous cells carcinoma. Eur J Med Chem 2018; 143:583-590. [DOI: 10.1016/j.ejmech.2017.11.067] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 11/22/2017] [Accepted: 11/24/2017] [Indexed: 02/04/2023]
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47
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Ihmels H, Löhl K, Paululat T, Uebach S. NMR-spectroscopic investigation of the complex between tetraazoniapentapheno[6,7-h]pentaphene and quadruplex DNA Tel26. NEW J CHEM 2018. [DOI: 10.1039/c8nj01931b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The tetraazoniapentapheno[6,7-h]pentaphene binds to the hybrid-1 quadruplex structure of the oligonucleotide Tel26 by terminal π stacking, likely on top of the A3–A9–A21 triplet.
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Affiliation(s)
- Heiko Ihmels
- Department of Chemistry and Biology
- University of Siegen
- Siegen 57068
- Germany
| | - Katharina Löhl
- Department of Chemistry and Biology
- University of Siegen
- Siegen 57068
- Germany
| | - Thomas Paululat
- Department of Chemistry and Biology
- University of Siegen
- Siegen 57068
- Germany
| | - Sandra Uebach
- Department of Chemistry and Biology
- University of Siegen
- Siegen 57068
- Germany
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48
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de Almeida SMV, Ribeiro AG, de Lima Silva GC, Ferreira Alves JE, Beltrão EIC, de Oliveira JF, de Carvalho LB, Alves de Lima MDC. DNA binding and Topoisomerase inhibition: How can these mechanisms be explored to design more specific anticancer agents? Biomed Pharmacother 2017; 96:1538-1556. [DOI: 10.1016/j.biopha.2017.11.054] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 11/07/2017] [Accepted: 11/07/2017] [Indexed: 12/11/2022] Open
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49
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Boga S, Bouzada D, García Peña D, Vázquez López M, Vázquez ME. Sequence-Specific DNA Recognition with Designed Peptides. European J Org Chem 2017. [DOI: 10.1002/ejoc.201700988] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Sonia Boga
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica; Universidade de Santiago de Compostela; 15782 Santiago de Compostela Spain
| | - David Bouzada
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica; Universidade de Santiago de Compostela; 15782 Santiago de Compostela Spain
| | - Diego García Peña
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica; Universidade de Santiago de Compostela; 15782 Santiago de Compostela Spain
| | - Miguel Vázquez López
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Inorgánica; Universidade de Santiago de Compostela; 15782 Santiago de Compostela Spain
| | - M. Eugenio Vázquez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica; Universidade de Santiago de Compostela; 15782 Santiago de Compostela Spain
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50
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Arslantas A, Agirtas MS. A Comparative Study on DNA Binding Properties of 2,10,16,24-Tetrakis 4-(4-hydroxyphenyl)-1-phenylethyl) phenoxy)-Substituted Co(II) and Mg(II) Phthalocyanine Compounds. ChemistrySelect 2017. [DOI: 10.1002/slct.201701224] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Ali Arslantas
- Biomedical Engineering Department; School of Engineering; Karabuk University; 78050 Karabuk Turkey
| | - Mehmet Salih Agirtas
- Department of Chemistry; Faculty of Science; Yüzüncü Yıl University; 65080 Van Turkey
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