1
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Nguyen VT, Huynh TKC, Ho GTT, Nguyen THA, Le Anh Nguyen T, Dao DQ, Mai TVT, Huynh LK, Hoang TKD. Metal complexes of benzimidazole-derived as potential anti-cancer agents: synthesis, characterization, combined experimental and computational studies. ROYAL SOCIETY OPEN SCIENCE 2022; 9:220659. [PMID: 36147940 PMCID: PMC9490329 DOI: 10.1098/rsos.220659] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 08/26/2022] [Indexed: 05/10/2023]
Abstract
In this study, a series of 14 Cu (II), Zn (II), Ni (II) and Ag (I) complexes containing bis-benzimidazole derivatives were successfully designed and synthesized from 2-(1H-benzimidazole-2-yl)-phenol derivatives and corresponding metal salt solutions. The compound structures were identified by FT-IR, 1H-NMR, powder X-ray diffraction and ESI-MS analyses, and the presence of the metal in the complexes was confirmed by ultraviolet-visible spectroscopy and ICP optical emission spectrometry. Electronic structure calculations were also carried out to describe the detailed structures in addition to the electronic absorption spectra of the ligands. The cytotoxic activity of the complexes was evaluated against three human cancer cell lines: lung (A549), breast (MDA-MB-231) and prostate (PC3) cancer cells. All complexes inhibited anti-proliferative cancer cells better than free ligands, especially Zn (II) and Ag (I) complexes, which are most sensitive to MDA-MB-231 cells. In addition, showing the growth inhibition of three cancer cell lines with IC50 < 10.4 µM, complexes C1 , C3 and C14 could be considered potential multi-targeted anti-cancer agents.
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Affiliation(s)
- Van-Thanh Nguyen
- Institute of Chemical Technology – VAST, 1A Thanh Loc 29 Street, Thanh Loc Ward, District 12, Ho Chi Minh City 700000, Vietnam
| | - Thi-Kim-Chi Huynh
- Institute of Chemical Technology – VAST, 1A Thanh Loc 29 Street, Thanh Loc Ward, District 12, Ho Chi Minh City 700000, Vietnam
- Graduate University of Science and Technology – VAST, 18 Hoang Quoc Viet Street, Nghia Do Ward, Cau Giay District, Hanoi 100000, Vietnam
| | - Gia-Thien-Thanh Ho
- Institute of Chemical Technology – VAST, 1A Thanh Loc 29 Street, Thanh Loc Ward, District 12, Ho Chi Minh City 700000, Vietnam
- Ton Duc Thang University, 19 Nguyen Huu Tho Street, Tan Phong Ward, District 7, Ho Chi Minh City 700000, Vietnam
| | - Thi-Hong-An Nguyen
- Institute of Chemical Technology – VAST, 1A Thanh Loc 29 Street, Thanh Loc Ward, District 12, Ho Chi Minh City 700000, Vietnam
| | - Thi Le Anh Nguyen
- Institute of Research and Development, Duy Tan University, Da Nang 50000, Vietnam
| | - Duy Quang Dao
- Institute of Research and Development, Duy Tan University, Da Nang 50000, Vietnam
| | - Tam V. T. Mai
- Institute for Computational Science and Technology, SBI Building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City 700000, Vietnam
- University of Science, Ho Chi Minh City, 227 Nguyen Van Cu Street, Ward 4, District 5, Ho Chi Minh City 700000, Vietnam
- Vietnam National University, Ho Chi Minh City 700000, Vietnam
| | - Lam K. Huynh
- University of Science, Ho Chi Minh City, 227 Nguyen Van Cu Street, Ward 4, District 5, Ho Chi Minh City 700000, Vietnam
- International University, Block 6, Linh Trung Ward, Thu Duc District, Ho Chi Minh City 700000, Vietnam
| | - Thi-Kim-Dung Hoang
- Institute of Chemical Technology – VAST, 1A Thanh Loc 29 Street, Thanh Loc Ward, District 12, Ho Chi Minh City 700000, Vietnam
- Graduate University of Science and Technology – VAST, 18 Hoang Quoc Viet Street, Nghia Do Ward, Cau Giay District, Hanoi 100000, Vietnam
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2
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Nguyen VT, Huynh TKC, Ho GTT, Nguyen THA, Le Anh Nguyen T, Dao DQ, Mai TVT, Huynh LK, Hoang TKD. Metal complexes of benzimidazole-derived as potential anti-cancer agents: synthesis, characterization, combined experimental and computational studies. ROYAL SOCIETY OPEN SCIENCE 2022; 9:220659. [PMID: 36147940 DOI: 10.6084/m9.figshare.c.6197452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 08/26/2022] [Indexed: 05/25/2023]
Abstract
In this study, a series of 14 Cu (II), Zn (II), Ni (II) and Ag (I) complexes containing bis-benzimidazole derivatives were successfully designed and synthesized from 2-(1H-benzimidazole-2-yl)-phenol derivatives and corresponding metal salt solutions. The compound structures were identified by FT-IR, 1H-NMR, powder X-ray diffraction and ESI-MS analyses, and the presence of the metal in the complexes was confirmed by ultraviolet-visible spectroscopy and ICP optical emission spectrometry. Electronic structure calculations were also carried out to describe the detailed structures in addition to the electronic absorption spectra of the ligands. The cytotoxic activity of the complexes was evaluated against three human cancer cell lines: lung (A549), breast (MDA-MB-231) and prostate (PC3) cancer cells. All complexes inhibited anti-proliferative cancer cells better than free ligands, especially Zn (II) and Ag (I) complexes, which are most sensitive to MDA-MB-231 cells. In addition, showing the growth inhibition of three cancer cell lines with IC50 < 10.4 µM, complexes C1 , C3 and C14 could be considered potential multi-targeted anti-cancer agents.
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Affiliation(s)
- Van-Thanh Nguyen
- Institute of Chemical Technology - VAST, 1A Thanh Loc 29 Street, Thanh Loc Ward, District 12, Ho Chi Minh City 700000, Vietnam
| | - Thi-Kim-Chi Huynh
- Institute of Chemical Technology - VAST, 1A Thanh Loc 29 Street, Thanh Loc Ward, District 12, Ho Chi Minh City 700000, Vietnam
- Graduate University of Science and Technology - VAST, 18 Hoang Quoc Viet Street, Nghia Do Ward, Cau Giay District, Hanoi 100000, Vietnam
| | - Gia-Thien-Thanh Ho
- Institute of Chemical Technology - VAST, 1A Thanh Loc 29 Street, Thanh Loc Ward, District 12, Ho Chi Minh City 700000, Vietnam
- Ton Duc Thang University, 19 Nguyen Huu Tho Street, Tan Phong Ward, District 7, Ho Chi Minh City 700000, Vietnam
| | - Thi-Hong-An Nguyen
- Institute of Chemical Technology - VAST, 1A Thanh Loc 29 Street, Thanh Loc Ward, District 12, Ho Chi Minh City 700000, Vietnam
| | - Thi Le Anh Nguyen
- Institute of Research and Development, Duy Tan University, Da Nang 50000, Vietnam
| | - Duy Quang Dao
- Institute of Research and Development, Duy Tan University, Da Nang 50000, Vietnam
| | - Tam V T Mai
- Institute for Computational Science and Technology, SBI Building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City 700000, Vietnam
- University of Science, Ho Chi Minh City, 227 Nguyen Van Cu Street, Ward 4, District 5, Ho Chi Minh City 700000, Vietnam
- Vietnam National University, Ho Chi Minh City 700000, Vietnam
| | - Lam K Huynh
- University of Science, Ho Chi Minh City, 227 Nguyen Van Cu Street, Ward 4, District 5, Ho Chi Minh City 700000, Vietnam
- International University, Block 6, Linh Trung Ward, Thu Duc District, Ho Chi Minh City 700000, Vietnam
| | - Thi-Kim-Dung Hoang
- Institute of Chemical Technology - VAST, 1A Thanh Loc 29 Street, Thanh Loc Ward, District 12, Ho Chi Minh City 700000, Vietnam
- Graduate University of Science and Technology - VAST, 18 Hoang Quoc Viet Street, Nghia Do Ward, Cau Giay District, Hanoi 100000, Vietnam
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3
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Jhan CR, Satange R, Wang SC, Zeng JY, Horng YC, Jin P, Neidle S, Hou MH. Targeting the ALS/FTD-associated A-DNA kink with anthracene-based metal complex causes DNA backbone straightening and groove contraction. Nucleic Acids Res 2021; 49:9526-9538. [PMID: 33836081 PMCID: PMC8450080 DOI: 10.1093/nar/gkab227] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 03/16/2021] [Accepted: 03/26/2021] [Indexed: 12/22/2022] Open
Abstract
The use of a small molecule compound to reduce toxic repeat RNA transcripts or their translated aberrant proteins to target repeat-expanded RNA/DNA with a G4C2 motif is a promising strategy to treat C9orf72-linked disorders. In this study, the crystal structures of DNA and RNA–DNA hybrid duplexes with the -GGGCCG- region as a G4C2 repeat motif were solved. Unusual groove widening and sharper bending of the G4C2 DNA duplex A-DNA conformation with B-form characteristics inside was observed. The G4C2 RNA–DNA hybrid duplex adopts a more typical rigid A form structure. Detailed structural analysis revealed that the G4C2 repeat motif of the DNA duplex exhibits a hydration shell and greater flexibility and serves as a ‘hot-spot’ for binding of the anthracene-based nickel complex, NiII(Chro)2 (Chro = Chromomycin A3). In addition to the original GGCC recognition site, NiII(Chro)2 has extended specificity and binds the flanked G:C base pairs of the GGCC core, resulting in minor groove contraction and straightening of the DNA backbone. We have also shown that Chro-metal complexes inhibit neuronal toxicity and suppresses locomotor deficits in a Drosophila model of C9orf72-associated ALS. The approach represents a new direction for drug discovery against ALS and FTD diseases by targeting G4C2 repeat motif DNA.
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Affiliation(s)
- Cyong-Ru Jhan
- Department of Life Sciences, National Chung-Hsing University, Taichung 402, Taiwan
| | - Roshan Satange
- Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung 402, Taiwan.,Institute of Genomics and Bioinformatics; National Chung Hsing University, Taichung 402, Taiwan
| | - Shun-Ching Wang
- Institute of Genomics and Bioinformatics; National Chung Hsing University, Taichung 402, Taiwan
| | - Jing-Yi Zeng
- Institute of Genomics and Bioinformatics; National Chung Hsing University, Taichung 402, Taiwan
| | - Yih-Chern Horng
- Department of Chemistry, National Changhua University of Education, Changhua 50058, Taiwan
| | - Peng Jin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Stephen Neidle
- The School of Pharmacy, University College London, London, WC1N 1AX, United Kingdom
| | - Ming-Hon Hou
- Department of Life Sciences, National Chung-Hsing University, Taichung 402, Taiwan.,Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung 402, Taiwan.,Institute of Genomics and Bioinformatics; National Chung Hsing University, Taichung 402, Taiwan
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4
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Kacim K, Jelsch C, Lucas C, Lefebvre F, Kaminsky W, Ben Nasr C, Kaabi K. Synthesis, crystal structure determination, DFT calculation, and Hirshfeld surface analysis of a new Zn(II) complex with the guaninium ligand. J COORD CHEM 2020. [DOI: 10.1080/00958972.2020.1844192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Klai Kacim
- Laboratoire de Chimie des Matériaux, Faculté des Sciences de Bizerte, Université de Carthage, Zarzouna, Tunisie
| | - Christian Jelsch
- CRM, CNRS, Institut Jean Barriol, Université de Lorraine, Vandoeuvre les Nancy Cedex, France
| | - Christine Lucas
- Ecole Supérieure de Chimie Physique Electronique, Laboratoire de Chimie Organométallique de Surface (LCOMS), Villeurbanne Cedex, France
| | - Frédéric Lefebvre
- Ecole Supérieure de Chimie Physique Electronique, Laboratoire de Chimie Organométallique de Surface (LCOMS), Villeurbanne Cedex, France
| | - Werner Kaminsky
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Cherif Ben Nasr
- Laboratoire de Chimie des Matériaux, Faculté des Sciences de Bizerte, Université de Carthage, Zarzouna, Tunisie
| | - Kamel Kaabi
- Laboratoire de Chimie des Matériaux, Faculté des Sciences de Bizerte, Université de Carthage, Zarzouna, Tunisie
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5
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Satange R, Chang CK, Hou MH. A survey of recent unusual high-resolution DNA structures provoked by mismatches, repeats and ligand binding. Nucleic Acids Res 2019; 46:6416-6434. [PMID: 29945186 PMCID: PMC6061790 DOI: 10.1093/nar/gky561] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 06/08/2018] [Indexed: 12/20/2022] Open
Abstract
The structure of the DNA duplex is arguably one of the most important biological structures elucidated in modern history. DNA duplex structure is closely associated with essential biological functions such as DNA replication and RNA transcription. In addition to the classical A-, B- and Z-DNA conformations, DNA duplexes are capable of assuming a variety of alternative conformations depending on the sequence and environmental context. A considerable number of these unusual DNA duplex structures have been identified in the past decade, and some of them have been found to be closely associated with different biological functions and pathological conditions. In this manuscript, we review a selection of unusual DNA duplex structures, particularly those originating from base pair mismatch, repetitive sequence motifs and ligand-induced structures. Although the biological significance of these novel structures has not yet been established in most cases, the illustrated conformational versatility of DNA could have relevance for pharmaceutical or nanotechnology development. A perspective on the future directions of this field is also presented.
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Affiliation(s)
- Roshan Satange
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, Taiwan.,Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Chung-Ke Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Ming-Hon Hou
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, Taiwan.,Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung, Taiwan
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6
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Andrić JM, Stanković IM, Zarić SD. Binding of metal ions and water molecules to nucleic acid bases: the influence of water molecule coordination to a metal ion on water-nucleic acid base hydrogen bonds. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2019; 75:301-309. [PMID: 32830651 DOI: 10.1107/s2052520619001999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 02/04/2019] [Indexed: 06/11/2023]
Abstract
The interactions of nucleic acid bases with non-coordinated and coordinated water molecules were studied by analyzing data in the Protein Data Bank (PDB) and by quantum chemical calculations. The analysis of the data in the crystal structures from the PDB indicates that hydrogen bonds involving oxygen or nitrogen atoms of nucleic acid bases and water molecules are shorter when water is bonded to a metal ion. These results are in agreement with the quantum chemical calculations on geometries and interaction energies of hydrogen bonds; the calculations on model systems show that hydrogen bonds of nucleic acid bases with water bonded to a metal ion are stronger than hydrogen bonds with non-coordinated water. These calculated values are similar to the strength of hydrogen bonds between nucleic acid bases. The results presented in this paper may be relevant to understand the role of water molecules and metal ions in the process of replication and stabilization of nucleic acids and also to understand the possible toxicity of metal ion interactions with nucleic acids.
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Affiliation(s)
- Jelena M Andrić
- Innovation center of the Faculty of Chemistry, Studentski trg 12-16, 11000 Belgrade, Serbia
| | | | - Snežana D Zarić
- Faculty of Chemistry, University of Belgrade, Studentski trg 12-16, 11000 Belgrade, Serbia
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7
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Chen YW, Satange R, Wu PC, Jhan CR, Chang CK, Chung KR, Waring MJ, Lin SW, Hsieh LC, Hou MH. Co II(Chromomycin)₂ Complex Induces a Conformational Change of CCG Repeats from i-Motif to Base-Extruded DNA Duplex. Int J Mol Sci 2018; 19:ijms19092796. [PMID: 30227633 PMCID: PMC6164834 DOI: 10.3390/ijms19092796] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 09/07/2018] [Indexed: 01/07/2023] Open
Abstract
We have reported the propensity of a DNA sequence containing CCG repeats to form a stable i-motif tetraplex structure in the absence of ligands. Here we show that an i-motif DNA sequence may transition to a base-extruded duplex structure with a GGCC tetranucleotide tract when bound to the (CoII)-mediated dimer of chromomycin A3, CoII(Chro)₂. Biophysical experiments reveal that CCG trinucleotide repeats provide favorable binding sites for CoII(Chro)₂. In addition, water hydration and divalent metal ion (CoII) interactions also play a crucial role in the stabilization of CCG trinucleotide repeats (TNRs). Our data furnish useful structural information for the design of novel therapeutic strategies to treat neurological diseases caused by repeat expansions.
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Affiliation(s)
- Yu-Wen Chen
- Institute of Biotechnology, National Chung-Hsing University, Taichung 402, Taiwan.
| | - Roshan Satange
- Institute of Genomics and Bioinformatics, National Chung-Hsing University, Taichung 402, Taiwan.
- Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung 402, Taiwan.
| | - Pei-Ching Wu
- Institute of Genomics and Bioinformatics, National Chung-Hsing University, Taichung 402, Taiwan.
| | - Cyong-Ru Jhan
- Department of Life Sciences, National Chung-Hsing University, Taichung 402, Taiwan.
| | - Chung-Ke Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan.
| | - Kuang-Ren Chung
- Department of Plant Pathology, National Chung-Hsing University, Taichung 402, Taiwan.
| | - Michael J Waring
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK.
| | - Sheng-Wei Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan.
| | - Li-Ching Hsieh
- Institute of Genomics and Bioinformatics, National Chung-Hsing University, Taichung 402, Taiwan.
- Advanced Plant Biotechnology Center, National Chung-Hsing University, Taichung 402, Taiwan.
| | - Ming-Hon Hou
- Institute of Biotechnology, National Chung-Hsing University, Taichung 402, Taiwan.
- Institute of Genomics and Bioinformatics, National Chung-Hsing University, Taichung 402, Taiwan.
- Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung 402, Taiwan.
- Department of Life Sciences, National Chung-Hsing University, Taichung 402, Taiwan.
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8
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Divalent cations are dispensable for binding to DNA of a novel positively charged olivomycin A derivative. PLoS One 2018; 13:e0191923. [PMID: 29420558 PMCID: PMC5805246 DOI: 10.1371/journal.pone.0191923] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 01/08/2018] [Indexed: 11/19/2022] Open
Abstract
The current model of binding of the antitumor antibiotic olivomycin A (1) to GC-rich DNA regions presumes that coordination of the magnesium divalent cation with drug dimers is necessary for binding of 1 into the minor groove of the DNA duplex. Previously we have synthesized the derivatives of 1 termed ‘short acid’ (2) and its N,N-dimethylaminoethylamide (3). The latter compound demonstrated an improved tolerance in vivo compared to 1 and good therapeutic potency in animal models. We herein report that compound 3 is able to form stable complexes with DNA in the absence of Mg2+, in striking contrast to 1 whose binding to the DNA absolutely requires Mg2+. The mode of binding of 3 to DNA is similar in the presence or absence of Mg2+ as determined by circular dichroism. The affinity to DNA of 3 in Mg2+-free solution was similar to that of 1 or 3 in the presence of Mg2+ at low ionic strength. Non-electrostatic contributions to total free energy of binding of 1 and 3 to DNA were comparable for Mg2+-free complexes. Our data strongly suggest that electrostatic interaction of the positively charged 3 can compensate for the absence of divalent ions in complexes with DNA. This new property of the olivomycin A derivative expands the mechanistic knowledge of the modes of interaction with DNA of small molecular weight drug candidates.
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9
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Tseng WH, Chang CK, Wu PC, Hu NJ, Lee GH, Tzeng CC, Neidle S, Hou MH. Induced-Fit Recognition of CCG Trinucleotide Repeats by a Nickel-Chromomycin Complex Resulting in Large-Scale DNA Deformation. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201703989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Wen-Hsuan Tseng
- Institute of Genomics and Bioinformatics; National Chung Hsing University; 250 Kuo-kuang Rd. Taichung Taiwan
| | - Chung-ke Chang
- Institute of Biomedical Sciences; Academia Sinica; 128 Sec. 2, Academia Rd. Nankang Taipei Taiwan
| | - Pei-Ching Wu
- Institute of Genomics and Bioinformatics; National Chung Hsing University; 250 Kuo-kuang Rd. Taichung Taiwan
| | - Nien-Jen Hu
- Institute of Biochemistry; National Chung Hsing University; 250 Kuo-kuang Rd. Taichung Taiwan
| | - Gene-Hsiang Lee
- Instrumentation Center; College of Science; National Taiwan University; No.1, Sec. 4, Roosevelt Rd. Taipei Taiwan
| | - Ching-Cherng Tzeng
- Department of Pathology; Chi Mei Medical Center; No.901, Zhonghua Rd. Tainan Taiwan
| | - Stephen Neidle
- The School of Pharmacy; University College London; London WC1N 1AX UK
| | - Ming-Hon Hou
- Institute of Genomics and Bioinformatics; National Chung Hsing University; 250 Kuo-kuang Rd. Taichung Taiwan
- Institute of Biotechnology; National Chung Hsing University; 250 Kuo-kuang Rd. Taichung Taiwan
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10
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Tseng WH, Chang CK, Wu PC, Hu NJ, Lee GH, Tzeng CC, Neidle S, Hou MH. Induced-Fit Recognition of CCG Trinucleotide Repeats by a Nickel-Chromomycin Complex Resulting in Large-Scale DNA Deformation. Angew Chem Int Ed Engl 2017; 56:8761-8765. [PMID: 28544401 DOI: 10.1002/anie.201703989] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Indexed: 01/23/2023]
Abstract
Small-molecule compounds targeting trinucleotide repeats in DNA have considerable potential as therapeutic or diagnostic agents against many neurological diseases. NiII (Chro)2 (Chro=chromomycin A3) binds specifically to the minor groove of (CCG)n repeats in duplex DNA, with unique fluorescence features that may serve as a probe for disease detection. Crystallographic studies revealed that the specificity originates from the large-scale spatial rearrangement of the DNA structure, including extrusion of consecutive bases and backbone distortions, with a sharp bending of the duplex accompanied by conformational changes in the NiII chelate itself. The DNA deformation of CCG repeats upon binding forms a GGCC tetranucleotide tract, which is recognized by NiII (Chro)2 . The extruded cytosine and last guanine nucleotides form water-mediated hydrogen bonds, which aid in ligand recognition. The recognition can be accounted for by the classic induced-fit paradigm.
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Affiliation(s)
- Wen-Hsuan Tseng
- Institute of Genomics and Bioinformatics, National Chung Hsing University, 250 Kuo-kuang Rd., Taichung, Taiwan
| | - Chung-Ke Chang
- Institute of Biomedical Sciences, Academia Sinica, 128 Sec. 2, Academia Rd. Nankang, Taipei, Taiwan
| | - Pei-Ching Wu
- Institute of Genomics and Bioinformatics, National Chung Hsing University, 250 Kuo-kuang Rd., Taichung, Taiwan
| | - Nien-Jen Hu
- Institute of Biochemistry, National Chung Hsing University, 250 Kuo-kuang Rd., Taichung, Taiwan
| | - Gene-Hsiang Lee
- Instrumentation Center, College of Science, National Taiwan University, No.1, Sec. 4, Roosevelt Rd., Taipei, Taiwan
| | - Ching-Cherng Tzeng
- Department of Pathology, Chi Mei Medical Center, No.901, Zhonghua Rd., Tainan, Taiwan
| | - Stephen Neidle
- The School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Ming-Hon Hou
- Institute of Genomics and Bioinformatics, National Chung Hsing University, 250 Kuo-kuang Rd., Taichung, Taiwan
- Institute of Biotechnology, National Chung Hsing University, 250 Kuo-kuang Rd., Taichung, Taiwan
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11
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Carvalho A, Chu J, Meinguet C, Kiss R, Vandenbussche G, Masereel B, Wouters J, Kornienko A, Pelletier J, Mathieu V. A harmine-derived beta-carboline displays anti-cancer effects in vitro by targeting protein synthesis. Eur J Pharmacol 2017; 805:25-35. [PMID: 28322844 DOI: 10.1016/j.ejphar.2017.03.034] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 03/13/2017] [Accepted: 03/15/2017] [Indexed: 12/17/2022]
Abstract
Growing evidence indicates that protein synthesis is deregulated in cancer onset and progression and targeting this process might be a selective way to combat cancers. While harmine is known to inhibit DYRK1A and intercalate into the DNA, tri-substitution was shown previously to modify its activity profile in favor of protein synthesis inhibition. In this study, we thus evaluated the optimized derivative CM16 in vitro anti-cancer effects unfolding its protein synthesis inhibition activity. Indeed, the growth inhibitory profile of CM16 in the NCI 60-cancer-cell-line-panel correlated with those of other compounds described as protein synthesis inhibitors. Accordingly, CM16 decreased in a time- and concentration-dependent manner the translation of neosynthesized proteins in vitro while it did not affect mRNA transcription. CM16 rapidly penetrated into the cell in the perinuclear region of the endoplasmic reticulum where it appears to target translation initiation as highlighted by ribosomal disorganization. More precisely, we found that the mRNA expression levels of the initiation factors EIF1AX, EIF3E and EIF3H differ when comparing resistant or sensitive cell models to CM16. Additionally, CM16 induced eIF2α phosphorylation. Those effects could explain, at least partly, the CM16 cytostatic anti-cancer effects observed in vitro while neither cell cycle arrest nor DNA intercalation could be demonstrated. Therefore, targeting protein synthesis initiation with CM16 could represent a new promising alternative to current cancer therapies due to the specific alterations of the translation machinery in cancer cells as recently evidenced with respect to EIF1AX and eIF3 complex, the potential targets identified in this present study.
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Affiliation(s)
- Annelise Carvalho
- Laboratoire de Cancérologie et Toxicologie Expérimentale, Faculté de Pharmacie, Université Libre de Bruxelles, Brussels, Belgium
| | - Jennifer Chu
- Department of Biochemistry, McGill University, Montreal, Québec, Canada
| | - Céline Meinguet
- Namur Medicine and Drug Innovation Center (NAMEDIC-NARILIS), Université de Namur, Namur, Belgium
| | - Robert Kiss
- Laboratoire de Cancérologie et Toxicologie Expérimentale, Faculté de Pharmacie, Université Libre de Bruxelles, Brussels, Belgium
| | - Guy Vandenbussche
- Laboratory for the Structure and Function of Biological Membranes, Faculté des Sciences, Université Libre de Bruxelles, Brussels, Belgium
| | - Bernard Masereel
- Namur Medicine and Drug Innovation Center (NAMEDIC-NARILIS), Université de Namur, Namur, Belgium
| | - Johan Wouters
- Namur Medicine and Drug Innovation Center (NAMEDIC-NARILIS), Université de Namur, Namur, Belgium
| | - Alexander Kornienko
- Department of Chemistry and Biochemistry, Texas State University, 601 University Drive, San Marcos, TX 78666, USA
| | - Jerry Pelletier
- Department of Biochemistry, McGill University, Montreal, Québec, Canada
| | - Véronique Mathieu
- Laboratoire de Cancérologie et Toxicologie Expérimentale, Faculté de Pharmacie, Université Libre de Bruxelles, Brussels, Belgium.
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Guimarães LA, Jimenez PC, Sousa TDS, Freitas HPS, Rocha DD, Wilke DV, Martín J, Reyes F, Deusdênia Loiola Pessoa O, Costa-Lotufo LV. Chromomycin A2 induces autophagy in melanoma cells. Mar Drugs 2014; 12:5839-55. [PMID: 25486109 PMCID: PMC4278204 DOI: 10.3390/md12125839] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 11/17/2014] [Accepted: 11/20/2014] [Indexed: 12/19/2022] Open
Abstract
The present study highlights the biological effects of chromomycin A2 toward metastatic melanoma cells in culture. Besides chromomycin A2, chromomycin A3 and demethylchromomycin A2 were also identified from the extract derived from Streptomyces sp., recovered from Paracuru Beach, located in the northeast region of Brazil. The cytotoxic activity of chromomycin A2 was evaluated across a panel of human tumor cell lines, which found IC50 values in the nM-range for exposures of 48 and 72 h. MALME-3M, a metastatic melanoma cell line, showed the highest sensitivity to chromomycin A2 after 48h incubation, and was chosen as a model to investigate this potent cytotoxic effect. Treatment with chromomycin A2 at 30 nM reduced cell proliferation, but had no significant effect upon cell viability. Additionally, chromomycin A2 induced accumulation of cells in G0/G1 phase of the cell cycle, with consequent reduction of S and G2/M and unbalanced expression of cyclins. Chromomycin A2 treated cells depicted several cellular fragments resembling autophagosomes and increased expression of proteins LC3-A and LC3-B. Moreover, exposure to chromomycin A2 also induced the appearance of acidic vacuolar organelles in treated cells. These features combined are suggestive of the induction of autophagy promoted by chromomycin A2, a feature not previously described for chromomycins.
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Affiliation(s)
| | | | - Thiciana da Silva Sousa
- Department of Organic and Inorganic Chemistry, Federal University of Ceara, Fortaleza, CE 60021-970, Brazil.
| | - Hozana Patrícia S Freitas
- Department of Organic and Inorganic Chemistry, Federal University of Ceara, Fortaleza, CE 60021-970, Brazil.
| | - Danilo Damasceno Rocha
- Department of Physiology and Pharmacology, Federal University of Ceara, Fortaleza, Ceará 60430-270, Brazil.
| | - Diego Veras Wilke
- Marine Sciences Institute, Federal University of Ceara, Fortaleza, Ceara 60165-081, Brazil.
| | - Jesús Martín
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Granada 18016, Spain.
| | - Fernando Reyes
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Granada 18016, Spain.
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Lo YS, Tseng WH, Chuang CY, Hou MH. The structural basis of actinomycin D-binding induces nucleotide flipping out, a sharp bend and a left-handed twist in CGG triplet repeats. Nucleic Acids Res 2013; 41:4284-94. [PMID: 23408860 PMCID: PMC3627577 DOI: 10.1093/nar/gkt084] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The potent anticancer drug actinomycin D (ActD) functions by intercalating into DNA at GpC sites, thereby interrupting essential biological processes including replication and transcription. Certain neurological diseases are correlated with the expansion of (CGG)n trinucleotide sequences, which contain many contiguous GpC sites separated by a single G:G mispair. To characterize the binding of ActD to CGG triplet repeat sequences, the structural basis for the strong binding of ActD to neighbouring GpC sites flanking a G:G mismatch has been determined based on the crystal structure of ActD bound to ATGCGGCAT, which contains a CGG triplet sequence. The binding of ActD molecules to GCGGC causes many unexpected conformational changes including nucleotide flipping out, a sharp bend and a left-handed twist in the DNA helix via a two site-binding model. Heat denaturation, circular dichroism and surface plasmon resonance analyses showed that adjacent GpC sequences flanking a G:G mismatch are preferred ActD-binding sites. In addition, ActD was shown to bind the hairpin conformation of (CGG)16 in a pairwise combination and with greater stability than that of other DNA intercalators. Our results provide evidence of a possible biological consequence of ActD binding to CGG triplet repeat sequences.
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Affiliation(s)
- Yu-Sheng Lo
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan
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The binding of the Co(II) complex of dimeric chromomycin A3 to GC sites with flanking G:G mismatches. J Inorg Biochem 2012; 121:28-36. [PMID: 23333714 DOI: 10.1016/j.jinorgbio.2012.12.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Revised: 12/12/2012] [Accepted: 12/12/2012] [Indexed: 01/09/2023]
Abstract
Some neurological diseases are correlated with expansion of (CXG)n trinucleotide repeats, which contain many contiguous GpC flanked by mismatched X/X base pair. This study focused on the binding of the Co(II) complex of dimeric chromomycin A3(Chro), Co(II)(Chro)2, to DNA with CXG trinucleotide repeats. The present study showed that GC sites with flanking G:G mismatches provide an excellent binding site for Co(II)(Chro)2 as shown by surface plasmon resonance and fluorescence analysis, compared to GC sites with flanking A:A, T:T, or C:C mismatches. In addition, we measured the ability of Co(II)(Chro)2 to act on the hairpin DNA of (CGG)16. We observed that Co(II)(Chro)2 could stabilize and trap the cruciform conformation of (CGG)16. Furthermore, two Co(II)(Chro)2 molecules may bind at the two GpC sites separated by at least one GC site in the hairpin structure of (CGG)16. In a synthetic self-priming DNA model, 5'-(CGG)16(CCG)6-3', Co(II)(Chro)2 can interfere with the expansion process of CGG triplet repeats, as shown by a gel electrophoretic expansion assay. Here, we first report the acting of Co(II)(Chro)2, the groove-binding drug, to trinucleotide repeats. Our results provide the possible biological consequence of Co(II)(Chro)2 bound to CGG triplet repeat sequences.
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Johnson IM, Prakash H, Prathiba J, Raghunathan R, Malathi R. Spectral analysis of naturally occurring methylxanthines (theophylline, theobromine and caffeine) binding with DNA. PLoS One 2012; 7:e50019. [PMID: 23236361 PMCID: PMC3517612 DOI: 10.1371/journal.pone.0050019] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Accepted: 10/17/2012] [Indexed: 12/13/2022] Open
Abstract
Nucleic acids exist in a dynamic equilibrium with a number of molecules that constantly interact with them and regulate the cellular activities. The inherent nature of the structure and conformational integrity of these macromolecules can lead to altered biological activity through proper targeting of nucleic acids binding ligands or drug molecules. We studied the interaction of naturally occurring methylxanthines such as theophylline, theobromine and caffeine with DNA, using UV absorption and Fourier transform infrared (FTIR) spectroscopic methods, and especially monitored their binding affinity in the presence of Mg(2+) and during helix-coil transitions of DNA by temperature (T(m)) or pH melting profiles. The study indicates that all these molecules effectively bind to DNA in a dose dependent manner. The overall binding constants of DNA-theophylline = 3.5×10(3) M(-1), DNA-theobromine = 1.1×10(3) M(-1), and DNA-Caffeine = 3.8×10(3) M(-1). On the other hand T(m)/pH melting profiles showed 24-35% of enhanced binding activity of methylxanthines during helix-coil transitions of DNA rather than to its native double helical structure. The FTIR analysis divulged that theophylline, theobromine and caffeine interact with all the base pairs of DNA (A-T; G-C) and phosphate group through hydrogen bond (H-bond) interaction. In the presence of Mg(2+), methylxanthines altered the structure of DNA from B to A-family. However, the B-family structure of DNA remained unaltered in DNA-methylxanthines complexes or in the absence of Mg(2+). The spectral analyses indicated the order of binding affinity as "caffeine≥theophylline>theobromine" to the native double helical DNA, and "theophylline≥theobromine>caffeine to the denatured form of DNA and in the presence of divalent metal ions.
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Affiliation(s)
- Irudayam Maria Johnson
- Department of Physiology, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
- Department of Genetics, Taramani Campus, University of Madras, Chennai, India
- * E-mail: (IMJ); (RM)
| | - Halan Prakash
- National Centre for Ultrafast Processes, Taramani Campus, University of Madras, Chennai, India
| | - Jeyaguru Prathiba
- Department of Genetics, Taramani Campus, University of Madras, Chennai, India
| | | | - Raghunathan Malathi
- Department of Genetics, Taramani Campus, University of Madras, Chennai, India
- * E-mail: (IMJ); (RM)
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Wang SY, Lee YL, Lai YH, Chen JJW, Wu WL, Yuann JMP, Su WL, Chuang SM, Hou MH. Spermine attenuates the action of the DNA intercalator, actinomycin D, on DNA binding and the inhibition of transcription and DNA replication. PLoS One 2012; 7:e47101. [PMID: 23144800 PMCID: PMC3493566 DOI: 10.1371/journal.pone.0047101] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Accepted: 09/10/2012] [Indexed: 12/23/2022] Open
Abstract
The anticancer activity of DNA intercalators is related to their ability to intercalate into the DNA duplex with high affinity, thereby interfering with DNA replication and transcription. Polyamines (spermine in particular) are almost exclusively bound to nucleic acids and are involved in many cellular processes that require nucleic acids. Until now, the effects of polyamines on DNA intercalator activities have remained unclear because intercalation is the most important mechanism employed by DNA-binding drugs. Herein, using actinomycin D (ACTD) as a model, we have attempted to elucidate the effects of spermine on the action of ACTD, including its DNA-binding ability, RNA and DNA polymerase interference, and its role in the transcription and replication inhibition of ACTD within cells. We found that spermine interfered with the binding and stabilization of ACTD to DNA. The presence of increasing concentrations of spermine enhanced the transcriptional and replication activities of RNA and DNA polymerases, respectively, in vitro treated with ActD. Moreover, a decrease in intracellular polyamine concentrations stimulated by methylglyoxal-bis(guanylhydrazone) (MGBG) enhanced the ACTD-induced inhibition of c-myc transcription and DNA replication in several cancer cell lines. The results indicated that spermine attenuates ACTD binding to DNA and its inhibition of transcription and DNA replication both in vitro and within cells. Finally, a synergistic antiproliferative effect of MGBG and ACTD was observed in a cell viability assay. Our findings will be of significant relevance to future developments in combination with cancer therapy by enhancing the anticancer activity of DNA interactors through polyamine depletion.
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Affiliation(s)
- Sheng-Yu Wang
- Department of Life Science, National Chung Hsing University, Taichung, Taiwan
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, Taiwan
| | - Yueh-Luen Lee
- National Institute of Cancer Research, National Health Research Institutes, Miaoli, Taiwan
| | - Yi-Hua Lai
- Institute of Biomedical Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Jeremy J. W. Chen
- Institute of Biomedical Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Wen-Lin Wu
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, Taiwan
| | - Jeu-Ming P. Yuann
- Department of Biotechnology, Ming Chuan University, Taoyuan County, Taiwan
| | - Wang-Lin Su
- Department of Life Science, National Chung Hsing University, Taichung, Taiwan
| | - Show-Mei Chuang
- Institute of Biomedical Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Ming-Hon Hou
- Department of Life Science, National Chung Hsing University, Taichung, Taiwan
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, Taiwan
- * E-mail:
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Hsu CW, Kuo CF, Chuang SM, Hou MH. Elucidation of the DNA-interacting properties and anticancer activity of a Ni(II)-coordinated mithramycin dimer complex. Biometals 2012; 26:1-12. [DOI: 10.1007/s10534-012-9589-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 10/03/2012] [Indexed: 02/03/2023]
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